count: 4008
list:
- accessibility: Open access
  additionDate: '2025-07-04T16:10:32.821423Z'
  biotoolsCURIE: biotools:16smicrobiomemlfs
  biotoolsID: 16smicrobiomemlfs
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: igarachv@ugr.es
    fundrefid: null
    gridid: null
    name: Ignacio Garach Vélez
    note: null
    orcidid: https://orcid.org/0009-0006-6618-7949
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://github.com/nach00gar/16SMicrobiomeMLFS
  description: 'Code and supporting data for the article: "Exploring the role of normalization
    and feature selection in microbiome disease classification pipelines."'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/nach00gar/16SMicrobiomeMLFS
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-04T16:10:32.823947Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/nach00gar/16SMicrobiomeMLFS
  maturity: Emerging
  name: 16SMicrobiomeMLFS
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: igarachv
  publication: []
  relation: []
  toolType:
  - Script
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2018-05-28T14:50:09Z'
  biotoolsCURIE: biotools:deepsig
  biotoolsID: deepsig
  collectionID:
  - Bologna Biocomputing Group
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-ITA-BOLOGNA
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: http://biocomp.unibo.it
  - email: castrense.savojardo2@unibo.it
    fundrefid: null
    gridid: null
    name: Castrense Savojardo
    note: null
    orcidid: https://orcid.org/0000-0002-7359-0633
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    url: null
  - email: pierluigi.martelli@unibo.it
    fundrefid: null
    gridid: null
    name: Pier Luigi Martelli
    note: null
    orcidid: https://orcid.org/0000-0002-0274-5669
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://biocomp.unibo.it
  description: Prediction of secretory signal peptides in protein sequences
  documentation:
  - note: null
    type:
    - Command-line options
    url: https://github.com/BolognaBiocomp/deepsig
  download:
  - note: null
    type: Source code
    url: https://github.com/BolognaBiocomp/deepsig
    version: 1.2.5
  - note: null
    type: Container file
    url: https://hub.docker.com/r/bolognabiocomp/deepsig
    version: 1.2.5
  editPermission:
    authors:
    - savo
    - ELIXIR-ITA-BOLOGNA
    type: group
  elixirCommunity: []
  elixirNode:
  - Italy
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence (raw)
        uri: http://edamontology.org/data_2974
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: null
    operation:
    - term: Protein signal peptide detection
      uri: http://edamontology.org/operation_0418
    output:
    - data:
        term: Protein report
        uri: http://edamontology.org/data_0896
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://busca.biocomp.unibo.it/deepsig/
  homepage_status: 0
  language:
  - Python
  - C++
  lastUpdate: '2025-06-19T11:55:09.017105Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: DeepSig
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ELIXIR-ITA-BOLOGNA
  publication:
  - doi: 10.1093/bioinformatics/btx818
    metadata:
      abstract: Motivation The identification of signal peptides in protein sequences
        is an important step toward protein localization and function characterization.
        Results Here, we present DeepSig, an improved approach for signal peptide
        detection and cleavage-site prediction based on deep learning methods. Comparative
        benchmarks performed on an updated independent dataset of proteins show that
        DeepSig is the current best performing method, scoring better than other available
        state-of-the-art approaches on both signal peptide detection and precise cleavage-site
        identification. Availability and implementation DeepSig is available as both
        standalone program and web server at https://deepsig.biocomp.unibo.it. All
        datasets used in this study can be obtained from the same website.
      authors:
      - name: Savojardo C.
      - name: Martelli P.L.
      - name: Fariselli P.
      - name: Casadio R.
      citationCount: 96
      date: '2018-05-15T00:00:00Z'
      journal: Bioinformatics
      title: 'DeepSig: Deep learning improves signal peptide detection in proteins'
    note: null
    pmcid: PMC5946842
    pmid: '29280997'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  validated: 1
  version:
  - 1.2.5
- accessibility: Open access (with restrictions)
  additionDate: '2021-07-06T20:27:27Z'
  biotoolsCURIE: biotools:nanoplot
  biotoolsID: nanoplot
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Wouter De Coster
    note: null
    orcidid: https://orcid.org/0000-0002-5248-8197
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://gigabaseorgigabyte.wordpress.com/
  description: NanoPlot is a tool with various visualizations of sequencing data in
    bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for
    long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences
  documentation:
  - note: null
    type:
    - Command-line options
    url: https://github.com/wdecoster/NanoPlot
  download:
  - note: null
    type: Command-line specification
    url: https://anaconda.org/bioconda/nanoplot
    version: null
  - note: null
    type: Command-line specification
    url: https://pypi.org/project/NanoPlot/
    version: null
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
      - term: nucleotide
        uri: http://edamontology.org/format_1207
    note: null
    operation:
    - term: Scatter plot plotting
      uri: http://edamontology.org/operation_2940
    - term: Box-Whisker plot plotting
      uri: http://edamontology.org/operation_2943
    output: []
  homepage: https://github.com/wdecoster/NanoPlot
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-06-18T12:31:48.762608Z'
  license: GPL-3.0
  link:
  - note: Issue tracker and most up to date software version
    type:
    - Repository
    url: https://github.com/wdecoster/NanoPlot
  - note: Web service with more limited options compared to the command line tool
    type:
    - Service
    url: http://nanoplot.bioinf.be/
  maturity: Mature
  name: NanoPlot
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: wdecoster
  publication:
  - doi: 10.1093/bioinformatics/bty149
    metadata:
      abstract: 'Summary: Here we describe NanoPack, a set of tools developed for
        visualization and processing of long-read sequencing data from Oxford Nanopore
        Technologies and Pacific Biosciences. Availability and implementation: The
        NanoPack tools are written in Python3 and released under the GNU GPL3.0 License.
        The source code can be found at https://github.com/wdecoster/nanopack, together
        with links to separate scripts and their documentation. The scripts are compatible
        with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available
        as a graphical user interface, a web service at http://nanoplot.bioinf.be
        and command line tools.'
      authors:
      - name: De Coster W.
      - name: D'Hert S.
      - name: Schultz D.T.
      - name: Cruts M.
      - name: Van Broeckhoven C.
      citationCount: 1840
      date: '2018-08-01T00:00:00Z'
      journal: Bioinformatics
      title: 'NanoPack: Visualizing and processing long-read sequencing data'
    note: null
    pmcid: PMC6061794
    pmid: '29547981'
    type:
    - Method
    version: null
  relation:
  - biotoolsID: nanopack
    type: includedIn
  toolType:
  - Command-line tool
  - Web application
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - v.1.42.0
- accessibility: Open access
  additionDate: '2021-05-26T21:13:32Z'
  biotoolsCURIE: biotools:nextdenovo
  biotoolsID: nextdenovo
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: support@nextomics.org
    fundrefid: null
    gridid: null
    name: Nextomics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Primary contact
    url: null
  description: NextDenovo is a string graph-based de novo assembler for long reads
    (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu
    (no correction step for PacBio Hifi reads), but requires significantly less computing
    resources and storages.
  documentation:
  - note: null
    type:
    - User manual
    url: https://nextdenovo.readthedocs.io/en/latest/
  download:
  - note: null
    type: Source code
    url: https://github.com/Nextomics/NextDenovo/releases/tag/2.5.2
    version: null
  editPermission:
    authors:
    - jw
    - ELIXIR-CZ
    - Keiler_Collier
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    output:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: Sequence assembly format (text)
        uri: http://edamontology.org/format_2561
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/Nextomics/NextDenovo
  homepage_status: 0
  language:
  - Python
  - C
  lastUpdate: '2025-06-18T12:20:23.607241Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/Nextomics/NextDenovo/issues
  maturity: Mature
  name: NextDenovo
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1101/2023.03.09.531669.
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version:
  - v.2.5.2
- accessibility: Open access
  additionDate: '2021-05-27T09:04:45Z'
  biotoolsCURIE: biotools:quickmerge
  biotoolsID: quickmerge
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Mahul Chakraborty
    note: null
    orcidid: https://orcid.org/0000-0003-2414-9187
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://mahulchakraborty.wordpress.com/
  description: Quickmerge is a program that uses complementary information from genomes
    assembled with long reads in order to improve contiguity, and works with assemblies
    derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even
    work with hybrid assemblies made by combining long reads and Illumina short reads.
  documentation: []
  download: []
  editPermission:
    authors:
    - ELIXIR-CZ
    - Keiler_Collier
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: merge_wrapper.py -pre output_prefix assembly_1.fa assembly_2.fa
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: 'Runs whole merge process on an input assembly.

      Assembly 2 will be used to fill gaps in assembly 1.'
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: Scaffolding
      uri: http://edamontology.org/operation_3216
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/mahulchak/quickmerge
  homepage_status: 0
  language:
  - C++
  - C
  lastUpdate: '2025-06-18T12:17:20.983962Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/mahulchak/quickmerge/issues
  - note: null
    type:
    - Repository
    url: https://github.com/mahulchak/quickmerge
  maturity: null
  name: quickmerge
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1534/g3.118.200162
    metadata:
      abstract: Accurate and comprehensive characterization of genetic variation is
        essential for deciphering the genetic basis of diseases and other phenotypes.
        A vast amount of genetic variation stems from largescale sequence changes
        arising from the duplication, deletion, inversion, and translocation of sequences.
        In the past 10 years, high-throughput short reads have greatly expanded our
        ability to assay sequence variation due to single nucleotide polymorphisms.
        However, a recent de novo assembly of a second Drosophila melanogaster reference
        genome has revealed that short read genotyping methods miss hundreds of structural
        variants, including those affecting phenotypes. While genomes assembled using
        highcoverage long reads can achieve high levels of contiguity and completeness,
        concerns about cost, errors, and low yield have limited widespread adoption
        of such sequencing approaches. Here we resequenced the reference strain of
        D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for
        24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we
        assembled a highly contiguous de novo genome. The addition of inexpensive
        paired reads and subsequent scaffolding using an optical map technology achieved
        an assembly with completeness and contiguity comparable to the D. melanogaster
        reference assembly. Comparison of our assembly to the reference assembly of
        ISO1 uncovered a number of structural variants (SVs), including novel LTR
        transposable element insertions and duplications affecting genes with developmental,
        behavioral, and metabolic functions. Collectively, these SVs provide a snapshot
        of the dynamics of genome evolution. Furthermore, our assembly and comparison
        to the D. melanogaster reference genome demonstrates that high-quality de
        novo assembly of reference genomes and comprehensive variant discovery using
        such assemblies are now possible by a single lab for under $1,000 (USD).
      authors:
      - name: Solares E.A.
      - name: Chakraborty M.
      - name: Miller D.E.
      - name: Kalsow S.
      - name: Hall K.
      - name: Perera A.G.
      - name: Emerson J.J.
      - name: Scott Hawley R.
      citationCount: 70
      date: '2018-10-01T00:00:00Z'
      journal: 'G3: Genes, Genomes, Genetics'
      title: Rapid low-cost assembly of the drosophila melanogaster reference genome
        using low-coverage, long-read sequencing
    note: null
    pmcid: PMC6169397
    pmid: '30018084'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Structural variation
    uri: http://edamontology.org/topic_3175
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  validated: 0
  version:
  - v.0.3
- accessibility: Open access
  additionDate: '2017-08-20T16:34:27Z'
  biotoolsCURIE: biotools:pavian
  biotoolsID: pavian
  collectionID:
  - Animal and Crop Genomics
  - Biodiversity
  - microbiome
  confidence_flag: null
  cost: null
  credit:
  - email: fbreitw1@jhmi.edu
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Web application for exploring metagenomics classification results,
    with a special focus on infectious disease diagnosis. Pinpointing pathogens in
    metagenomics classification results is often complicated by host and laboratory
    contaminants as well as many non-pathogenic microbiota. Researchers can analyze,
    display and transform results from the Kraken and Centrifuge classifiers using
    interactive tables, heatmaps and flow diagrams.
  documentation:
  - note: null
    type:
    - User manual
    url: https://ccb.jhu.edu/software/pavian/index.shtml?t=manual
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    note: null
    operation:
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format: []
  homepage: https://ccb.jhu.edu/software/pavian/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-06-17T15:12:54.095225Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/fbreitwieser/pavian/tree/master
  maturity: null
  name: Pavian
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: admin
  publication:
  - doi: 10.1101/084715
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  validated: 1
  version: []
- accessibility: null
  additionDate: '2025-06-02T12:24:30.535794Z'
  biotoolsCURIE: biotools:wtv
  biotoolsID: wtv
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: "A CLI/python library that selects characteristic qualitative ions\
    \ based on \nhttps://github.com/yuanhonglun/WTV_2.0"
  documentation:
  - note: null
    type:
    - User manual
    url: https://recetox.github.io/wtv/
  download:
  - note: null
    type: Source code
    url: https://github.com/RECETOX/wtv
    version: null
  - note: null
    type: Software package
    url: https://pypi.org/project/wtv/
    version: null
  - note: null
    type: Tool wrapper (Galaxy)
    url: https://github.com/RECETOX/galaxytools/tree/master/tools/wtv
    version: null
  editPermission:
    authors:
    - recetox-specdatri
    type: group
  elixirCommunity:
  - Metabolomics
  elixirNode:
  - Czech Republic
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: wtv-cli --msp_path input.msp --outpath output --mz_min 35 --mz_max 400 ...
    input:
    - data:
        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
      - term: MSP
        uri: http://edamontology.org/format_4039
    note: null
    operation:
    - term: Feature selection
      uri: http://edamontology.org/operation_3936
    output:
    - data:
        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
      - term: MSP
        uri: http://edamontology.org/format_4039
  homepage: https://recetox.github.io/wtv/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-06-12T09:26:29.793603Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/RECETOX/wtv
  maturity: Emerging
  name: wtv
  operatingSystem: []
  otherID: []
  owner: acquayefrank
  publication:
  - doi: 10.1016/j.molp.2024.04.012
    metadata:
      abstract: Volatilomics is essential for understanding the biological functions
        and fragrance contributions of plant volatiles. However, the annotation coverage
        achieved using current untargeted and widely targeted volatomics (WTV) methods
        has been limited by low sensitivity and/or low acquisition coverage. Here,
        we introduce WTV 2.0, which enabled the construction of a high-coverage library
        containing 2111 plant volatiles, and report the development of a comprehensive
        selective ion monitoring (cSIM) acquisition method, including the selection
        of characteristic qualitative ions with the minimal ion number for each compound
        and an optimized segmentation method, that can acquire the smallest but sufficient
        number of ions for most plant volatiles, as well as the automatic qualitative
        and semi-quantitative analysis of cSIM data. Importantly, the library and
        acquisition method we developed can be self-expanded by incorporating compounds
        not present in the library, utilizing the obtained cSIM data. We showed that
        WTV 2.0 increases the median signal-to-noise ratio by 7.6-fold compared with
        the untargeted method, doubled the annotation coverage compared with the untargeted
        and WTV 1.0 methods in tomato fruit, and led to the discovery of menthofuran
        as a novel flavor compound in passion fruit. WTV 2.0 is a Python library with
        a user-friendly interface and is applicable to profiling of volatiles and
        primary metabolites in any species.
      authors:
      - name: Yuan H.
      - name: Jiangfang Y.
      - name: Liu Z.
      - name: Su R.
      - name: Li Q.
      - name: Fang C.
      - name: Huang S.
      - name: Liu X.
      - name: Fernie A.R.
      - name: Luo J.
      citationCount: 12
      date: '2024-06-03T00:00:00Z'
      journal: Molecular Plant
      title: 'WTV2.0: A high-coverage plant volatilomics method with a comprehensive
        selective ion monitoring acquisition mode'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  validated: 0
  version:
  - 0.0.2
- accessibility: null
  additionDate: '2017-08-20T15:17:20Z'
  biotoolsCURIE: biotools:bracken
  biotoolsID: bracken
  collectionID:
  - Animal and Crop Genomics
  confidence_flag: null
  cost: null
  credit:
  - email: jlu26@jhmi.edu
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2
    While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken
    allows estimation of abundance at a single level using those classifications (e.g.
    Bracken can estimate abundance of species within a sample).
  documentation:
  - note: null
    type:
    - User manual
    url: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
  download: []
  editPermission:
    authors:
    - animalandcropgenomics
    - ELIXIR-CZ
    - bebatut
    - vashokan
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output: []
  homepage: https://ccb.jhu.edu/software/bracken/
  homepage_status: 0
  language:
  - Perl
  - Python
  lastUpdate: '2025-06-11T12:25:29.118910Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/jenniferlu717/Bracken
  - note: null
    type:
    - Issue tracker
    url: https://github.com/jenniferlu717/Bracken/issues
  maturity: null
  name: Bracken
  operatingSystem:
  - Linux
  otherID: []
  owner: admin
  publication:
  - doi: 10.7717/peerj-cs.104
    metadata:
      abstract: Metagenomic experiments attempt to characterize microbial communities
        using high-throughput DNA sequencing. Identification of the microorganisms
        in a sample provides information about the genetic profile, population structure,
        and role of microorganisms within an environment. Until recently, most metagenomics
        studies focused on high-level characterization at the level of phyla, or alternatively
        sequenced the 16S ribosomalRNAgene that is present in bacterial species. As
        the cost of sequencing has fallen, though, metagenomics experiments have increasingly
        used unbiased shotgun sequencing to capture all the organisms in a sample.
        This approach requires a method for estimating abundance directly from the
        raw read data. Here we describe a fast, accurate new method that computes
        the abundance at the species level using the reads collected in a metagenomics
        experiment. Bracken (Bayesian Reestimation of Abundance after Classification
        with KrakEN) uses the taxonomic assignments made by Kraken, a very fast read-level
        classifier, along with information about the genomes themselves to estimate
        abundance at the species level, the genus level, or above. We demonstrate
        that Bracken can produce accurate species- and genus-level abundance estimates
        even when a sample contains multiple near-identical species.
      authors:
      - name: Lu J.
      - name: Breitwieser F.P.
      - name: Thielen P.
      - name: Salzberg S.L.
      citationCount: 1084
      date: '2017-01-01T00:00:00Z'
      journal: PeerJ Computer Science
      title: 'Bracken: Estimating species abundance in metagenomics data'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: kraken2
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2021-05-26T20:42:18Z'
  biotoolsCURIE: biotools:maldi_quant
  biotoolsID: maldi_quant
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: mail@sebastiangibb.de
    fundrefid: null
    gridid: null
    name: Sebastian Gibb
    note: null
    orcidid: https://orcid.org/0000-0001-7406-4443
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Korbinian Strimmer
    note: null
    orcidid: https://orcid.org/0000-0001-7917-2056
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: MALDIquant is a complete analysis pipeline for matrix-assisted laser
    desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass
    spectrometry data. In addition to commonly used plotting and processing methods
    it includes distinctive features, namely baseline subtraction methods such as
    morphological filters (TopHat) or the statistics-sensitive non-linear iterative
    peak-clipping algorithm (SNIP), peak alignment using warping functions, handling
    of replicated measurements as well as allowing spectra with different resolutions.
  documentation:
  - note: null
    type:
    - General
    url: https://cran.r-project.org/web/packages/MALDIquant/MALDIquant.pdf
  download: []
  editPermission:
    authors:
    - sizhengZhao
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: imzML metadata file
        uri: http://edamontology.org/format_3682
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: ibd
        uri: http://edamontology.org/format_3839
    note: null
    operation:
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    - term: Spectrum calculation
      uri: http://edamontology.org/operation_3860
    - term: Peak detection
      uri: http://edamontology.org/operation_3215
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  - cmd: null
    input:
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: imzML metadata file
        uri: http://edamontology.org/format_3682
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: ibd
        uri: http://edamontology.org/format_3839
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
  - cmd: null
    input:
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: imzML metadata file
        uri: http://edamontology.org/format_3682
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: ibd
        uri: http://edamontology.org/format_3839
    note: null
    operation:
    - term: Mass spectra calibration
      uri: http://edamontology.org/operation_3627
    output:
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: imzML metadata file
        uri: http://edamontology.org/format_3682
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: ibd
        uri: http://edamontology.org/format_3839
  homepage: https://cran.r-project.org/package=MALDIquant
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-06-05T11:28:57.497366Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/sgibb/MALDIquant/
  - note: null
    type:
    - Issue tracker
    url: https://github.com/sgibb/MALDIquant/issues
  - note: null
    type:
    - Other
    url: http://strimmerlab.org/software/maldiquant/
  maturity: null
  name: MALDIquant
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1093/bioinformatics/bts447
    metadata:
      abstract: MALDIquant is an R package providing a complete and modular analysis
        pipeline for quantitative analysis of mass spectrometry data. MALDIquant is
        specifically designed with application in clinical diagnostics in mind and
        implements sophisticated routines for importing raw data, preprocessing, non-linear
        peak alignment and calibration. It also handles technical replicates as well
        as spectra with unequal resolution. © The Author 2012. Published by Oxford
        University Press. All rights reserved.
      authors:
      - name: Gibb S.
      - name: Strimmer K.
      citationCount: 499
      date: '2012-09-01T00:00:00Z'
      journal: Bioinformatics
      title: 'Maldiquant: A versatile R package for the analysis of mass spectrometry
        data'
    note: null
    pmcid: null
    pmid: '22796955'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  - Workflow
  topic:
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-04-18T15:04:18.411979Z'
  biotoolsCURIE: biotools:dicom_tags_extractor
  biotoolsID: dicom_tags_extractor
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: BC|Platforms
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: 'The tool scans the imaging DICOM files of a defined directory at the
    series level, and produces as output one single JSON file containing all the DICOM
    tags for each detected series.

    If a list of selected DICOM tags is provided, the tool can also produce one single
    csv file containing the listed DICOM tags.

    To use this tool, the user can download an executable file (.exe). Two execution
    modes are available : manual execution and command line execution.

    For the tool to scan data successfully, it is important that : 1/ the extension
    “.dcm” is visible, as the tool only scans those files, and discard any other;
    2/ each DICOM series has its own folder, as the tool gets a single .dcm file from
    each folder and extracts the tags.'
  documentation: []
  download:
  - note: '1- Install ORAS tool (https://oras.land/docs/installation).

      2- Login in the registry using the command oras login harbor.eucaim.cancerimage.eu,
      and provide a username and a token

      3- Download the file by using the command oras pull harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_tag_extraction:1.0'
    type: Software package
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data formatting
      uri: http://edamontology.org/operation_0335
    output: []
  homepage: https://www.bcplatforms.com/
  homepage_status: 0
  language: []
  lastUpdate: '2025-06-04T11:29:09.107990Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Other
    url: https://www.bcplatforms.com/
  maturity: Emerging
  name: DICOM tags extractor
  operatingSystem: []
  otherID: []
  owner: lsaint-aubert
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version: []
- accessibility: null
  additionDate: '2024-09-06T14:19:58.602565Z'
  biotoolsCURIE: biotools:bdpn
  biotoolsID: bdpn
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: anna.zhukova@pasteur.fr
    fundrefid: null
    gridid: null
    name: Anna Zhukova
    note: null
    orcidid: https://orcid.org/0000-0003-2200-7935
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://research.pasteur.fr/en/member/anna-zhukova/
  description: Estimator of epidemiological parameters under the Birth-Death with
    Contact Tracing (BD-CT) model from phylogenetic trees and a non-parametric CT
    detection test.
  documentation:
  - note: null
    type:
    - Command-line options
    url: https://pypi.org/project/bdct
  download:
  - note: null
    type: Source code
    url: https://github.com/evolbioinfo/bdct
    version: null
  - note: null
    type: Downloads page
    url: https://pypi.org/project/bdct
    version: null
  - note: null
    type: Container file
    url: https://hub.docker.com/r/evolbioinfo/bdct
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    note: null
    operation:
    - term: Statistical inference
      uri: http://edamontology.org/operation_3658
    output:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
  homepage: https://github.com/evolbioinfo/bdct
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-06-02T14:34:59.109392Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/evolbioinfo/bdct
  maturity: null
  name: bdct
  operatingSystem: []
  otherID: []
  owner: azhukova
  publication:
  - doi: 10.1371/journal.pcbi.1012461
    metadata: null
    note: null
    pmcid: null
    pmid: '40440423'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Public health and epidemiology
    uri: http://edamontology.org/topic_3305
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2019-05-27T16:59:15Z'
  biotoolsCURIE: biotools:SLiM_software
  biotoolsID: SLiM_software
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: messer@cornell.edu
    fundrefid: null
    gridid: null
    name: Philipp Messer
    note: null
    orcidid: https://orcid.org/0000-0001-8453-9377
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://messerlab.org
  - email: bhaller@benhaller.com
    fundrefid: null
    gridid: null
    name: Benjamin C. Haller
    note: null
    orcidid: https://orcid.org/0000-0003-1874-8327
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://benhaller.com
  description: Evolutionary simulation framework that combines a powerful engine for
    population genetic simulations with the capability of modeling arbitrarily complex
    evolutionary scenarios.  Includes a graphical modeling environment.
  documentation:
  - note: The manual for SLiM itself
    type:
    - User manual
    url: http://benhaller.com/slim/SLiM_Manual.pdf
  - note: The manual for Eidos, the scripting language used by SLiM
    type:
    - User manual
    url: http://benhaller.com/slim/Eidos_Manual.pdf
  - note: Quick reference sheets for SLiM and Eidos
    type:
    - Quick start guide
    url: http://benhaller.com/slim/SLiMEidosRefSheets.zip
  download:
  - note: A source archive for the command-line `slim` tool only.  Complete source
      code is on GitHub, but most platforms have an installer anyway; see the manual,
      chapter 2, for installation instructions.
    type: Source code
    url: http://benhaller.com/slim/SLiM.zip
    version: null
  - note: The GitHub page for the current release version, to obtain full source code.
    type: Downloads page
    url: https://github.com/MesserLab/SLiM/releases/latest
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Run individual-based eco-evolutionary simulations with explicit genetics
    operation:
    - term: DNA substitution modelling
      uri: http://edamontology.org/operation_0550
    - term: Sequence generation
      uri: http://edamontology.org/operation_0230
    - term: Ecological modelling
      uri: http://edamontology.org/operation_3946
    output: []
  homepage: https://messerlab.org/slim/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-04-18T17:40:38.228809Z'
  license: GPL-3.0
  link:
  - note: SLiM home page in the Messer Lab website
    type:
    - Software catalogue
    url: https://messerlab.org/slim/
  - note: GitHub repository for SLiM
    type:
    - Repository
    url: https://github.com/MesserLab/SLiM
  - note: Discussion forum for SLiM questions
    type:
    - Discussion forum
    url: https://groups.google.com/g/slim-discuss
  - note: Announcements mailing list
    type:
    - Mailing list
    url: https://groups.google.com/g/slim-announce
  maturity: Mature
  name: SLiM
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: bchaller
  publication:
  - doi: 10.1093/molbev/msy228
    metadata:
      abstract: With the desire to model population genetic processes under increasingly
        realistic scenarios, forward genetic simulations have become a critical part
        of the toolbox of modern evolutionary biology. The SLiM forward genetic simulation
        framework is one of the most powerful and widely used tools in this area.
        However, its foundation in the Wright-Fisher model has been found to pose
        an obstacle to implementing many types of models; it is difficult to adapt
        the Wright-Fisher model, with its many assumptions, to modeling ecologically
        realistic scenarios such as explicit space, overlapping generations, individual
        variation in reproduction, density-dependent population regulation, individual
        variation in dispersal or migration, local extinction and recolonization,
        mating between subpopulations, age structure, fitness-based survival and hard
        selection, emergent sex ratios, and so forth. In response to this need, we
        here introduce SLiM 3, which contains two key advancements aimed at abolishing
        these limitations. First, the new non-Wright-Fisher or "nonWF" model type
        provides a much more flexible foundation that allows the easy implementation
        of all of the above scenarios and many more. Second, SLiM 3 adds support for
        continuous space, including spatial interactions and spatial maps of environmental
        variables. We provide a conceptual overview of these new features, and present
        several example models to illustrate their use.
      authors:
      - name: Haller B.C.
      - name: Messer P.W.
      citationCount: 504
      date: '2019-03-01T00:00:00Z'
      journal: Molecular Biology and Evolution
      title: 'SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model'
    note: 'B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond
      the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637.'
    pmcid: PMC6389312
    pmid: '30517680'
    type:
    - Other
    version: null
  - doi: 10.1093/molbev/msy237
    metadata:
      abstract: The SLiM forward genetic simulation framework has proved to be a powerful
        and flexible tool for population genetic modeling. However, as a complex piece
        of software with many features that allow simulating a diverse assortment
        of evolutionary models, its initial learning curve can be difficult. Here
        we provide a step-by-step demonstration of how to build a simple evolutionary
        model in SLiM 3, to help new users get started. We will begin with a panmictic
        neutral model, and build up to a model of the evolution of a polygenic quantitative
        trait under selection for an environmental phenotypic optimum.
      authors:
      - name: Haller B.C.
      - name: Messer P.W.
      citationCount: 12
      date: '2019-05-01T00:00:00Z'
      journal: Molecular Biology and Evolution
      title: Evolutionary Modeling in SLiM 3 for Beginners
    note: B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners.
      Molecular Biology and Evolution 36(5), 1101–1109.
    pmcid: PMC6501880
    pmid: '30590560'
    type:
    - Usage
    version: null
  - doi: 10.1111/1755-0998.12968
    metadata:
      abstract: 'There is an increasing demand for evolutionary models to incorporate
        relatively realistic dynamics, ranging from selection at many genomic sites
        to complex demography, population structure, and ecological interactions.
        Such models can generally be implemented as individual-based forward simulations,
        but the large computational overhead of these models often makes simulation
        of whole chromosome sequences in large populations infeasible. This situation
        presents an important obstacle to the field that requires conceptual advances
        to overcome. The recently developed tree-sequence recording method (Kelleher,
        Thornton, Ashander, & Ralph, 2018), which stores the genealogical history
        of all genomes in the simulated population, could provide such an advance.
        This method has several benefits: (1) it allows neutral mutations to be omitted
        entirely from forward-time simulations and added later, thereby dramatically
        improving computational efficiency; (2) it allows neutral burn-in to be constructed
        extremely efficiently after the fact, using “recapitation”; (3) it allows
        direct examination and analysis of the genealogical trees along the genome;
        and (4) it provides a compact representation of a population''s genealogy
        that can be analysed in Python using the msprime package. We have implemented
        the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary
        simulation software package) and extended it to allow the recording of non-neutral
        mutations, greatly broadening the utility of this method. To demonstrate the
        versatility and performance of this approach, we showcase several practical
        applications that would have been beyond the reach of previously existing
        methods, opening up new horizons for the modelling and exploration of evolutionary
        processes.'
      authors:
      - name: Haller B.C.
      - name: Galloway J.
      - name: Kelleher J.
      - name: Messer P.W.
      - name: Ralph P.L.
      citationCount: 109
      date: '2019-03-01T00:00:00Z'
      journal: Molecular Ecology Resources
      title: Tree-sequence recording in SLiM opens new horizons for forward-time simulation
        of whole genomes
    note: B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019).
      Tree-sequence recording in SLiM opens new horizons for forward-time simulation
      of whole genomes. Molecular Ecology Resources 19(2), 552–566.
    pmcid: PMC6393187
    pmid: '30565882'
    type:
    - Method
    version: null
  - doi: 10.1086/723601
    metadata:
      abstract: The SLiM software framework for genetically explicit forward simulation
        has been widely used in population genetics. However, it has been largely
        restricted to modeling only a single species, which has limited its broader
        utility in evolutionary biology. Indeed, to our knowledge no general-purpose,
        flexible modeling framework exists that provides support for simulating multiple
        species while also providing other key features, such as explicit genetics
        and continuous space. The lack of such software has limited our ability to
        model higher biological levels such as communities, eco-systems, coevolutionary
        and eco-evolutionary processes, and bio-diversity, which is crucial for many
        purposes, from extending our basic understanding of evolutionary ecology to
        informing conservation and management decisions. We here announce the release
        of SLiM 4, which fills this important gap by adding support for multiple species,
        including ecological interactions between species such as predation, parasitism,
        and mutualism, and illustrate its new features with examples.
      authors:
      - name: Haller B.C.
      - name: Messer P.W.
      citationCount: 79
      date: '2023-05-01T00:00:00Z'
      journal: American Naturalist
      title: 'SLiM 4: Multispecies Eco-Evolutionary Modeling'
    note: 'B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary
      modeling. The American Naturalist 201(5), E127–E139.'
    pmcid: PMC10793872
    pmid: '37130229'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  validated: 0
  version:
  - '5.0'
- accessibility: Open access
  additionDate: '2024-04-16T14:14:05.166974Z'
  biotoolsCURIE: biotools:mudoger
  biotoolsID: mudoger
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: ulisses.rocha@ufz.de
    fundrefid: null
    gridid: null
    name: Ulisses Rocha
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: The Multi-Domain Genome Recovery v1.0 (MuDoGeR v1.0) framework is a
    tool developed to help users to recover Metagenome-Assembled Genomes and Uncultivated
    Viral Genomes from whole-genome sequence (WGS) samples simultaneously. The MuDoGeR
    v1.0 framework acts as a wrapper for several tools. It was designed to be an easy-to-use
    tool that outputs ready-to-use comprehensive files.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output: []
  homepage: https://github.com/mdsufz/MuDoGeR
  homepage_status: 0
  language:
  - Shell
  - R
  - Python
  lastUpdate: '2025-04-09T07:23:51.614291Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/mdsufz/MuDoGeR
  maturity: null
  name: MuDoGeR
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1111/1755-0998.13904
    metadata:
      abstract: Several computational frameworks and workflows that recover genomes
        from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is
        difficult for scientists with little bioinformatics experience to evaluate
        quality, annotate genes, dereplicate, assign taxonomy and calculate relative
        abundance and coverage of genomes belonging to different domains. MuDoGeR
        is a user-friendly tool tailored for those familiar with Unix command-line
        environment that makes it easy to recover genomes of prokaryotes, eukaryotes
        and viruses from metagenomes, either alone or in combination. We tested MuDoGeR
        using 24 individual-isolated genomes and 574 metagenomes, demonstrating the
        applicability for a few samples and high throughput. While MuDoGeR can recover
        eukaryotic viral sequences, its characterization is predominantly skewed towards
        bacterial and archaeal viruses, reflecting the field's current state. However,
        acting as a dynamic wrapper, the MuDoGeR is designed to constantly incorporate
        updates and integrate new tools, ensuring its ongoing relevance in the rapidly
        evolving field. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR.
        Additionally, MuDoGeR is also available as a Singularity container.
      authors:
      - name: Rocha U.
      - name: CoelhoKasmanas J.
      - name: Kallies R.
      - name: Saraiva J.P.
      - name: Toscan R.B.
      - name: Stefanic P.
      - name: Bicalho M.F.
      - name: BorimCorrea F.
      - name: Basturk M.N.
      - name: Fousekis E.
      - name: VianaBarbosa L.M.
      - name: Plewka J.
      - name: Probst A.J.
      - name: Baldrian P.
      - name: Stadler P.F.
      citationCount: 5
      date: '2024-02-01T00:00:00Z'
      journal: Molecular Ecology Resources
      title: 'MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy'
    note: null
    pmcid: null
    pmid: '37994269'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-04-08T11:23:25.060891Z'
  biotoolsCURIE: biotools:checkm2
  biotoolsID: checkm2
  collectionID:
  - NFDI4Microbiota
  confidence_flag: null
  cost: null
  credit: []
  description: 'Rapid assessment of genome bin quality using machine learning.


    CheckM2 uses two distinct machine learning models to predict genome completeness.
    The ''general'' gradient boost model is able to generalize well and is intended
    to be used on organisms not well represented in GenBank or RefSeq (roughly, when
    an organism is novel at the level of order, class or phylum). The ''specific''
    neural network model is more accurate when predicting completeness of organisms
    more closely related to the reference training set (roughly, when an organism
    belongs to a known species, genus or family). CheckM2 uses a cosine similarity
    calculation to automatically determine the appropriate completeness model for
    each input genome, but you can also force the use of a particular completeness
    model, or get the prediction outputs for both. There is only one contamination
    model (based on gradient boost) which is applied regardless of taxonomic novelty
    and works well across all cases.'
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://github.com/chklovski/CheckM2
  download:
  - note: null
    type: Biological data
    url: https://doi.org/10.5281/zenodo.14897628
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/chklovski/CheckM2
  homepage_status: 0
  language: []
  lastUpdate: '2025-04-08T11:23:25.063938Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Other
    url: https://www.nature.com/articles/s41592-023-01940-w
  maturity: Mature
  name: CheckM2
  operatingSystem:
  - Linux
  otherID: []
  owner: Kasmanas
  publication:
  - doi: 10.1038/s41592-023-01940-w
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-03-31T08:50:20.800385Z'
  biotoolsCURIE: biotools:csdr
  biotoolsID: csdr
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Differential gene coexpression analysis based on the Conserved, Specific,
    and Differentiated (CSD) method
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://almaaslab.github.io/csdR/
  homepage_status: 0
  language: []
  lastUpdate: '2025-03-31T09:00:57.202555Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://www.bioconductor.org/packages/release/bioc/html/csdR.html
  - note: null
    type:
    - Repository
    url: https://github.com/AlmaasLab/csdR
  maturity: Mature
  name: csdR
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: japet
  publication:
  - doi: 10.1186/s12859-022-04605-1
    metadata:
      abstract: 'Background: Differential co-expression network analysis has become
        an important tool to gain understanding of biological phenotypes and diseases.
        The CSD algorithm is a method to generate differential co-expression networks
        by comparing gene co-expressions from two different conditions. Each of the
        gene pairs is assigned conserved (C), specific (S) and differentiated (D)
        scores based on the co-expression of the gene pair between the two conditions.
        The result of the procedure is a network where the nodes are genes and the
        links are the gene pairs with the highest C-, S-, and D-scores. However, the
        existing CSD-implementations suffer from poor computational performance, difficult
        user procedures and lack of documentation. Results: We created the R-package
        csdR aimed at reaching good performance together with ease of use, sufficient
        documentation, and with the ability to play well with other tools for data
        analysis. csdR was benchmarked on a realistic dataset with 20,645 genes. After
        verifying that the chosen number of iterations gave sufficient robustness,
        we tested the performance against the two existing CSD implementations. csdR
        was superior in performance to one of the implementations, whereas the other
        did not run. Our implementation can utilize multiple processing cores. However,
        we were unable to achieve more than ∼ 2.7 parallel speedup with saturation
        reached at about 10 cores. Conclusion: The results suggest that csdR is a
        useful tool for differential co-expression analysis and is able to generate
        robust results within a workday on datasets of realistic sizes when run on
        a workstation or compute server.'
      authors:
      - name: Pettersen J.P.
      - name: Almaas E.
      citationCount: 3
      date: '2022-12-01T00:00:00Z'
      journal: BMC Bioinformatics
      title: csdR, an R package for differential co-expression analysis
    note: null
    pmcid: PMC8858518
    pmid: '35183100'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Gene regulation
    uri: http://edamontology.org/topic_0204
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-03-22T00:35:21.183948Z'
  biotoolsCURIE: biotools:deepannotation
  biotoolsID: deepannotation
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: The python package 'DeepAnnotation' can be used to perform genomic
    selection (GS), which is a promising breeding strategy for agricultural breeding.
    DeepAnnotation predicts phenotypes from comprehensive multi-omics functional annotations
    with interpretable deep learning framework.
  documentation: []
  download:
  - note: GitHub repository
    type: Downloads page
    url: https://github.com/mawenlong2016/DeepAnnotation
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/mawenlong2016/DeepAnnotation
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-03-22T00:35:21.186342Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/mawenlong2016/DeepAnnotation
  maturity: null
  name: DeepAnnotation
  operatingSystem: []
  otherID: []
  owner: mawenlong2025
  publication: []
  relation: []
  toolType:
  - Command-line tool
  - Script
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-03-20T09:46:51.356874Z'
  biotoolsCURIE: biotools:spacedust
  biotoolsID: spacedust
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Spacedust is a modular toolkit for identification of conserved gene
    clusters among multiple genomes based on homology and conservation of gene neighborhood.
    Spacedust adapts the fast and sensitive structure comparisons of Foldseek and
    homology search capabilities of MMseqs2. It introduces a novel approach of aggregating
    sets of homologous hits between pairs of genomes and identifies cluster of hits
    with conserved gene neighborhood between each using agglomerative hierarchical
    clustering algorithm.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/soedinglab/spacedust/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-03-20T09:46:51.359476Z'
  license: GPL-3.0
  link: []
  maturity: Emerging
  name: Spacedust
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: milot-mirdita
  publication:
  - doi: 10.1101/2024.10.02.616292v1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-03-17T15:56:34.552871Z'
  biotoolsCURIE: biotools:chewbbaca
  biotoolsID: chewbbaca
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: chewBBACA is a software suite for the creation and evaluation of core
    genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
  documentation:
  - note: null
    type:
    - User manual
    url: https://chewbbaca.readthedocs.io/en/latest/index.html
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Multilocus sequence typing
      uri: http://edamontology.org/operation_3840
    output: []
  homepage: https://github.com/B-UMMI/chewBBACA
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-03-19T14:47:22.843193Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: chewBBaca
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: EngyNasr
  publication:
  - doi: 10.1099/MGEN.0.000166
    metadata:
      abstract: Gene-by-gene approaches are becoming increasingly popular in bacterial
        genomic epidemiology and outbreak detection. However, there is a lack of open-source
        scalable software for schema definition and allele calling for these methodologies.
        The chewBBACA suite was designed to assist users in the creation and evaluation
        of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent
        allele calling in bacterial strains of interest. chewBBACA performs the schema
        creation and allele calls on complete or draft genomes resulting from de novo
        assemblers. The chewBBACA software uses Python 3.4 or higher and can run on
        a laptop or in high performance clusters making it useful for both small laboratories
        and large reference centers. ChewBBACA is available at https://github.com/B-UMMI/chewBBACA.
      authors:
      - name: Silva M.
      - name: Machado M.P.
      - name: Silva D.N.
      - name: Rossi M.
      - name: Moran-Gilad J.
      - name: Santos S.
      - name: Ramirez M.
      - name: Carrico J.A.
      citationCount: 276
      date: '2018-03-01T00:00:00Z'
      journal: Microbial genomics
      title: 'chewBBACA: A complete suite for gene-by-gene schema creation and strain
        identification'
    note: null
    pmcid: PMC5885018
    pmid: '29543149'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-03-12T15:38:32.218141Z'
  biotoolsCURIE: biotools:gtestimate
  biotoolsID: gtestimate
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: GTestimate is a scRNA-seq normalization method. In contrast to other
    methods it uses the Simple Good-Turing estimator for the per cell relative gene
    expression estimation.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/Martin-Fahrenberger/GTestimate
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: GTestimate()
    input:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format: []
    note: GTestimate is provided as an R-package containing the GTestimate() function.
    operation:
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    output:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
  homepage: https://github.com/Martin-Fahrenberger/GTestimate
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-03-12T15:38:32.221353Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    - Repository
    url: https://github.com/Martin-Fahrenberger/GTestimate
  maturity: Mature
  name: GTestimate
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: martin_fahrenberger
  publication:
  - doi: 10.1101/2024.07.02.601501
    metadata: null
    note: preprint version 2
    pmcid: null
    pmid: null
    type:
    - Method
    version: '2'
  relation: []
  toolType:
  - Library
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-02-07T18:01:50.963394Z'
  biotoolsCURIE: biotools:autobigs.cli
  biotoolsID: autobigs.cli
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A command-line interface (CLI) based program that allows quickly batched
    requests for obtaining MLST profiles on multiple FASTA sequences and exporting
    it as a convenient CSV. Capable of querying a variety of MLST databases from both
    Institut Pasteur and PubMLST.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://pypi.org/project/autoBIGS.cli/
  homepage_status: 0
  language: []
  lastUpdate: '2025-03-04T20:00:40.298949Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/RealYHD/autoBIGS.cli
  maturity: Emerging
  name: AutoBIGS.CLI
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: RealYHD
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - 0.3.1
  - 0.4.0
  - 0.4.1
  - 0.4.2
  - 0.4.3
  - 0.4.4
  - 0.5.0
  - 0.6.0
  - 0.6.1
  - 0.6.2
- accessibility: Open access
  additionDate: '2025-03-03T13:46:56.613465Z'
  biotoolsCURIE: biotools:mosim
  biotoolsID: mosim
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: sotacam@eio.upv.es
    fundrefid: null
    gridid: null
    name: Sonia Tarazona
    note: null
    orcidid: https://orcid.org/0000-0001-5346-1407
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Maintainer
    url: null
  description: MOSim (Multi-Omics Simulation) package simulates multi-omic experiments
    that mimic regulatory mechanisms within the cell, allowing flexible experimental
    design including time course and multiple groups.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output: []
  homepage: https://bioconductor.org/packages/release/bioc/html/MOSim.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-03-04T15:12:34.696650Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ConesaLab/MOSim
  - note: null
    type:
    - Issue tracker
    url: https://github.com/ConesaLab/MOSim/issues
  maturity: Emerging
  name: MOSim
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: biostatomics1
  publication:
  - doi: 10.1101/421834
    metadata: null
    note: This is a preprint accesible at bioRxiv. When the paper is published it
      will be updated
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Multiomics
    uri: http://edamontology.org/topic_4021
  - term: Simulation experiment
    uri: http://edamontology.org/topic_3524
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - 2.2.0
- accessibility: Open access
  additionDate: '2021-01-18T09:08:27Z'
  biotoolsCURIE: biotools:metidfyr
  biotoolsID: metidfyr
  collectionID: []
  confidence_flag: tool
  cost: null
  credit: []
  description: 'Open-Source R Package to Decipher Small-Molecule Drugs Metabolism
    Through High Resolution Mass Spectrometry.


    MetIDfyR is an open-source, cross-platform and versatile R script to predict and
    detect metabolites in mass spectrometry data (mzML) based on the raw formula of
    the drug of interest.'
  documentation:
  - note: null
    type:
    - Quick start guide
    - Installation instructions
    - Citation instructions
    url: https://github.com/agnesbrnb/MetIDfyR
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: mzML
        uri: http://edamontology.org/format_3244
    - data:
        term: Chemical formula
        uri: http://edamontology.org/data_0846
      format: []
    note: null
    operation:
    - term: Natural product identification
      uri: http://edamontology.org/operation_3803
    - term: Phasing
      uri: http://edamontology.org/operation_3454
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
  homepage: https://github.com/agnesbrnb/MetIDfyR
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-02-27T15:46:01.807140Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: MetIDfyR
  operatingSystem: []
  otherID: []
  owner: agnesbarnabe
  publication:
  - doi: 10.1021/acs.analchem.0c02281
    metadata:
      abstract: With recent advances in analytical chemistry, liquid chromatography
        high-resolution tandem mass spectrometry (LC-HRMS/MS) has become an essential
        tool for metabolite discovery and detection. Even if most of the common drug
        transformations have already been extensively described, manual search of
        drug metabolites in LC-HRMS/MS datasets is still a common practice in toxicology
        laboratories, complicating metabolite discovery. Furthermore, the availability
        of free open-source software for metabolite discovery is still limited. In
        this article, we present MetIDfyR, an open-source and cross-platform R package
        for in silico drug phase I/II biotransformation prediction and mass-spectrometric
        data mining. MetIDfyR has proven its efficacy for advanced metabolite identification
        in semi-complex and complex mixtures in in vitro or in vivo drug studies and
        is freely available at github.com/agnesblch/MetIDfyR.
      authors:
      - name: Delcourt V.
      - name: Barnabe A.
      - name: Loup B.
      - name: Garcia P.
      - name: Andre F.
      - name: Chabot B.
      - name: Trevisiol S.
      - name: Moulard Y.
      - name: Popot M.-A.
      - name: Bailly-Chouriberry L.
      citationCount: 10
      date: '2020-10-06T00:00:00Z'
      journal: Analytical Chemistry
      title: 'MetIDfyR: An Open-Source R Package to Decipher Small-Molecule Drug Metabolism
        through High-Resolution Mass Spectrometry'
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Script
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Drug metabolism
    uri: http://edamontology.org/topic_3375
  - term: Analytical chemistry
    uri: http://edamontology.org/topic_3370
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2022-08-28T00:23:42.459646Z'
  biotoolsCURIE: biotools:magneto
  biotoolsID: magneto
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: samuel.chaffron@ls2n.fr
    fundrefid: null
    gridid: null
    name: Samuel Chaffron
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Benjamin Churcheward
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Audrey Bihouée
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Guillaume Fertin
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: hugo.lefeuvre@univ-nantes.fr
    fundrefid: null
    gridid: null
    name: Hugo Lefeuvre
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: An automated workflow for genome-resolved metagenomics
  documentation:
  - note: null
    type:
    - User manual
    url: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto/-/wikis/home
  download:
  - note: null
    type: Source code
    url: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto/-/releases/1.2
    version: '1.2'
  - note: null
    type: Software package
    url: https://anaconda.org/bioconda/magneto
    version: '1.2'
  editPermission:
    authors:
    - hugo-lefeuvre
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: magneto run all --profile config/slurm/ --config target=single_assembly --rerun-incomplete
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: GZIP format
        uri: http://edamontology.org/format_3989
    note: null
    operation:
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    - term: Sequence trimming
      uri: http://edamontology.org/operation_3192
    - term: Read pre-processing
      uri: http://edamontology.org/operation_3219
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    - term: Gene prediction
      uri: http://edamontology.org/operation_2454
    output:
    - data:
        term: Taxonomic classification
        uri: http://edamontology.org/data_1872
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Gene report
        uri: http://edamontology.org/data_0916
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-02-24T16:29:20.503951Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto
  maturity: null
  name: MAGNETO
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Jennifer
  publication:
  - doi: 10.1128/msystems.00432-22
    metadata:
      abstract: 'Metagenome-assembled genomes (MAGs) represent individual genomes
        recovered from metagenomic data. MAGs are extremely useful to analyze uncultured
        microbial genomic diversity, as well as to characterize associated functional
        and metabolic potential in natural environments. Recent computational developments
        have considerably improved MAG reconstruction but also emphasized several
        limitations, such as the nonbinning of sequence regions with repetitions or
        distinct nucleotidic composition. Different assembly and binning strategies
        are often used; however, it still remains unclear which assembly strategy,
        in combination with which binning approach, offers the best performance for
        MAG recovery. Several workflows have been proposed in order to reconstruct
        MAGs, but users are usually limited to single-metagenome assembly or need
        to manually define sets of metagenomes to coassemble prior to genome binning.
        Here, we present MAGNETO, an automated workflow dedicated to MAG reconstruction,
        which includes a fully-automated coassembly step informed by optimal clustering
        of metagenomic distances, and implements complementary genome binning strategies,
        for improving MAG recovery. MAGNETO is implemented as a Snakemake workflow
        and is available at: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto.
        IMPORTANCE Genome-resolved metagenomics has led to the discovery of previously
        untapped biodiversity within the microbial world. As the development of computational
        methods for the recovery of genomes from metagenomes continues, existing strategies
        need to be evaluated and compared to eventually lead to standardized computational
        workflows. In this study, we compared commonly used assembly and binning strategies
        and assessed their performance using both simulated and real metagenomic data
        sets. We propose a novel approach to automate coassembly, avoiding the requirement
        for a priori knowledge to combine metagenomic information. The comparison
        against a previous coassembly approach demonstrates a strong impact of this
        step on genome binning results, but also the benefits of informing coassembly
        for improving the quality of recovered genomes. MAGNETO integrates complementary
        assembly-binning strategies to optimize genome reconstruction and provides
        a complete reads-to-genomes workflow for the growing microbiome research community.'
      authors:
      - name: Churcheward B.
      - name: Millet M.
      - name: Bihouee A.
      - name: Fertin G.
      - name: Chaffron S.
      citationCount: 8
      date: '2022-08-01T00:00:00Z'
      journal: mSystems
      title: 'MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics'
    note: null
    pmcid: PMC9426564
    pmid: '35703559'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  validated: 1
  version:
  - '1.2'
- accessibility: Open access
  additionDate: '2023-11-09T14:07:47.020033Z'
  biotoolsCURIE: biotools:enquire
  biotoolsID: enquire
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: luca.musella@uk-erlangen.de
    fundrefid: null
    gridid: null
    name: Luca Musella
    note: null
    orcidid: https://orcid.org/0009-0008-1870-5670
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    url: http://sysbiomed-erlangen.weebly.com/
  - email: null
    fundrefid: null
    gridid: null
    name: Max Widmann
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Julio Vera
    note: null
    orcidid: https://orcid.org/0000-0002-3076-5122
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: ENQUIRE (Expanding Networks by Querying Unexpectedly Inter-Related
    Entities) offers an alternative to manual literature curation and database mining
    to study complex biomedical phenomena. ENQUIRE generates a co-occurrence network
    of genes and biomedical ontologies (MeSH) using a corpus of publications as input.
    The algorithm iteratively reconstructs and expands the network by generating PubMed
    queries from significant interrelations, until it obtains an interconnected network
    of genes and MeSH relevant to the input corpus.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/Muszeb/ENQUIRE#readme
  download:
  - note: null
    type: Downloads page
    url: https://doi.org/10.6084/m9.figshare.24434845.v10
    version: 3.0.1
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: '`apptainer run ENQUIRE.sif <script_name> [options]`'
    input:
    - data:
        term: Annotated text
        uri: http://edamontology.org/data_3779
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    note: Run one of the scripts contained in the ENQUIRE suite via the Apptainer/Singularity
      Image File (SIF).
    operation:
    - term: Named-entity and concept recognition
      uri: http://edamontology.org/operation_3280
    - term: Network analysis
      uri: http://edamontology.org/operation_3927
    - term: Relation extraction
      uri: http://edamontology.org/operation_3625
    - term: Network visualisation
      uri: http://edamontology.org/operation_3925
    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    - term: Pathway analysis
      uri: http://edamontology.org/operation_3928
    output:
    - data:
        term: Annotated text
        uri: http://edamontology.org/data_3779
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Statistical estimate score
        uri: http://edamontology.org/data_0951
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: PNG
        uri: http://edamontology.org/format_3603
  homepage: https://zenodo.org/records/12734778
  homepage_status: 0
  language:
  - Bash
  - Python
  - R
  lastUpdate: '2025-02-12T11:17:06.811354Z'
  license: GPL-3.0
  link:
  - note: Github Repository.
    type:
    - Repository
    url: https://github.com/Muszeb/ENQUIRE
  - note: SIF image (Apptainer/Singularity).
    type:
    - Repository
    url: https://figshare.com/articles/software/ENQUIRE/24434845?file=48081496
  - note: Docker Image.
    type:
    - Repository
    url: https://hub.docker.com/r/muszeb/enquire
  maturity: Emerging
  name: ENQUIRE
  operatingSystem:
  - Linux
  otherID: []
  owner: LucaMusella
  publication:
  - doi: 10.1101/2023.09.10.556351
    metadata: null
    note: BioRxiv preprint
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  - doi: 10.1371/journal.pcbi.1012745
    metadata: null
    note: Publication in PLOS Computational Biology.
    pmcid: null
    pmid: null
    type:
    - Method
    version: 3.0.1
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Natural language processing
    uri: http://edamontology.org/topic_0218
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  validated: 0
  version:
  - 1.0.0
  - 2.0.0
  - 3.0.1
- accessibility: null
  additionDate: '2025-02-12T09:09:36.042710Z'
  biotoolsCURIE: biotools:anndata2ri
  biotoolsID: anndata2ri
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: RPy2 converter from AnnData to SingleCellExperiment and back.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://icb-anndata2ri.readthedocs-hosted.com/en/latest/
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output: []
  homepage: https://github.com/theislab/anndata2ri
  homepage_status: 0
  language:
  - Python
  - R
  lastUpdate: '2025-02-12T09:09:40.845206Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/theislab/anndata2ri
  maturity: null
  name: anndata2ri
  operatingSystem: []
  otherID: []
  owner: pavanvidem
  publication: []
  relation:
  - biotoolsID: anndata
    type: uses
  - biotoolsID: singlecellexperiment
    type: uses
  toolType:
  - Library
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-01-30T06:22:50.776690Z'
  biotoolsCURIE: biotools:mygod
  biotoolsID: mygod
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Charlotte Andre
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Mark HOEBEKE
    note: null
    orcidid: https://orcid.org/0000-0001-6311-9752
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Nicolas HENRY
    note: null
    orcidid: https://orcid.org/0000-0002-7702-1382
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Cyril NOEL
    note: null
    orcidid: https://orcid.org/0000-0002-7139-4073
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Patrick DURAND
    note: null
    orcidid: https://orcid.org/0000-0002-5597-4457
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Erwan CORRE
    note: null
    orcidid: https://orcid.org/0000-0001-6354-2278
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: 'MyGOD is a Web-based visual exploration tool. It has been designed
    to enable scientists to easily build dynamic and composite graphical representations
    of biodiversity data supplemented with environmental data (ex.: physico-chemical
    measurements). Anonymous visitors have access to all data and all types of graphical
    representations offered by MyGOD. Authenticated users benefit for additional feautures:
    they can save all the settings of the dashboards they have composed for later
    reuse, they can promote their dashboards as gallery entries which makes them publicly
    accessible; and, if they have the appropriate permissions, they can directly import
    new datasets into MyGOD. Developement of MyGOD has been funded by the BioGenOuest
    network, and the Institut Français de Bioinformatique, and been carried out by
    personnel of the ABiMS platform, with contributions from the Service de Bioinformatique
    de l''IFREMER and the Mediterranean Institute of Oceanography.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://mygod.sb-roscoff.fr/public/doc/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Marine Metagenomics
  elixirNode:
  - France
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://mygod.sb-roscoff.fr/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-01-30T06:22:50.779377Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.com/mygod-biodiv
  - note: null
    type:
    - Service
    url: https://mygod.sb-roscoff.fr/public/
  maturity: Emerging
  name: 'MyGOD : Manipulate your Genomic Observatory Data'
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: corre_erwan
  publication:
  - doi: 10.5281/zenodo.6451438
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  - Bioinformatics portal
  - Workbench
  topic:
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Metabarcoding
    uri: http://edamontology.org/topic_4038
  - term: Marine biology
    uri: http://edamontology.org/topic_3387
  validated: 0
  version: []
- accessibility: null
  additionDate: '2021-01-18T10:23:20Z'
  biotoolsCURIE: biotools:metabomaps
  biotoolsID: metabomaps
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: meina.neumann-schaal@dsmz.de
    fundrefid: null
    gridid: null
    name: Meina Neumann-Schaal
    note: null
    orcidid: https://orcid.org/0000-0002-1641-019X
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'Pathway sharing and multi-omics data visualization in metabolic context.


    MetaboMAPS is a web project for manipulating metabolic pathways in SVG format.
    MetaboMAPS consists of two main parts: the visualization tool, where users can
    plot their own data set, and the plot box editor, where users can add or change
    the areas for visualization (plot boxes) and assign identifiers to them.'
  documentation: []
  download: []
  editPermission:
    authors:
    - JKoblitz
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Expression profile pathway mapping
      uri: http://edamontology.org/operation_0533
    - term: Metabolic pathway prediction
      uri: http://edamontology.org/operation_3929
    - term: Pathway visualisation
      uri: http://edamontology.org/operation_3926
    - term: Box-Whisker plot plotting
      uri: http://edamontology.org/operation_2943
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output: []
  homepage: https://metabomaps.brenda-enzymes.org
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2025-01-23T15:00:32.268669Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/JuliaHelmecke/MetaboMAPS
  maturity: null
  name: MetaboMAPS
  operatingSystem: []
  otherID: []
  owner: Niclaskn
  publication:
  - doi: 10.12688/F1000RESEARCH.23427.1
    metadata: null
    note: null
    pmcid: PMC7383707
    pmid: '32765840'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  - Web application
  topic:
  - term: Endocrinology and metabolism
    uri: http://edamontology.org/topic_3407
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2015-11-05T20:13:20Z'
  biotoolsCURIE: biotools:elixir_elearning_portal
  biotoolsID: elixir_elearning_portal
  collectionID:
  - ELIXIR-SI
  - eLearning
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: University of Ljubljana, Faculty of Medicine
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: elixir@mf.uni-lj.si
    fundrefid: null
    gridid: null
    name: ELIXIR Slovenia
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Support
    - Contributor
    url: null
  - email: brane.leskosek@mf.uni-lj.si
    fundrefid: null
    gridid: null
    name: Brane L. Leskosek
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  description: ELIXIR-SI eLearning Platform (EeLP) is a learning management system
    (LMS) continuously administered and maintained by ELIXIR Slovenia. EeLP is an
    open educational resource that enables all-in-one-place access to materials, tools
    and services for any ELIXIR-related course.
  documentation:
  - note: null
    type:
    - General
    url: https://elixir.mf.uni-lj.si/
  download: []
  editPermission:
    authors:
    - elixir.si
    - brane
    - M
    type: group
  elixirCommunity: []
  elixirNode:
  - Slovenia
  elixirPlatform:
  - Training
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: Binary format
        uri: http://edamontology.org/format_2333
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: 'Learning materials can be deposited in many formats: pdf, pptx, txt, mp3,
      mp4, zip'
    operation:
    - term: Deposition
      uri: http://edamontology.org/operation_3431
    output: []
  - cmd: null
    input: []
    note: All learning materials deposited on the platform (files and folders in all
      formats) can be downloaded by platform users.
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output: []
  homepage: https://elixir.mf.uni-lj.si
  homepage_status: 0
  language: []
  lastUpdate: '2025-01-22T08:26:32.140794Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: ELIXIR eLearning Platform
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: elixir.si
  publication: []
  relation: []
  toolType:
  - Workbench
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  validated: 1
  version:
  - '1.0'
- accessibility: null
  additionDate: '2025-01-15T00:33:16.334452Z'
  biotoolsCURIE: biotools:atsrga_arabidopsis_thaliana_stress_rsponsive_genes_atlas
  biotoolsID: atsrga_arabidopsis_thaliana_stress_rsponsive_genes_atlas
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: AtSRGA is a user-friendly application enabling users to retrieve stress-responsive
    genes in Arabidopsis thaliana. AtSRGA presents stress-responsive genes in a heatmap
    format based on a stress responsiveness measure (SRscore, see section 2-3 of tutorial).
    It facilitates the comparative analysis of individual stress responses and groups
    of genes responsive to multiple stress conditions. Researchers can identify groups
    of genes with similar patterns by examining the SRscore pattern of a gene of interest
    across 11 stress conditions. AtSRGA will enhance the screening of biologically
    significant stress-responsive genes in Arabidopsis in functional genomics research.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/fusk-kpu/StressResponseGenesAtlas/raw/main/AtSRGA_tutorial_en.pdf
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://huggingface.co/spaces/fusk-kpu/AtSRGA
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-01-15T00:41:02.475884Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/fusk-kpu/StressResponseGenesAtlas
  maturity: null
  name: AtSRGA (Arabidopsis thaliana Stress Rsponsive Genes Atlas)
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: atfukush
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Microarray experiment
    uri: http://edamontology.org/topic_3518
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-01-08T04:55:10.922667Z'
  biotoolsCURIE: biotools:diffcorr
  biotoolsID: diffcorr
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: afukushima@kpu.ac.jp
    fundrefid: null
    gridid: null
    name: Atsushi Fukushima
    note: null
    orcidid: http://orcid.org/0000-0001-9015-1694
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: An R package to analyze and visualize differential correlations in
    biological networks. This package can explore differential correlations between
    2 conditions in the context of post-genomics data types, namely transcriptomics
    and metabolomics. DiffCorr is simple to use in calculating differential correlations
    and is suitable for the first step towards inferring causal relationships and
    detecting biomarker candidates.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://cran.r-project.org/web/packages/DiffCorr/vignettes/DiffCorr.html
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://CRAN.R-project.org/package=DiffCorr
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-01-08T05:23:17.072582Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/afukushima/DiffCorr
  maturity: null
  name: DiffCorr
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: atfukush
  publication:
  - doi: 10.1016/j.gene.2012.11.028
    metadata:
      abstract: 'Large-scale "omics" data, such as microarrays, can be used to infer
        underlying cellular regulatory networks in organisms, enabling us to better
        understand the molecular basis of disease and important traits. Correlation
        approaches, such as a hierarchical cluster analysis, have been widely used
        to analyze omics data. In addition to the changes in the mean levels of molecules
        in the omics data, it is important to know about the changes in the correlation
        relationship among molecules between 2 experimental conditions. The development
        of a tool to identify differential correlation patterns in omics data in an
        efficient and unbiased manner is therefore desirable. We developed the DiffCorr
        package, a simple method for identifying pattern changes between 2 experimental
        conditions in correlation networks, which builds on a commonly used association
        measure, such as Pearson''s correlation coefficient. DiffCorr calculates correlation
        matrices for each dataset, identifies the first principal component-based
        "eigen-molecules" in the correlation networks, and tests differential correlation
        between the 2 groups based on Fisher''s z-test. We illustrated its utility
        by demonstrating biologically relevant, differentially correlated molecules
        in transcriptome coexpression and metabolite-to-metabolite correlation networks.
        DiffCorr can explore differential correlations between 2 conditions in the
        context of post-genomics data types, namely transcriptomics and metabolomics.
        DiffCorr is simple to use in calculating differential correlations and is
        suitable for the first step towards inferring causal relationships and detecting
        biomarker candidates. The package can be downloaded from the following website:
        http://diffcorr.sourceforge.net/. © 2012 Elsevier B.V.'
      authors:
      - name: Fukushima A.
      citationCount: 131
      date: '2013-04-10T00:00:00Z'
      journal: Gene
      title: 'DiffCorr: An R package to analyze and visualize differential correlations
        in biological networks'
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Omics
    uri: http://edamontology.org/topic_3391
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Microarray experiment
    uri: http://edamontology.org/topic_3518
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - 0.4.4
- accessibility: Open access
  additionDate: '2021-05-08T17:25:21Z'
  biotoolsCURIE: biotools:bakta
  biotoolsID: bakta
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: oliver.schwengers@cb.jlug.de
    fundrefid: null
    gridid: null
    name: Oliver Schwengers
    note: null
    orcidid: https://orcid.org/0000-0003-4216-2721
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://github.com/oschwengers
  - email: null
    fundrefid: null
    gridid: null
    name: Justus Liebig University Giessen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uni-giessen.de
  description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/oschwengers/bakta/blob/main/README.md
  - note: null
    type:
    - Contributions policy
    url: https://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.md
  - note: null
    type:
    - Code of conduct
    url: https://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.md
  - note: null
    type:
    - User manual
    url: https://bakta.readthedocs.io/
  download:
  - note: Mandatory annotation database
    type: Other
    url: https://zenodo.org/records/7669534
    version: v5.1
  editPermission:
    authors:
    - ELIXIR-CZ
    - bebatut
    type: group
  elixirCommunity: []
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fasta
    input:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence features metadata
        uri: http://edamontology.org/data_2914
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF3
        uri: http://edamontology.org/format_1975
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Hidden Markov model
        uri: http://edamontology.org/data_1364
      format:
      - term: HMMER3
        uri: http://edamontology.org/format_3329
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output:
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: GenBank format
        uri: http://edamontology.org/format_1936
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GFF3
        uri: http://edamontology.org/format_1975
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Nucleic acid sequence record
        uri: http://edamontology.org/data_2887
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://github.com/oschwengers/bakta
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-12-23T21:48:50.049892Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/oschwengers/bakta
  - note: null
    type:
    - Issue tracker
    url: https://github.com/oschwengers/bakta/issues
  - note: null
    type:
    - Other
    url: https://bioconda.github.io/recipes/bakta/README.html
  - note: null
    type:
    - Service
    url: https://bakta.computational.bio
  maturity: Mature
  name: Bakta
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: oschwengers
  publication:
  - doi: 10.1099/mgen.0.000685
    metadata:
      abstract: Command-line annotation software tools have continuously gained popularity
        compared to centralized online services due to the worldwide increase of sequenced
        bacterial genomes. However, results of existing command-line software pipelines
        heavily depend on taxon-specific databases or sufficiently well annotated
        reference genomes. Here, we introduce Bakta, a new command-line software tool
        for the robust, taxon-independent, thorough and, nonetheless, fast annotation
        of bacterial genomes. Bakta conducts a comprehensive annotation workflow including
        the detection of small proteins taking into account replicon metadata. The
        annotation of coding sequences is accelerated via an alignment-free sequence
        identification approach that in addition facilitates the precise assignment
        of public database cross-references. Annotation results are exported in GFF3
        and International Nucleotide Sequence Database Collaboration (INSDC)-compliant
        flat files, as well as comprehensive JSON files, facilitating automated downstream
        analysis. We compared Bakta to other rapid contemporary command-line annotation
        software tools in both targeted and taxonomically broad benchmarks including
        isolates and metagenomic-assembled genomes. We demonstrated that Bakta outperforms
        other tools in terms of functional annotations, the assignment of functional
        categories and database cross-references, whilst providing comparable wall-clock
        runtimes. Bakta is implemented in Python 3 and runs on MacOS and Linux systems.
        It is freely available under a GPLv3 license at https://​github.​com/​oschwengers/​bakta.
        An accompanying web version is available at https://​bakta.​computational.​bio.
      authors:
      - name: Schwengers O.
      - name: Jelonek L.
      - name: Dieckmann M.A.
      - name: Beyvers S.
      - name: Blom J.
      - name: Goesmann A.
      citationCount: 323
      date: '2021-01-01T00:00:00Z'
      journal: Microbial Genomics
      title: 'Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free
        sequence identification'
    note: null
    pmcid: PMC8743544
    pmid: '34739369'
    type:
    - Primary
    version: '1.1'
  relation:
  - biotoolsID: diamond
    type: uses
  - biotoolsID: hmmer3
    type: uses
  - biotoolsID: infernal
    type: uses
  - biotoolsID: trnascan-se
    type: uses
  - biotoolsID: blast
    type: uses
  - biotoolsID: aragorn
    type: uses
  - biotoolsID: pilercr
    type: uses
  - biotoolsID: deepsig
    type: uses
  toolType:
  - Command-line tool
  - Web application
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - v1.10.3
- accessibility: null
  additionDate: '2017-01-17T14:50:59Z'
  biotoolsCURIE: biotools:esiprot
  biotoolsID: esiprot
  collectionID:
  - ms-utils
  - Proteomics
  confidence_flag: null
  cost: null
  credit:
  - email: robert.winkler@ira.cinvestav.mx
    fundrefid: null
    gridid: null
    name: Robert Winkler
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  - email: webmaster@ms-utils.org
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Documentor
    url: http://ms-utils.org
  description: Charge state determination and molecular weight calculation for low
    resolution electrospray ionization data.
  documentation:
  - note: null
    type:
    - General
    url: http://www.lababi.bioprocess.org/index.php/lababi-software/84-esiprot
  download:
  - note: null
    type: Source code
    url: http://www.bioprocess.org/esiprot/esiprot.zip
    version: null
  - note: null
    type: Source code
    url: http://www.bioprocess.org/esiprot/esiprot.zip
    version: null
  editPermission:
    authors:
    - proteomics.bio.tools
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Peptide mass fingerprint
        uri: http://edamontology.org/data_0944
      format:
      - term: Mass spectrometry data format
        uri: http://edamontology.org/format_3245
    note: null
    operation:
    - term: Protein molecular weight calculation
      uri: http://edamontology.org/operation_0398
    - term: Protein fragment weight comparison
      uri: http://edamontology.org/operation_2929
    - term: Deisotoping
      uri: http://edamontology.org/operation_3629
    output:
    - data:
        term: Peptide mass fingerprint
        uri: http://edamontology.org/data_0944
      format:
      - term: Mass spectrometry data format
        uri: http://edamontology.org/format_3245
  homepage: https://nube-gran.de/esiprot
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-12-13T13:53:01.317118Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Mirror
    url: http://www.bioprocess.org/esiprot/esiprot_form.php
  - note: null
    type:
    - Software catalogue
    url: http://ms-utils.org
  maturity: null
  name: ESIprot
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: msutils_import
  publication:
  - doi: 10.1002/rcm.4384
    metadata:
      abstract: Electrospray ionization (ESI) ion trap mass spectrometers with relatively
        low resolution are frequently used for the analysis of natural products and
        peptides. Although ESI spectra of multiply charged protein molecules also
        can be measured on this type of devices, only average spectra are produced
        for the majority of naturally occurring proteins. Evaluating such ESI protein
        spectra would provide valuable information about the native state of investigated
        proteins. However, no suitable and freely available software could be found
        which allows the charge state determination and molecular weight calculation
        of single proteins from average ESI-MS data. Therefore, an algorithm based
        on standard deviation optimization (scatter minimization) was implemented
        for the analysis of protein ESI-MS data. The resulting software ESIprot was
        tested with ESI-MS data of six intact reference proteins between 12.4 and
        66.7kDa. In all cases, the correct charge states could be determined. The
        obtained absolute mass errors were in a range between -0.2 and 1.2Da, the
        relative errors below 30ppm. The possible mass accuracy allows for valid conclusions
        about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates
        an extraordinary robustness and allows spectral interpretation from as little
        as two peaks, given sufficient quality of the provided m/z data, without the
        necessity for peak intensity data. ESIprot is independent from the raw data
        format and the computer platform, making it a versatile tool for mass spectrometrists.
        The program code was released under the open-source GPLv3 license to support
        future developments of mass spectrometry software. © 2010 John Wiley & Sons,
        Ltd.
      authors:
      - name: Winkler R.
      citationCount: 75
      date: '2010-01-01T00:00:00Z'
      journal: Rapid Communications in Mass Spectrometry
      title: 'ESIprot: A universal tool for charge state determination and molecular
        weight calculation of proteins from electrospray ionization mass spectrometry
        data'
    note: null
    pmcid: null
    pmid: '20049890'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Desktop application
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2024-12-12T11:51:31.339824Z'
  biotoolsCURIE: biotools:gimp_image_annotator
  biotoolsID: gimp_image_annotator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: gimp-image-annotator or GIÀ, a lightweight GIMP plug-in to alllow for
    computer vision-assisted image annotation using the powerful GIMP selection toolbox.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output: []
  homepage: https://github.com/kieranatkins/gimp-image-annotator
  homepage_status: 0
  language: []
  lastUpdate: '2024-12-12T11:53:52.946776Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/kieranatkins/gimp-image-annotator
  maturity: null
  name: GIMP Image Annotator
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: kieranatkins
  publication: []
  relation: []
  toolType:
  - Plug-in
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-12-12T10:54:48.364970Z'
  biotoolsCURIE: biotools:morphpod
  biotoolsID: morphpod
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: "MorphPod: Deep learning phenotyping of Arabidopsis fruit morphology\
    \ - \n\nDeep learning model weights and inference code to detect Arabidopsis thaliana\
    \ siliques in scans of stem material. Phenotyping code to extract length, diameter\
    \ area and volume metrics of siliques from model outputs.\n\nAssociated with the\
    \ manuscript \"Unlocking the Power of AI for Phenotyping Fruit Morphology in Arabidopsis\"\
    \ by Atkins et al."
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output: []
  homepage: https://github.com/kieranatkins/silique-detector
  homepage_status: 0
  language: []
  lastUpdate: '2024-12-12T11:04:25.814879Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: MorphPod
  operatingSystem: []
  otherID: []
  owner: kieranatkins
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Phenomics
    uri: http://edamontology.org/topic_3298
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-11-29T08:54:53.859484Z'
  biotoolsCURIE: biotools:plant_mitochondrial_dna_long-read_assembly_pipeline_polap
  biotoolsID: plant_mitochondrial_dna_long-read_assembly_pipeline_polap
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Polap is a specialized pipeline designed to assemble plant mitochondrial
    DNA (mtDNA) using the Flye long-read assembler, supplemented by organellar gene
    annotation to guide contig selection. Inspired by ptGAUL (a chloroplast assembly
    pipeline), Polap integrates Flye's capabilities with gene annotation to identify
    and assemble mtDNA contigs from whole-genome data.
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://github.com/goshng/polap/archive/refs/tags/0.3.7.3.tar.gz
    version: null
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ-like format
        uri: http://edamontology.org/format_2545
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    - term: Genome alignment
      uri: http://edamontology.org/operation_3182
    output:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: Sequence assembly format
        uri: http://edamontology.org/format_2055
  homepage: https://github.com/goshng/polap
  homepage_status: 0
  language:
  - Bash
  - Python
  - R
  lastUpdate: '2024-11-29T08:54:53.861975Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/goshng/polap
  maturity: Emerging
  name: Plant Mitochondrial DNA Long-read Assembly Pipeline (POLAP)
  operatingSystem:
  - Linux
  otherID: []
  owner: goshng
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version:
  - v0.3.7.3
- accessibility: Open access
  additionDate: '2019-02-13T17:01:40Z'
  biotoolsCURIE: biotools:Jalview
  biotoolsID: Jalview
  collectionID:
  - ELIXIR-UK
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Jim Procter
    note: null
    orcidid: https://orcid.org/0000-0002-7865-7382
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.lifesci.dundee.ac.uk/people/jim-procter
  - email: null
    fundrefid: null
    gridid: null
    name: Geoff Barton
    note: null
    orcidid: https://orcid.org/0000-0002-9014-5355
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://www.lifesci.dundee.ac.uk/people/geoff-barton
  description: Jalview is a free program for multiple sequence alignment editing,
    visualisation and analysis. Use it to view and edit sequence alignments, analyse
    them with phylogenetic trees and principal components analysis (PCA) plots and
    explore molecular structures and annotation.
  documentation:
  - note: null
    type:
    - Citation instructions
    url: https://www.jalview.org/about/citation
  - note: Hands-on exercises, Training courses and Training videos
    type:
    - Training material
    url: https://www.jalview.org/training/
  - note: null
    type:
    - FAQ
    url: https://www.jalview.org/help/faq
  - note: null
    type:
    - User manual
    url: https://www.jalview.org/help/documentation/
  download:
  - note: null
    type: Downloads page
    url: https://www.jalview.org/download
    version: null
  - note: null
    type: Source code
    url: https://www.jalview.org/download/source/
    version: null
  - note: Binaries for all platforms
    type: Binaries
    url: https://www.jalview.org/download/?os=all
    version: null
  - note: null
    type: Icon
    url: https://www.jalview.org/favicon.svg
    version: null
  - note: Executable JAR file
    type: Binaries
    url: https://www.jalview.org/download/other/jar/
    version: null
  editPermission:
    authors:
    - ben_s
    - jimprocter
    type: group
  elixirCommunity: []
  elixirNode:
  - UK
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: GFF2-seq
        uri: http://edamontology.org/format_1938
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: RNAML
        uri: http://edamontology.org/format_3311
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: mmCIF
        uri: http://edamontology.org/format_1477
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: Format
        uri: http://edamontology.org/format_1915
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: 'Other Input formats:

      AMSA (.amsa);

      JnetFile (.concise, .jnet);

      PFAM (.pfam);

      Substitution matrix (.matrix);

      Jalview Project File (.jvp);

      Jalview Feature File (.features, .jvfeatures);

      Jalview Annotations File (.annotations, .jvannotations);

      Predicted Aligned Error (PAE) Matrix File (.json)

      ...

      Other Output formats:

      PFAM (.pfam);

      BioJS (.biojs) (interactive HTML/Javascript);

      Jalview Project File (.jvp);'
    operation:
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: Format
        uri: http://edamontology.org/format_1915
  homepage: https://www.jalview.org/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-28T10:07:42.658684Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Discussion forum
    url: https://discourse.jalview.org/
  - note: null
    type:
    - Issue tracker
    url: https://issues.jalview.org/
  - note: Latest development version
    type:
    - Other
    url: https://www.jalview.org/development/jalview_develop/
  - note: null
    type:
    - Repository
    url: https://source.jalview.org/crucible/browse/jalview
  - note: Twitter feed
    type:
    - Social media
    url: https://twitter.com/Jalview
  - note: YouTube training videos
    type:
    - Social media
    url: https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw
  maturity: Mature
  name: Jalview
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ben_s
  publication:
  - doi: 10.1093/bioinformatics/btp033
    metadata: null
    note: null
    pmcid: PMC2672624
    pmid: '19151095'
    type: []
    version: null
  relation:
  - biotoolsID: jabaws
    type: uses
  - biotoolsID: chimera
    type: uses
  - biotoolsID: chimerax
    type: uses
  - biotoolsID: pymol
    type: uses
  - biotoolsID: bioconda
    type: includedIn
  - biotoolsID: 3d-beacons
    type: uses
  - biotoolsID: uniprot
    type: uses
  - biotoolsID: pfam
    type: uses
  - biotoolsID: ensembl
    type: uses
  - biotoolsID: pdb
    type: uses
  - biotoolsID: rfam
    type: uses
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 1
  version:
  - 2.11.4.1
- accessibility: null
  additionDate: '2015-08-23T14:07:20Z'
  biotoolsCURIE: biotools:verifybamid
  biotoolsID: verifybamid
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: University of Michigan
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: sanger.ac.uk
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Hyun Min Kang
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: http://genome.sph.umich.edu/wiki/VerifyBamID
  - email: null
    fundrefid: null
    gridid: null
    name: Hyun Min Kang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://genome.sph.umich.edu/wiki/VerifyBamID
  - email: null
    fundrefid: null
    gridid: null
    name: verifyBamID Google Group
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://groups.google.com/forum/#!forum/verifybamid
  description: Software that verifies whether the reads in particular file match previously
    known genotypes for an individual (or group of individuals), and checks whether
    the reads are contaminated as a mixture of two samples. It can detect sample contamination
    and swaps when external genotypes are available. When external genotypes are not
    available, it still robustly detects sample swaps.
  documentation:
  - note: null
    type:
    - General
    url: http://genome.sph.umich.edu/wiki/VerifyBamID
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment (nucleic acid)
        uri: http://edamontology.org/data_1383
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: Sequence reads from RNA-Seq, DNA-Seq or ChIP-Seq experiment. VCF file containing
      external genotypes. VerifyBamID provides a series of text files that is informative
      to determine whether the sample is possibly contaminated or swapped.
    operation:
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format: []
  homepage: http://genome.sph.umich.edu/wiki/VerifyBamID
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2024-11-25T16:22:08.146597Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: verifyBamID
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: ka8@sanger.ac.uk
  publication:
  - doi: 10.1016/j.ajhg.2012.09.004
    metadata: null
    note: null
    pmcid: PMC3487130
    pmid: '23103226'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 1
  version:
  - 1.1.2
- accessibility: null
  additionDate: '2016-06-07T13:24:40Z'
  biotoolsCURIE: biotools:gemmapper
  biotoolsID: gemmapper
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Paolo Ribeca
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Santiago Marco Sola
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Lab Roderic Guigo Group
    note: 'Lab Roderic Guigo Group: Computational Biology of RNA processing @ Centre
      for Genomic Regulation Parc de Recerca Biomedica: Dr. Aiguader, 88, 08003 Barcelona'
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: crg.eu
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: paolo.ribeca@pirbright.ac.uk
    fundrefid: null
    gridid: null
    name: Paolo Ribeca
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: 'A set of very optimized tools for indexing/querying huge genomes/files.
    Provided so far: a very fast exact mapper, and an unconstrained split-mapper'
  documentation:
  - note: null
    type:
    - General
    url: http://algorithms.cnag.cat/wiki/The_GEM_library
  download:
  - note: null
    type: Binaries
    url: https://sourceforge.net/projects/gemlibrary/files/gem-library/Binary%20pre-release%203/
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTQ-like format (text)
        uri: http://edamontology.org/format_2182
    note: Because of ever-increasing throughput requirements of sequencing data, most
      existing short-read aligners have been designed to focus on speed at the expense
      of accuracy. The Genome Multitool (GEM) mapper can leverage string matching
      by filtration to search the alignment space more efficiently, simultaneously
      delivering precision (performing fully tunable exhaustive searches that return
      all existing matches, including gapped ones) and speed (being several times
      faster than comparable state-of-the-art tools).
    operation:
    - term: Mapping
      uri: http://edamontology.org/operation_2429
    output:
    - data:
        term: Alignment
        uri: http://edamontology.org/data_1916
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: SAM
        uri: http://edamontology.org/format_2573
  homepage: https://sourceforge.net/projects/gemlibrary/
  homepage_status: 0
  language:
  - Perl
  - Python
  - C
  lastUpdate: '2024-11-25T16:17:09.101669Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: The GEM (GEnome Multi-tool) Library (GEM Mapper)
  operatingSystem:
  - Linux
  otherID: []
  owner: francisco.camara@crg.eu
  publication:
  - doi: 10.1038/nmeth.2221
    metadata: null
    note: null
    pmcid: null
    pmid: '23103880'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2017-01-13T13:16:21Z'
  biotoolsCURIE: biotools:seqsite
  biotoolsID: seqsite
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: zhangxg@tsinghua.edu.cn
    fundrefid: null
    gridid: null
    name: Xuegong Zhang (Corresponding)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://bioinfo.au.tsinghua.edu.cn/member/xzhang/XZhang_English.htm
  - email: wang-xi05@mails.thu.edu.cn
    fundrefid: null
    gridid: null
    name: Xi Wang (Software details/bugs)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://bioinfo.au.tsinghua.edu.cn/member/xwang/
  description: SeqSite is an efficient and easy-to-use software tool implementing
    a novel method for identifying and pinpointing transcription factor binding sites.
    It first detects transcription factor binding regions by clustering tags and statistical
    hypothesis testing, and locates every binding site in detected binding regions
    by modeling the tag profiles. It can pinpoint closely spaced adjacent binding
    sites from ChIP-seq data. This software is coded in C/C++, and supports major
    computer platforms.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Peak calling
      uri: http://edamontology.org/operation_3222
    output: []
  homepage: http://bioinfo.au.tsinghua.edu.cn/software/seqsite/
  homepage_status: 0
  language:
  - C++
  - C
  lastUpdate: '2024-11-25T16:16:56.491206Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: SeqSite
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1186/1752-0509-5-s2-s3
    metadata: null
    note: null
    pmcid: PMC3287483
    pmid: '22784574'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: ChIP-seq
    uri: http://edamontology.org/topic_3169
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-13T13:13:55Z'
  biotoolsCURIE: biotools:bsmap
  biotoolsID: bsmap
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: yxi@bcm.edu
    fundrefid: null
    gridid: null
    name: Y. Xi
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: short reads mapping software for bisulfite sequencing
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Read mapping
      uri: http://edamontology.org/operation_3198
    - term: Bisulfite mapping
      uri: http://edamontology.org/operation_3186
    output: []
  homepage: https://code.google.com/archive/p/bsmap/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2024-11-25T16:07:02.540260Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: BSMAP
  operatingSystem:
  - Linux
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1186/1471-2105-10-232
    metadata: null
    note: null
    pmcid: PMC2724425
    pmid: '19635165'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Epigenetics
    uri: http://edamontology.org/topic_3295
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-13T13:14:19Z'
  biotoolsCURIE: biotools:diffreps
  biotoolsID: diffreps
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: li.shen@mssm.edu
    fundrefid: null
    gridid: null
    name: Dr. Li Shen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://neuroscience.mssm.edu/shen/
  description: This software is developed to find different peaks in ChIP-seq. It
    scans the whole genome using a sliding window, performing millions of statistical
    tests and report the significant hits. It takes into account the biological variations
    within a group of samples and uses that information to enhance the statistical
    power. Considering biological variation is of high importance, especiallly for
    in vivo brain tissues.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/shenlab-sinai/diffreps
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output: []
  homepage: https://github.com/shenlab-sinai/diffreps
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2024-11-25T16:07:00.472112Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/diffreps-1-55-1-finding-differential-chromatin-modification-sites-chip-seq-data.html
  maturity: Mature
  name: diffReps
  operatingSystem:
  - Linux
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1371/journal.pone.0065598
    metadata: null
    note: null
    pmcid: PMC3677880
    pmid: '23762400'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Script
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: ChIP-seq
    uri: http://edamontology.org/topic_3169
  - term: Sample collections
    uri: http://edamontology.org/topic_3277
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-17T15:01:01Z'
  biotoolsCURIE: biotools:hmmcopy
  biotoolsID: hmmcopy
  collectionID:
  - BioConductor
  confidence_flag: null
  cost: null
  credit:
  - email: dalai@bccrc.ca
    fundrefid: null
    gridid: null
    name: Daniel Lai
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: sshah@bccrc.ca
    fundrefid: null
    gridid: null
    name: Sohrab Shah
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Corrects GC and mappability biases for readcounts (i.e. coverage) in
    non-overlapping windows of fixed length for single whole genome samples, yielding
    a rough estimate of copy number for further analysis.  Designed for rapid correction
    of high coverage whole genome tumour and normal samples.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/html/HMMcopy.html
  download:
  - note: null
    type: Source code
    url: http://bioconductor/packages/release/bioc/src/contrib/HMMcopy_1.16.0.tar.gz
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequencing error detection
      uri: http://edamontology.org/operation_3195
    output: []
  homepage: http://bioconductor.org/packages/release/bioc/html/HMMcopy.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-11-25T16:06:33.754141Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: HMMcopy
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: bioconductor_import
  publication:
  - doi: 10.1038/nmeth.3252
    metadata: null
    note: null
    pmcid: PMC4509590
    pmid: '25633503'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Genetics
    uri: http://edamontology.org/topic_3053
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 1
  version:
  - 1.16.0
- accessibility: null
  additionDate: '2017-01-17T15:05:47Z'
  biotoolsCURIE: biotools:hireadsprocessor
  biotoolsID: hireadsprocessor
  collectionID:
  - BioConductor
  confidence_flag: null
  cost: null
  credit:
  - email: malnirav@gmail.com
    fundrefid: null
    gridid: null
    name: Nirav V Malani
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Contains set of functions which allow users to process LM-PCR products
    sequenced using any platform. Given an excel/txt file containing parameters for
    demultiplexing and sample metadata, the functions automate trimming of adaptors
    and identification of the genomic product. Genomic products are further processed
    for QC and abundance quantification.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/html/hiReadsProcessor.html
  download:
  - note: null
    type: Source code
    url: http://bioconductor/packages/release/bioc/src/contrib/hiReadsProcessor_1.10.0.tar.gz
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output: []
  homepage: http://bioconductor.org/packages/release/bioc/html/hiReadsProcessor.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-11-25T16:03:31.100145Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: hiReadsProcessor
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: bioconductor_import
  publication:
  - doi: 10.1038/nmeth.3252
    metadata: null
    note: null
    pmcid: PMC4509590
    pmid: '25633503'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: PCR experiment
    uri: http://edamontology.org/topic_3519
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 1
  version:
  - 1.10.0
- accessibility: null
  additionDate: '2017-01-13T13:14:26Z'
  biotoolsCURIE: biotools:edena
  biotoolsID: edena
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: david.hernandez@genomic.ch
    fundrefid: null
    gridid: null
    name: Dr David HERNANDEZ
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: A program for assembling de novo bacterial genomes from short reads
    produced by Illumina sequencing platform.
  documentation: []
  download: []
  editPermission:
    authors:
    - ELIXIR-EE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output: []
  homepage: http://www.genomic.ch/edena
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:03:30.106943Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: EDENA
  operatingSystem:
  - Linux
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1101/gr.072033.107
    metadata: null
    note: null
    pmcid: PMC2336802
    pmid: '18332092'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version:
  - '3'
- accessibility: null
  additionDate: '2016-04-04T14:45:45Z'
  biotoolsCURIE: biotools:spliceaid-f
  biotoolsID: spliceaid-f
  collectionID:
  - ELIXIR-ITA-CNR
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-ITA-CNR
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: graziano.pesole@uniba.it
    fundrefid: null
    gridid: null
    name: Graziano Pesole
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: A database of human splicing factors and their binding sites.
  documentation:
  - note: null
    type:
    - General
    url: http://srv00.recas.ba.infn.it/SpliceAidF/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output: []
  homepage: http://srv00.recas.ba.infn.it/SpliceAidF/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:02:21.569606Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: SpliceAid-F
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ELIXIR-ITA-CNR
  publication:
  - doi: 10.1093/nar/gks997
    metadata: null
    note: null
    pmcid: PMC3531144
    pmid: '23118479'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-17T15:03:57Z'
  biotoolsCURIE: biotools:cnvtools
  biotoolsID: cnvtools
  collectionID:
  - BioConductor
  confidence_flag: null
  cost: null
  credit:
  - email: christopher.barnes@imperial.ac.uk
    fundrefid: null
    gridid: null
    name: Chris Barnes
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: This package is meant to facilitate the testing of Copy Number Variant
    data for genetic association, typically in case-control studies.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/html/CNVtools.html
  download:
  - note: null
    type: Source code
    url: http://bioconductor/packages/release/bioc/src/contrib/CNVtools_1.68.0.tar.gz
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Copy number estimation
      uri: http://edamontology.org/operation_3233
    output: []
  homepage: http://bioconductor.org/packages/release/bioc/html/CNVtools.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-11-25T16:01:43.686523Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: CNVtools
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: bioconductor_import
  publication:
  - doi: 10.1038/ng.206
    metadata: null
    note: null
    pmcid: PMC2784596
    pmid: '18776912'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - 1.68.0
- accessibility: null
  additionDate: '2017-01-17T15:00:10Z'
  biotoolsCURIE: biotools:cnvpanelizer
  biotoolsID: cnvpanelizer
  collectionID:
  - BioConductor
  confidence_flag: null
  cost: null
  credit:
  - email: thomas_wolf71@gmx.de
    fundrefid: null
    gridid: null
    name: Thomas Wolf
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: A method that allows for the use of a collection of non-matched normal
    tissue samples. Our approach uses a non-parametric bootstrap subsampling of the
    available reference samples to estimate the distribution of read counts from targeted
    sequencing. As inspired by random forest, this is combined with a procedure that
    subsamples the amplicons associated with each of the targeted genes. The obtained
    information allows us to reliably classify the copy number aberrations on the
    gene level.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/html/CNVPanelizer.html
  download:
  - note: null
    type: Source code
    url: http://bioconductor/packages/release/bioc/src/contrib/CNVPanelizer_1.4.0.tar.gz
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Copy number estimation
      uri: http://edamontology.org/operation_3233
    output: []
  homepage: http://bioconductor.org/packages/release/bioc/html/CNVPanelizer.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-11-25T16:01:42.466263Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: CNVPanelizer
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: bioconductor_import
  publication:
  - doi: 10.1038/nmeth.3252
    metadata: null
    note: null
    pmcid: PMC4509590
    pmid: '25633503'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - 1.4.0
- accessibility: null
  additionDate: '2017-01-17T15:05:37Z'
  biotoolsCURIE: biotools:cnvgsa
  biotoolsID: cnvgsa
  collectionID:
  - BioConductor
  confidence_flag: null
  cost: null
  credit:
  - email: joseph.r.lugo@gmail.com
    fundrefid: null
    gridid: null
    name: Joseph Lugo
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: This package is intended to facilitate gene-set association with rare
    CNVs in case-control studies.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/html/cnvGSA.html
  download:
  - note: null
    type: Source code
    url: http://bioconductor/packages/release/bioc/src/contrib/cnvGSA_1.18.0.tar.gz
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Copy number estimation
      uri: http://edamontology.org/operation_3233
    output: []
  homepage: http://bioconductor.org/packages/release/bioc/html/cnvGSA.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-11-25T16:01:41.521862Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: cnvGSA
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: bioconductor_import
  publication:
  - doi: 10.1038/nmeth.3252
    metadata: null
    note: null
    pmcid: PMC4509590
    pmid: '25633503'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  validated: 1
  version:
  - 1.18.0
- accessibility: null
  additionDate: '2017-01-17T15:02:20Z'
  biotoolsCURIE: biotools:lmgene
  biotoolsID: lmgene
  collectionID:
  - BioConductor
  confidence_flag: null
  cost: null
  credit:
  - email: bpdurbin@ucdavis.edu
    fundrefid: null
    gridid: null
    name: Blythe Durbin-Johnson
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: A package for analysis of microarray data using a linear model and
    glog data transformation.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/html/LMGene.html
  download:
  - note: null
    type: Source code
    url: http://bioconductor/packages/release/bioc/src/contrib/LMGene_2.30.0.tar.gz
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene expression analysis
      uri: http://edamontology.org/operation_2495
    output: []
  homepage: http://bioconductor.org/packages/release/bioc/html/LMGene.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-11-25T16:01:39.517258Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Mirror
    url: http://dmrocke.ucdavis.edu/software.html
  maturity: null
  name: LMGene
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: bioconductor_import
  publication:
  - doi: 10.1038/nmeth.3252
    metadata: null
    note: null
    pmcid: PMC4509590
    pmid: '25633503'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Microarray experiment
    uri: http://edamontology.org/topic_3518
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  validated: 1
  version:
  - 2.30.0
- accessibility: null
  additionDate: '2017-01-17T15:00:58Z'
  biotoolsCURIE: biotools:cntools
  biotoolsID: cntools
  collectionID:
  - BioConductor
  confidence_flag: null
  cost: null
  credit:
  - email: jzhang@jimmy.harvard.edu
    fundrefid: null
    gridid: null
    name: J. Zhang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: This package provides tools to convert the output of segmentation analysis
    using DNAcopy to a matrix structure with overlapping segments as rows and samples
    as columns so that other computational analyses can be applied to segmented data.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/html/CNTools.html
  download:
  - note: null
    type: Source code
    url: http://bioconductor/packages/release/bioc/src/contrib/CNTools_1.30.0.tar.gz
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence conversion
      uri: http://edamontology.org/operation_0233
    output: []
  homepage: http://bioconductor.org/packages/release/bioc/html/CNTools.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-11-25T16:01:37.546577Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: CNTools
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: bioconductor_import
  publication:
  - doi: 10.1038/nmeth.3252
    metadata: null
    note: null
    pmcid: PMC4509590
    pmid: '25633503'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - 1.30.0
next: ?page=2
previous: null
