count: 4551
list:
- accessibility: null
  additionDate: '2024-04-19T10:26:21.921850Z'
  biotoolsCURIE: biotools:mcptaggr
  biotoolsID: mcptaggr
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: f.tomoyuki@okayama-u.ac.jp
    fundrefid: null
    gridid: null
    name: Tomoyuki Furuta
    note: null
    orcidid: https://orcid.org/0000-0002-0869-6626
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: R package for accurate genotype calling in reduced representation sequencing
    data by eliminating error-prone markers based on genome comparison.
  documentation:
  - note: null
    type:
    - User manual
    url: https://tomoyukif.github.io/MCPtaggR/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    - term: Demultiplexing
      uri: http://edamontology.org/operation_3933
    - term: SNP detection
      uri: http://edamontology.org/operation_0484
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    output: []
  homepage: https://github.com/tomoyukif/MCPtaggR
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-04-19T10:26:21.924007Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: MCPtaggR
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/DNARES/DSAD027
    metadata:
      abstract: Reduced representation sequencing (RRS) offers cost-effective, high-throughput
        genotyping platforms such as genotyping-by-sequencing (GBS). RRS reads are
        typically mapped onto a reference genome. However, mapping reads harbouring
        mismatches against the reference can potentially result in mismapping and
        biased mapping, leading to the detection of error-prone markers that provide
        incorrect genotype information. We established a genotype-calling pipeline
        named mappable collinear polymorphic tag genotyping (MCPtagg) to achieve accurate
        genotyping by eliminating error-prone markers. MCPtagg was designed for the
        RRS-based genotyping of a population derived from a biparental cross. The
        MCPtagg pipeline filters out error-prone markers prior to genotype calling
        based on marker collinearity information obtained by comparing the genome
        sequences of the parents of a population to be genotyped. A performance evaluation
        on real GBS data from a rice F2 population confirmed its effectiveness. Furthermore,
        our performance test using a genome assembly that was obtained by genome sequence
        polishing on an available genome assembly suggests that our pipeline performs
        well with converted genomes, rather than necessitating de novo assembly. This
        demonstrates its flexibility and scalability. The R package, MCPtaggR, was
        developed to provide functions for the pipeline and is available at https://github.com/tomoyukif/MCPtaggR.
      authors:
      - name: Furuta T.
      - name: Yamamoto T.
      citationCount: 0
      date: '2024-02-01T00:00:00Z'
      journal: DNA Research
      title: 'MCPtaggR: R package for accurate genotype calling in reduced representation
        sequencing data by eliminating error-prone markers based on genome comparison'
    note: null
    pmcid: PMC10799318
    pmid: '38134958'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: Structural variation
    uri: http://edamontology.org/topic_3175
  validated: 0
  version: []
- accessibility: null
  additionDate: '2024-04-19T10:01:19.463835Z'
  biotoolsCURIE: biotools:predictonco
  biotoolsID: predictonco
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: jiri@chemi.muni.cz
    fundrefid: null
    gridid: null
    name: Jiri Damborsky
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: davidbednar1208@gmail.com
    fundrefid: null
    gridid: null
    name: David Bednar
    note: null
    orcidid: https://orcid.org/0000-0002-6803-0340
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: A web tool supporting decision-making in precision oncology by extending
    bioinformatics predictions with advanced computing and machine learning.
  documentation:
  - note: null
    type:
    - User manual
    url: https://loschmidt.chemi.muni.cz/predictonco/help
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Virtual screening
      uri: http://edamontology.org/operation_3938
    - term: Variant effect prediction
      uri: http://edamontology.org/operation_0331
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    output: []
  homepage: https://loschmidt.chemi.muni.cz/predictonco
  homepage_status: 0
  language: []
  lastUpdate: '2024-04-19T10:01:19.465909Z'
  license: null
  link: []
  maturity: null
  name: PredictONCO
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/BIB/BBAD441
    metadata:
      abstract: PredictONCO 1.0 is a unique web server that analyzes effects of mutations
        on proteins frequently altered in various cancer types. The server can assess
        the impact of mutations on the protein sequential and structural properties
        and apply a virtual screening to identify potential inhibitors that could
        be used as a highly individualized therapeutic approach, possibly based on
        the drug repurposing. PredictONCO integrates predictive algorithms and state-of-the-art
        computational tools combined with information from established databases.
        The user interface was carefully designed for the target specialists in precision
        oncology, molecular pathology, clinical genetics and clinical sciences. The
        tool summarizes the effect of the mutation on protein stability and function
        and currently covers 44 common oncological targets. The binding affinities
        of Food and Drug Administration/ European Medicines Agency -approved drugs
        with the wild-type and mutant proteins are calculated to facilitate treatment
        decisions. The reliability of predictions was confirmed against 108 clinically
        validated mutations. The server provides a fast and compact output, ideal
        for the often time-sensitive decision-making process in oncology. Three use
        cases of missense mutations, (i) K22A in cyclin-dependent kinase 4 identified
        in melanoma, (ii) E1197K mutation in anaplastic lymphoma kinase 4 identified
        in lung carcinoma and (iii) V765A mutation in epidermal growth factor receptor
        in a patient with congenital mismatch repair deficiency highlight how the
        tool can increase levels of confidence regarding the pathogenicity of the
        variants and identify the most effective inhibitors. The server is available
        at https://loschmidt.chemi.muni.cz/predictonco.
      authors:
      - name: Stourac J.
      - name: Borko S.
      - name: Khan R.T.
      - name: Pokorna P.
      - name: Dobias A.
      - name: Planas-Iglesias J.
      - name: Mazurenko S.
      - name: Pinto G.
      - name: Szotkowska V.
      - name: Sterba J.
      - name: Slaby O.
      - name: Damborsky J.
      - name: Bednar D.
      citationCount: 0
      date: '2024-01-01T00:00:00Z'
      journal: Briefings in Bioinformatics
      title: 'PredictONCO: A web tool supporting decision-making in precision oncology
        by extending the bioinformatics predictions with advanced computing and machine
        learning'
    note: null
    pmcid: PMC10709543
    pmid: '38066711'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Personalised medicine
    uri: http://edamontology.org/topic_3577
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Pathology
    uri: http://edamontology.org/topic_0634
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: null
  additionDate: '2024-04-19T08:02:22.142231Z'
  biotoolsCURIE: biotools:scipion_chem
  biotoolsID: scipion_chem
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: ddelhoyo@cnb.csic.es
    fundrefid: null
    gridid: null
    name: Daniel Del Hoyo
    note: null
    orcidid: https://orcid.org/0009-0005-3321-1810
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: An open platform for virtual drug screening.
  documentation:
  - note: null
    type:
    - User manual
    url: https://scipion-chem.github.io/docs/publications/scipion-chem_vds
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Virtual screening
      uri: http://edamontology.org/operation_3938
    - term: Protein-protein docking
      uri: http://edamontology.org/operation_3899
    - term: Epitope mapping
      uri: http://edamontology.org/operation_0416
    output: []
  homepage: https://github.com/scipion-chem
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-04-19T08:02:22.144325Z'
  license: AGPL-3.0
  link: []
  maturity: null
  name: Scipion-chem
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1021/ACS.JCIM.3C01085
    metadata:
      abstract: Virtual drug screening (VDS) tackles the problem of drug discovery
        by computationally reducing the number of potential pharmacological molecules
        that need to be tested experimentally to find a new drug. To do so, several
        approaches have been developed through the years, typically focusing on either
        the physicochemical characteristics of the receptor structure (structure-based
        virtual screening) or those of the potential ligands (ligand-based virtual
        screening). Scipion is a workflow engine well suited for structural studies
        of biological macromolecules. Here, we present Scipion-chem, a new branch
        oriented to VDS. A total of 11 plugins have already been integrated from the
        most common programs used in the field. They can be used through the Scipion
        graphical user interface to execute and analyze typical VDS tasks. In addition,
        we have developed several consensus protocols that combine results from the
        different integrated programs to generate more robust predictions. Backstage,
        Scipion also facilitates the interoperability of those different software
        packages while tracking all of the intermediate files, parameters, and user
        decisions. In summary, in this article, we present Scipion-chem. This accessible,
        interoperable, and traceable platform provides the user with all of the tools
        to carry out a successful VDS workflow. Scipion-chem is openly available at
        https://github.com/scipion-chem.
      authors:
      - name: Del Hoyo D.
      - name: Salinas M.
      - name: Lomas A.
      - name: Ulzurrun E.
      - name: Campillo N.E.
      - name: Sorzano C.O.
      citationCount: 0
      date: '2023-12-25T00:00:00Z'
      journal: Journal of Chemical Information and Modeling
      title: 'Scipion-Chem: An Open Platform for Virtual Drug Screening'
    note: null
    pmcid: PMC10751785
    pmid: '38052452'
    type: []
    version: null
  relation: []
  toolType:
  - Plug-in
  topic:
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Pharmacology
    uri: http://edamontology.org/topic_0202
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Cheminformatics
    uri: http://edamontology.org/topic_2258
  validated: 0
  version: []
- accessibility: null
  additionDate: '2024-04-19T07:46:31.537317Z'
  biotoolsCURIE: biotools:tcgaplot
  biotoolsID: tcgaplot
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: wangxiong@tjh.tjmu.edu.cn
    fundrefid: null
    gridid: null
    name: Xiong Wang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: An R package for integrative pan-cancer analysis and visualization
    of TCGA multi-omics data.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/tjhwangxiong/TCGAplot/blob/main/vignettes/TCGAplot.Rmd
  - note: null
    type:
    - User manual
    url: https://github.com/tjhwangxiong/TCGAplot/blob/main/vignettes/TCGAplot
  download:
  - note: null
    type: Software package
    url: https://github.com/tjhwangxiong/TCGAplot/releases/download/v4.0.0/TCGAplot_4.0.0.zip
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    - term: Scatter plot plotting
      uri: http://edamontology.org/operation_2940
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    - term: Expression correlation analysis
      uri: http://edamontology.org/operation_3463
    - term: Dot plot plotting
      uri: http://edamontology.org/operation_0490
    output: []
  homepage: https://github.com/tjhwangxiong/TCGAplot
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-04-19T07:46:50.933786Z'
  license: MIT
  link: []
  maturity: null
  name: TCGAplot
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1186/S12859-023-05615-3
    metadata:
      abstract: 'Background: Pan-cancer analysis examines both the commonalities and
        heterogeneity among genomic and cellular alterations across numerous types
        of tumors. Pan-cancer analysis of gene expression, tumor mutational burden
        (TMB), microsatellite instability (MSI), and tumor immune microenvironment
        (TIME), and methylation becomes available based on the multi-omics data from
        The Cancer Genome Atlas Program (TCGA). Some online tools provide analysis
        of gene and protein expression, mutation, methylation, and survival for TCGA
        data. However, these online tools were either Uni-functional or were not able
        to perform analysis of user-defined functions. Therefore, we created the TCGAplot
        R package to facilitate perform pan-cancer analysis and visualization of the
        built-in multi-omic TCGA data. Results: TCGAplot provides several functions
        to perform pan-cancer paired/unpaired differential gene expression analysis,
        pan-cancer correlation analysis between gene expression and TMB, MSI, TIME,
        and promoter methylation. Functions for visualization include paired/unpaired
        boxplot, survival plot, ROC curve, heatmap, scatter, radar chart, and forest
        plot. Moreover, gene set based pan-cancer and tumor specific analyses were
        also available. Finally, all these built-in multi-omic data could be extracted
        for implementation for user-defined functions, making the pan-cancer analysis
        much more convenient.\ Conclusions: We developed an R-package for integrative
        pan-cancer analysis and visualization of TCGA multi-omics data. The source
        code and pre-built package are available at GitHub (https://github.com/tjhwangxiong/TCGAplot).'
      authors:
      - name: Liao C.
      - name: Wang X.
      citationCount: 2
      date: '2023-12-01T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'TCGAplot: an R package for integrative pan-cancer analysis and visualization
        of TCGA multi-omics data'
    note: null
    pmcid: PMC10726608
    pmid: '38105215'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 0
  version: []
- accessibility: null
  additionDate: '2024-02-02T14:42:46.030561Z'
  biotoolsCURIE: biotools:hictk
  biotoolsID: hictk
  collectionID: []
  community: null
  confidence_flag: null
  cost: null
  credit: []
  description: Blazing fast toolkit to work with .hic and .cool files
  documentation:
  - note: null
    type:
    - User manual
    url: https://hictk.readthedocs.io/en/latest/index.html
  download:
  - note: null
    type: Downloads page
    url: https://github.com/paulsengroup/hictk/releases
    version: null
  - note: null
    type: Binaries
    url: https://anaconda.org/bioconda/hictk
    version: null
  - note: null
    type: Container file
    url: https://github.com/paulsengroup/hictk/pkgs/container/hictk
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/paulsengroup/hictk
  homepage_status: 0
  language: []
  lastUpdate: '2024-04-18T08:55:19.020424Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/paulsengroup/hictk
  - note: null
    type:
    - Issue tracker
    url: https://github.com/paulsengroup/hictk/issues
  maturity: null
  name: hictk
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: robomics
  publication:
  - doi: 10.1101/2023.11.26.568707
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: hictkpy
    type: usedBy
  - biotoolsID: hictkr
    type: usedBy
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 0.0.1
  - 0.0.2
  - 0.0.3
  - 0.0.4
  - 0.0.5
  - 0.0.6
  - 0.0.7
  - 0.0.8
  - 0.0.9
  - 0.0.10
  - 0.0.11
  - 0.0.12
- accessibility: Open access
  additionDate: '2024-04-16T14:10:00.623929Z'
  biotoolsCURIE: biotools:oggmap
  biotoolsID: oggmap
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: ullrich@evolbio.mpg.de
    fundrefid: null
    gridid: null
    name: Kristian K Ullrich
    note: null
    orcidid: https://orcid.org/0000-0003-4308-9626
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Nikoleta E Glytnasi
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Python package to extract gene ages per orthogroup and link them with
    single-cell RNA data.
  documentation:
  - note: null
    type:
    - User manual
    url: https://oggmap.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Dimensionality reduction
      uri: http://edamontology.org/operation_3935
    output: []
  homepage: https://github.com/kullrich/oggmap
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-04-16T14:10:00.646441Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: oggmap
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/BIOINFORMATICS/BTAD657
    metadata:
      abstract: 'Summary: For model species, single-cell RNA-based cell atlases are
        available. A good cell atlas includes all major stages in a species’ ontogeny,
        and soon, they will be standard even for nonmodel species. Here, we propose
        a Python package called oggmap, which allows for the easy extraction of an
        orthomap (gene ages per orthogroup) for any given query species from OrthoFinder
        and other gene family data resources, like homologous groups from eggNOG or
        PLAZA. oggmap provides extracted gene ages for more than thousand eukaryotic
        species which can be further used to calculate gene age-weighted expression
        data from scRNA sequencing objects using the Python Scanpy toolkit. Not limited
        to one transcriptome evolutionary index, oggmap can visualize the individual
        gene category (e.g. age class, nucleotide diversity bin) and their corresponding
        expression profiles to investigate scRNA-based cell type assignments in an
        evolutionary context.'
      authors:
      - name: Ullrich K.K.
      - name: Glytnasi N.E.
      citationCount: 1
      date: '2023-11-01T00:00:00Z'
      journal: Bioinformatics
      title: 'oggmap: a Python package to extract gene ages per orthogroup and link
        them with single-cell RNA data'
    note: null
    pmcid: PMC10663984
    pmid: '37952198'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-04-16T10:56:15.558018Z'
  biotoolsCURIE: biotools:stomicsdb
  biotoolsID: stomicsdb
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: makailong@cngb.org
    fundrefid: null
    gridid: null
    name: Kailong Ma
    note: null
    orcidid: https://orcid.org/0000-0002-9351-104X
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: xuxun@genomics.cn
    fundrefid: null
    gridid: null
    name: Xun Xu
    note: null
    orcidid: https://orcid.org/0000-0002-5338-5173
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: weixiaofeng@cngb.org
    fundrefid: null
    gridid: null
    name: Xiaofeng Wei
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Comprehensive database for spatial transcriptomics data sharing, analysis
    and visualization.
  documentation:
  - note: null
    type:
    - User manual
    url: https://stomics-data-archive.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Deposition
      uri: http://edamontology.org/operation_3431
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    output: []
  homepage: https://db.cngb.org/stomics/
  homepage_status: 0
  language: []
  lastUpdate: '2024-04-16T10:56:15.560225Z'
  license: null
  link: []
  maturity: null
  name: STOmicsDB
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/NAR/GKAD933
    metadata:
      abstract: Recent technological developments in spatial transcriptomics allow
        researchers to measure gene expression of cells and their spatial locations
        at the single-cell level, generating detailed biological insight into biological
        processes. A comprehensive database could facilitate the sharing of spatial
        transcriptomic data and streamline the data acquisition process for researchers.
        Here, we present the Spatial TranscriptOmics DataBase (STOmicsDB), a database
        that serves as a one-stop hub for spatial transcriptomics. STOmicsDB integrates
        218 manually curated datasets representing 17 species. We annotated cell types,
        identified spatial regions and genes, and performed cell-cell interaction
        analysis for these datasets. STOmicsDB features a user-friendly interface
        for the rapid visualization of millions of cells. To further facilitate the
        reusability and interoperability of spatial transcriptomic data, we developed
        standards for spatial transcriptomic data archiving and constructed a spatial
        transcriptomic data archiving system. Additionally, we offer a distinctive
        capability of customizing dedicated sub-databases in STOmicsDB for researchers,
        assisting them in visualizing their spatial transcriptomic analyses. We believe
        that STOmicsDB could contribute to research insights in the spatial transcriptomics
        field, including data archiving, sharing, visualization and analysis. STOmicsDB
        is freely accessible at https://db.cngb.org/stomics/.
      authors:
      - name: Xu Z.
      - name: Wang W.
      - name: Yang T.
      - name: Li L.
      - name: Ma X.
      - name: Chen J.
      - name: Wang J.
      - name: Huang Y.
      - name: Gould J.
      - name: Lu H.
      - name: Du W.
      - name: Sahu S.K.
      - name: Yang F.
      - name: Li Z.
      - name: Hu Q.
      - name: Hua C.
      - name: Hu S.
      - name: Liu Y.
      - name: Cai J.
      - name: You L.
      - name: Zhang Y.
      - name: Li Y.
      - name: Zeng W.
      - name: Chen A.
      - name: Wang B.
      - name: Liu L.
      - name: Chen F.
      - name: Ma K.
      - name: Xu X.
      - name: Wei X.
      citationCount: 6
      date: '2024-01-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'STOmicsDB: a comprehensive database for spatial transcriptomics data
        sharing, analysis and visualization'
    note: null
    pmcid: PMC10767841
    pmid: '37953328'
    type: []
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  - term: Biological databases
    uri: http://edamontology.org/topic_3071
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2017-01-13T13:16:12Z'
  biotoolsCURIE: biotools:samtools
  biotoolsID: samtools
  collectionID:
  - Rare Disease
  - Animal and Crop Genomics
  - SAMtools
  community:
    biolib:
      app_name: samtools
      author_name: SAMtools
      author_username: samtools
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: rd@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Richard Durbin
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Primary contact
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: SAMtools and BCFtools are widely used programs for processing and analysing
    high-throughput sequencing data. They include tools for file format conversion
    and manipulation, sorting, querying, statistics, variant calling, and effect analysis
    amongst other methods.
  documentation:
  - note: HowTos for samtools
    type:
    - Other
    url: http://www.htslib.org/doc/#howtos
  - note: null
    type:
    - User manual
    url: http://www.htslib.org/doc/#manual-pages
  - note: null
    type:
    - Installation instructions
    url: http://www.htslib.org/download/
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
  editPermission:
    authors:
    - ELIXIR-EE
    - animalandcropgenomics
    - alice
    - awhitwham
    - sergitobara
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: CRAM
        uri: http://edamontology.org/format_3462
    note: null
    operation:
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    - term: Editing
      uri: http://edamontology.org/operation_3096
    - term: Parsing
      uri: http://edamontology.org/operation_1812
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    - term: Sorting
      uri: http://edamontology.org/operation_3802
    - term: Filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: CRAM
        uri: http://edamontology.org/format_3462
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2024-04-16T10:22:46.809965Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/samtools
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/samtools/issues
  maturity: Mature
  name: SAMtools
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/bioinformatics/btp352
    metadata:
      abstract: 'Summary: The Sequence Alignment/Map (SAM) format is a generic alignment
        format for storing read alignments against reference sequences, supporting
        short and long reads (up to 128 Mbp) produced by different sequencing platforms.
        It is flexible in style, compact in size, efficient in random access and is
        the format in which alignments from the 1000 Genomes Project are released.
        SAM tools implements various utilities for post-processing alignments in the
        SAM format, such as indexing, variant caller and alignment viewer, and thus
        provides universal tools for processing read alignments. © 2009 The Author(s).'
      authors:
      - name: Li H.
      - name: Handsaker B.
      - name: Wysoker A.
      - name: Fennell T.
      - name: Ruan J.
      - name: Homer N.
      - name: Marth G.
      - name: Abecasis G.
      - name: Durbin R.
      citationCount: 37126
      date: '2009-08-01T00:00:00Z'
      journal: Bioinformatics
      title: The Sequence Alignment/Map format and SAMtools
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
    pmid: '19505943'
    type:
    - Primary
    version: null
  - doi: 10.1093/gigascience/giab008
    metadata:
      abstract: 'Background: SAMtools and BCFtools are widely used programs for processing
        and analysing high-throughput sequencing data. They include tools for file
        format conversion and manipulation, sorting, querying, statistics, variant
        calling, and effect analysis amongst other methods. Findings: The first version
        appeared online 12 years ago and has been maintained and further developed
        ever since, with many new features and improvements added over the years.
        The SAMtools and BCFtools packages represent a unique collection of tools
        that have been used in numerous other software projects and countless genomic
        pipelines. Conclusion: Both SAMtools and BCFtools are freely available on
        GitHub under the permissive MIT licence, free for both non-commercial and
        commercial use. Both packages have been installed >1 million times via Bioconda.
        The source code and documentation are available from https://www.htslib.org.'
      authors:
      - name: Danecek P.
      - name: Bonfield J.K.
      - name: Liddle J.
      - name: Marshall J.
      - name: Ohan V.
      - name: Pollard M.O.
      - name: Whitwham A.
      - name: Keane T.
      - name: McCarthy S.A.
      - name: Davies R.M.
      citationCount: 3084
      date: '2021-02-01T00:00:00Z'
      journal: GigaScience
      title: Twelve years of SAMtools and BCFtools
    note: Twelve years of SAMtools and BCFtools.
    pmcid: PMC7931819
    pmid: '33590861'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btr509
    metadata:
      abstract: 'Motivation: Most existing methods for DNA sequence analysis rely
        on accurate sequences or genotypes. However, in applications of the next-generation
        sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample
        low-coverage sequencing or somatic mutation discovery). These applications
        press for the development of new methods for analyzing sequence data with
        uncertainty. Results: We present a statistical framework for calling SNPs,
        discovering somatic mutations, inferring population genetical parameters and
        performing association tests directly based on sequencing data without explicit
        genotyping or linkage-based imputation. On real data, we demonstrate that
        our method achieves comparable accuracy to alternative methods for estimating
        site allele count, for inferring allele frequency spectrum and for association
        mapping. We also highlight the necessity of using symmetric datasets for finding
        somatic mutations and confirm that for discovering rare events, mismapping
        is frequently the leading source of errors. © The Author 2011. Published by
        Oxford University Press. All rights reserved.'
      authors:
      - name: Li H.
      citationCount: 3826
      date: '2011-11-01T00:00:00Z'
      journal: Bioinformatics
      title: A statistical framework for SNP calling, mutation discovery, association
        mapping and population genetical parameter estimation from sequencing data
    note: null
    pmcid: PMC3198575
    pmid: '21903627'
    type: []
    version: null
  relation:
  - biotoolsID: htslib
    type: uses
  toolType:
  - Suite
  - Command-line tool
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - '1.3'
  - 1.3.1
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - 1.16.1
  - '1.17'
  - '1.18'
  - '1.19'
  - 1.19.1
  - 1.19.2
  - '1.20'
- accessibility: Open access
  additionDate: '2017-08-20T16:07:58Z'
  biotoolsCURIE: biotools:htslib
  biotoolsID: htslib
  collectionID:
  - Animal and Crop Genomics
  community: null
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Primary contact
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: The main purpose of HTSlib is to provide access to genomic information
    files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF
    and BCF formats). The library also provides interfaces to access and index genome
    reference data in FASTA format and tab-delimited files with genomic coordinates.
    It is utilized and incorporated into both SAMtools and BCFtools.
  documentation:
  - note: null
    type:
    - User manual
    url: http://www.htslib.org/doc/#manual-pages
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
  editPermission:
    authors:
    - animalandcropgenomics
    - smoe
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2024-04-16T10:19:42.968075Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/htslib
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/htslib/issues
  maturity: Mature
  name: HTSlib
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/gigascience/giab007
    metadata:
      abstract: 'Background: Since the original publication of the VCF and SAM formats,
        an explosion of software tools have been created to process these data files.
        To facilitate this a library was produced out of the original SAMtools implementation,
        with a focus on performance and robustness. The file formats themselves have
        become international standards under the jurisdiction of the Global Alliance
        for Genomics and Health. Findings: We present a software library for providing
        programmatic access to sequencing alignment and variant formats. It was born
        out of the widely used SAMtools and BCFtools applications. Considerable improvements
        have been made to the original code plus many new features including newer
        access protocols, the addition of the CRAM file format, better indexing and
        iterators, and better use of threading. Conclusion: Since the original Samtools
        release, performance has been considerably improved, with a BAM read-write
        loop running 5 times faster and BAM to SAM conversion 13 times faster (both
        using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen
        HTSlib downloaded >1 million times from GitHub and conda. The C library has
        been used directly by an estimated 900 GitHub projects and has been incorporated
        into Perl, Python, Rust, and R, significantly expanding the number of uses
        via other languages. HTSlib is open source and is freely available from htslib.org
        under MIT/BSD license.'
      authors:
      - name: Bonfield J.K.
      - name: Marshall J.
      - name: Danecek P.
      - name: Li H.
      - name: Ohan V.
      - name: Whitwham A.
      - name: Keane T.
      citationCount: 116
      date: '2021-02-01T00:00:00Z'
      journal: GigaScience
      title: 'HTSlib: C library for reading/writing high-Throughput sequencing data'
    note: 'HTSlib: C library for reading/writing high-throughput sequencing data.'
    pmcid: PMC7931820
    pmid: '33594436'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: samtools
    type: usedBy
  - biotoolsID: bcftools
    type: usedBy
  toolType:
  - Library
  topic:
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - 1.2.1
  - '1.3'
  - 1.3.1
  - 1.3.2
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - 1.10.1
  - 1.10.2
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - '1.17'
  - '1.18'
  - '1.19'
  - '1.20'
- accessibility: Open access
  additionDate: '2021-01-20T10:58:38Z'
  biotoolsCURIE: biotools:phenpath
  biotoolsID: phenpath
  collectionID:
  - Rare Disease
  - Bologna Biocomputing Group
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: pierluigi.martelli@unibo.it
    fundrefid: null
    gridid: null
    name: Pier Luigi Martelli
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: giulia.babbi@unibo.it
    fundrefid: null
    gridid: null
    name: Giulia Babbi
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-ITA-BOLOGNA
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: 'A tool for characterizing biological functions underlying different
    phenotypes.


    a web server for associating phenotypes with molecular functional annotations.


    PhenPath includes a database and a tool:.

    '''
  documentation:
  - note: null
    type:
    - User manual
    url: http://phenpath.biocomp.unibo.it/phenpath/help_page.html
  download: []
  editPermission:
    authors:
    - ELIXIR-ITA-BOLOGNA
    type: group
  elixirCommunity: []
  elixirNode:
  - Italy
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Disease ID
        uri: http://edamontology.org/data_1150
      format: []
    - data:
        term: Disease name
        uri: http://edamontology.org/data_3668
      format: []
    - data:
        term: Phenotype name
        uri: http://edamontology.org/data_3275
      format: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Enrichment analysis
      uri: http://edamontology.org/operation_3501
    - term: Gene functional annotation
      uri: http://edamontology.org/operation_3672
    output:
    - data:
        term: Disease report
        uri: http://edamontology.org/data_1622
      format: []
  homepage: http://phenpath.biocomp.unibo.it
  homepage_status: 0
  language: []
  lastUpdate: '2024-03-11T16:45:53.823541Z'
  license: CC-BY-NC-4.0
  link: []
  maturity: Mature
  name: PhenPath
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: ELIXIR-ITA-BOLOGNA
  publication:
  - doi: 10.1186/S12864-019-5868-X
    metadata:
      abstract: 'Background: Many diseases are associated with complex patterns of
        symptoms and phenotypic manifestations. Parsimonious explanations aim at reconciling
        the multiplicity of phenotypic traits with the perturbation of one or few
        biological functions. For this, it is necessary to characterize human phenotypes
        at the molecular and functional levels, by exploiting gene annotations and
        known relations among genes, diseases and phenotypes. This characterization
        makes it possible to implement tools for retrieving functions shared among
        phenotypes, co-occurring in the same patient and facilitating the formulation
        of hypotheses about the molecular causes of the disease. Results: We introduce
        PhenPath, a new resource consisting of two parts: PhenPathDB and PhenPathTOOL.
        The former is a database collecting the human genes associated with the phenotypes
        described in Human Phenotype Ontology (HPO) and OMIM Clinical Synopses. Phenotypes
        are then associated with biological functions and pathways by means of NET-GE,
        a network-based method for functional enrichment of sets of genes. The present
        version considers only phenotypes related to diseases. PhenPathDB collects
        information for 18 OMIM Clinical synopses and 7137 HPO phenotypes, related
        to 4292 diseases and 3446 genes. Enrichment of Gene Ontology annotations endows
        some 87.7, 86.9 and 73.6% of HPO phenotypes with Biological Process, Molecular
        Function and Cellular Component terms, respectively. Furthermore, 58.8 and
        77.8% of HPO phenotypes are also enriched for KEGG and Reactome pathways,
        respectively. Based on PhenPathDB, PhenPathTOOL analyzes user-defined sets
        of phenotypes retrieving diseases, genes and functional terms which they share.
        This information can provide clues for interpreting the co-occurrence of phenotypes
        in a patient. Conclusions: The resource allows finding molecular features
        useful to investigate diseases characterized by multiple phenotypes, and by
        this, it can help researchers and physicians in identifying molecular mechanisms
        and biological functions underlying the concomitant manifestation of phenotypes.
        The resource is freely available at http://phenpath.biocomp.unibo.it.'
      authors:
      - name: Babbi G.
      - name: Martelli P.L.
      - name: Casadio R.
      citationCount: 8
      date: '2019-07-16T00:00:00Z'
      journal: BMC Genomics
      title: 'PhenPath: A tool for characterizing biological functions underlying
        different phenotypes'
    note: null
    pmcid: PMC6631446
    pmid: '31307376'
    type: []
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Pathology
    uri: http://edamontology.org/topic_0634
  - term: Public health and epidemiology
    uri: http://edamontology.org/topic_3305
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 0
  version: []
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