count: 6731
list:
- accessibility: null
  additionDate: '2023-06-07T03:22:25.847061Z'
  biotoolsCURIE: biotools:metabuli
  biotoolsID: metabuli
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Metabuli: specific and sensitive metagenomic classification via joint
    analysis of DNA and amino acid'
  documentation: []
  download: []
  editPermission:
    authors:
    - vashokan
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format: []
  homepage: https://metabuli.steineggerlab.com
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-02-12T14:21:25.897853Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/steineggerlab/Metabuli/issues
  - note: github repository
    type:
    - Repository
    url: https://github.com/steineggerlab/Metabuli
  maturity: Mature
  name: metabuli
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: milot-mirdita
  publication:
  - doi: 10.1038/s41592-024-02273-y
    metadata: null
    note: null
    pmcid: null
    pmid: '38769467'
    type: []
    version: null
  relation:
  - biotoolsID: mmseqs2
    type: uses
  - biotoolsID: gtdb
    type: uses
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  validated: 0
  version: []
- accessibility: null
  additionDate: '2018-06-27T22:03:41Z'
  biotoolsCURIE: biotools:sourmash
  biotoolsID: sourmash
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: ctbrown@ucdavis.edu
    fundrefid: null
    gridid: null
    name: C. Titus Brown
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://github.com/dib-lab/sourmash/
  description: Compute and compare MinHash signatures for DNA data sets.
  documentation: []
  download: []
  editPermission:
    authors:
    - luizirber
    - vashokan
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence (raw)
        uri: http://edamontology.org/data_2975
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    - term: Sequence distance matrix generation
      uri: http://edamontology.org/operation_0289
    output: []
  - 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: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
  homepage: https://sourmash.readthedocs.io/en/latest/
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-12T14:14:38.842520Z'
  license: BSD-3-Clause
  link:
  - note: github repository
    type:
    - Repository
    url: https://github.com/sourmash-bio/sourmash
  maturity: Emerging
  name: sourmash
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: diblab
  publication:
  - doi: 10.12688/f1000research.19675.1
    metadata: null
    note: null
    pmcid: PMC6720031
    pmid: '31508216'
    type: []
    version: null
  relation:
  - biotoolsID: gtdb
    type: uses
  toolType:
  - Library
  - Command-line tool
  topic:
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 1
  version:
  - 2.0a8
- accessibility: Open access
  additionDate: '2024-11-11T08:56:21.437836Z'
  biotoolsCURIE: biotools:liana
  biotoolsID: liana
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: LIANA+ is a scalable framework for inference of cell‑cell communication
    (CCC) from single-cell and spatially resolved omics data. It integrates multiple
    ligand‑receptor inference methods and expert curated resources into a unified
    pipeline, supports consensus ranking across methods, and facilitates differential
    and contextual CCC analyses. LIANA+ accepts AnnData/MuData formats and interfaces
    with single‑cell ecosystems like scverse for flexible, interoperable workflows.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://liana-py.readthedocs.io/en/latest/api.html
  - note: null
    type:
    - Installation instructions
    url: https://liana-py.readthedocs.io/en/latest/installation.html
  - note: null
    type:
    - Training material
    url: https://liana-py.readthedocs.io/en/latest/notebooks/index.html
  download: []
  editPermission:
    authors:
    - khaled4
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: HDF5
        uri: http://edamontology.org/format_3590
    note: null
    operation:
    - term: Expression profile clustering
      uri: http://edamontology.org/operation_0313
    - term: Principal component visualisation
      uri: http://edamontology.org/operation_2939
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    output:
    - data:
        term: Clustered expression profiles
        uri: http://edamontology.org/data_3768
      format: []
  homepage: https://liana-py.readthedocs.io/en/latest/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-05T16:22:37.314374Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/saezlab/liana-py
  maturity: null
  name: Liana+
  operatingSystem: []
  otherID: []
  owner: attilagabor
  publication:
  - doi: 10.1038/s41556-024-01469-w
    metadata: null
    note: The growing availability of single-cell and spatially resolved transcriptomics
      has led to the development of many approaches to infer cell-cell communication,
      each capturing only a partial view of the complex landscape of intercellular
      signalling. Here we present LIANA+, a scalable framework built around a rich
      knowledge base to decode coordinated inter- and intracellular signalling events
      from single- and multi-condition datasets in both single-cell and spatially
      resolved data. By extending and unifying established methodologies, LIANA+ provides
      a comprehensive set of synergistic components to study cell-cell communication
      via diverse molecular mediators, including those measured in multi-omics data.
      LIANA+ is accessible at https://github.com/saezlab/liana-py with extensive vignettes
      ( https://liana-py.readthedocs.io/ ) and provides an all-in-one solution to
      intercellular communication inference.
    pmcid: PMC11392821
    pmid: '39223377'
    type: []
    version: 1.7.1
  - doi: 10.1038/s41467-022-30755-0
    metadata: null
    note: null
    pmcid: PMC9184522
    pmid: '35680885'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Single-cell sequencing
    uri: http://edamontology.org/topic_4028
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Genetics
    uri: http://edamontology.org/topic_3053
  validated: 0
  version:
  - 1.7.1
- accessibility: Open access
  additionDate: '2016-02-03T14:20:28Z'
  biotoolsCURIE: biotools:brenda
  biotoolsID: brenda
  collectionID:
  - de.NBI
  - DSMZ Digital Diversity
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: BMBF
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  - email: contact@brenda-enzymes.org
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: grid.420081.f
    name: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
    note: null
    orcidid: null
    rorid: 02tyer376
    typeEntity: null
    typeRole: []
    url: https://www.dsmz.de/
  description: Internationally leading information system on all aspects of enzymes,
    including function, structure, involvement in diseases, application, engineering,
    and molecular properties. The database includes hundreds of milllions of enzyme
    data and is compiled from manual literature annotation, data integration from
    other databases and predicted enzyme functions and locations.
  documentation:
  - note: null
    type:
    - Terms of use
    url: http://www.brenda-enzymes.org/copy.php
  - note: null
    type:
    - Citation instructions
    url: http://www.brenda-enzymes.org/introduction.php
  - note: null
    type:
    - Training material
    url: https://www.brenda-enzymes.org/tutorial.php
  - note: null
    type:
    - Training material
    url: https://www.brenda-enzymes.org/help.php
  - note: null
    type:
    - FAQ
    url: https://www.brenda-enzymes.org/faq.php
  download: []
  editPermission:
    authors:
    - AJaede
    - juh22
    - lje
    type: group
  elixirCommunity: []
  elixirNode:
  - Germany
  elixirPlatform:
  - Data
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Organism name
        uri: http://edamontology.org/data_2909
      format: []
    - data:
        term: Compound name
        uri: http://edamontology.org/data_0990
      format: []
    - data:
        term: Gene name
        uri: http://edamontology.org/data_2299
      format: []
    - data:
        term: PDB ID
        uri: http://edamontology.org/data_1127
      format: []
    - data:
        term: UniProt ID
        uri: http://edamontology.org/data_2291
      format: []
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Reaction ID
        uri: http://edamontology.org/data_2108
      format: []
    - data:
        term: Pathway or network name
        uri: http://edamontology.org/data_2342
      format: []
    - data:
        term: Pathway or network accession
        uri: http://edamontology.org/data_2365
      format: []
    - data:
        term: PubMed ID
        uri: http://edamontology.org/data_1187
      format: []
    - data:
        term: Strain name
        uri: http://edamontology.org/data_1046
      format: []
    - data:
        term: NCBI taxonomy ID
        uri: http://edamontology.org/data_1179
      format: []
    - data:
        term: Ontology name
        uri: http://edamontology.org/data_1051
      format: []
    - data:
        term: Enzyme name
        uri: http://edamontology.org/data_1012
      format: []
    - data:
        term: EC number
        uri: http://edamontology.org/data_1011
      format: []
    - data:
        term: Enzyme kinetics data
        uri: http://edamontology.org/data_2024
      format: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Genome visualisation
      uri: http://edamontology.org/operation_3208
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    - term: Sequence database search
      uri: http://edamontology.org/operation_0338
    - term: Text mining
      uri: http://edamontology.org/operation_0306
    - term: Transmembrane protein visualisation
      uri: http://edamontology.org/operation_2241
    - term: Structural similarity search
      uri: http://edamontology.org/operation_0360
    - term: Transmembrane protein prediction
      uri: http://edamontology.org/operation_0269
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Pathway or network visualisation
      uri: http://edamontology.org/operation_3083
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Genome feature comparison
      uri: http://edamontology.org/operation_3194
    - term: Literature search
      uri: http://edamontology.org/operation_0305
    output:
    - data:
        term: UniProt ID
        uri: http://edamontology.org/data_2291
      format: []
    - data:
        term: PDB ID
        uri: http://edamontology.org/data_1127
      format: []
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Reaction ID
        uri: http://edamontology.org/data_2108
      format: []
    - data:
        term: Pathway or network name
        uri: http://edamontology.org/data_2342
      format: []
    - data:
        term: Pathway or network accession
        uri: http://edamontology.org/data_2365
      format: []
    - data:
        term: Strain name
        uri: http://edamontology.org/data_1046
      format: []
    - data:
        term: Organism name
        uri: http://edamontology.org/data_2909
      format: []
    - data:
        term: NCBI taxonomy ID
        uri: http://edamontology.org/data_1179
      format: []
    - data:
        term: SCOP domain identifier
        uri: http://edamontology.org/data_1039
      format: []
    - data:
        term: CATH identifier
        uri: http://edamontology.org/data_2700
      format: []
    - data:
        term: Enzyme name
        uri: http://edamontology.org/data_1012
      format: []
    - data:
        term: EC number
        uri: http://edamontology.org/data_1011
      format: []
    - data:
        term: Enzyme kinetics data
        uri: http://edamontology.org/data_2024
      format: []
  homepage: http://www.brenda-enzymes.org
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-05T07:01:46.010390Z'
  license: CC-BY-4.0
  link:
  - note: null
    type:
    - Other
    url: https://www.dsmz.de/
  - note: null
    type:
    - Service
    url: https://hub.dsmz.de/#/
  - note: null
    type:
    - Service
    url: https://www.brenda-enzymes.org/
  - note: null
    type:
    - Helpdesk
    url: https://brenda-enzymes.org/support.php
  maturity: Mature
  name: BRENDA
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: matkrull
  publication:
  - doi: 10.1093/nar/gkaf1113
    metadata: null
    note: null
    pmcid: PMC12807770
    pmid: '41206471'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkaa1025
    metadata: null
    note: null
    pmcid: PMC7779020
    pmid: '33211880'
    type: []
    version: null
  - doi: 10.1093/nar/gky1048
    metadata: null
    note: null
    pmcid: PMC6323942
    pmid: '30395242'
    type: []
    version: null
  - doi: 10.1016/j.jbiotec.2017.04.020
    metadata: null
    note: null
    pmcid: null
    pmid: '28438579'
    type: []
    version: null
  - doi: 10.1093/nar/gku1068
    metadata: null
    note: null
    pmcid: PMC4383907
    pmid: '25378310'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gkn820
    metadata: null
    note: null
    pmcid: PMC2686525
    pmid: '18984617'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gkq1089
    metadata: null
    note: null
    pmcid: PMC3013686
    pmid: '21062828'
    type:
    - Other
    version: null
  - doi: 10.1186/1471-2105-12-329
    metadata: null
    note: null
    pmcid: PMC3166944
    pmid: '21827651'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gkh081
    metadata: null
    note: null
    pmcid: PMC308815
    pmid: '14681450'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gks1049
    metadata: null
    note: null
    pmcid: PMC3531171
    pmid: '23203881'
    type:
    - Other
    version: null
  - doi: 10.1016/s0968-0004(01)02027-8
    metadata: null
    note: null
    pmcid: null
    pmid: '11796225'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gkl972
    metadata: null
    note: null
    pmcid: PMC1899097
    pmid: '17202167'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/30.1.47
    metadata: null
    note: null
    pmcid: PMC99121
    pmid: '11752250'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gkq968
    metadata: null
    note: null
    pmcid: PMC3013802
    pmid: '21030441'
    type:
    - Other
    version: null
  relation:
  - biotoolsID: bto
    type: includes
  toolType:
  - Database portal
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  - term: Enzymes
    uri: http://edamontology.org/topic_0821
  - term: Biology
    uri: http://edamontology.org/topic_3070
  - term: Biotechnology
    uri: http://edamontology.org/topic_3297
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Biomedical science
    uri: http://edamontology.org/topic_3344
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2017-05-24T12:15:33Z'
  biotoolsCURIE: biotools:sarek
  biotoolsID: sarek
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: maxime.garcia@scilifelab.se
    fundrefid: null
    gridid: null
    name: Maxime U. Garcia
    note: null
    orcidid: https://orcid.org/0000-0003-2827-9261
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://maxulysse.github.io/
  - email: szilveszter.juhos@scilifelab.se
    fundrefid: null
    gridid: null
    name: Szilvester Juhos
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Science for Life Laboratory - SciLifeLab
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole: []
    url: https://www.scilifelab.se/
  - email: null
    fundrefid: null
    gridid: null
    name: National Genomics Infrastructure - NGI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole: []
    url: https://ngisweden.scilifelab.se/
  - email: null
    fundrefid: null
    gridid: null
    name: National Bioinformatics Infrastructure Sweden - NBIS
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole: []
    url: https://nbis.se/
  - email: null
    fundrefid: null
    gridid: null
    name: Barntumörbanken
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole: []
    url: https://ki.se/forskning/barntumorbanken
  description: Sarek is part of nf-core and has changed to the nf-core-sarek id.
  documentation:
  - note: null
    type:
    - General
    url: https://nf-co.re/sarek
  - note: null
    type:
    - User manual
    url: https://nf-co.re/sarek/usage
  - note: null
    type:
    - Installation instructions
    url: https://nf-co.re/usage/installation
  - note: null
    type:
    - Terms of use
    url: https://github.com/nf-core/sarek/blob/master/LICENSE
  download: []
  editPermission:
    authors:
    - malinlarsson
    - szilva
    - fhanssen
    - ewels
    - JoseEspinosa
    - gelpi@ub.edu
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence (raw)
        uri: http://edamontology.org/data_3497
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
    note: null
    operation:
    - term: Sample comparison
      uri: http://edamontology.org/operation_3731
    - term: Sequence annotation
      uri: http://edamontology.org/operation_0361
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: https://nf-co.re/sarek
  homepage_status: 0
  language:
  - Groovy
  lastUpdate: '2026-02-04T22:38:39.196636Z'
  license: MIT
  link:
  - note: Github Repository
    type:
    - Repository
    url: https://github.com/nf-core/sarek
  - note: Slack channel
    type:
    - Social media
    url: https://nfcore.slack.com/channels/sarek
  maturity: Mature
  name: Sarek
  operatingSystem:
  - Linux
  otherID: []
  owner: MaxUlysse
  publication:
  - doi: 10.1101/316976
    metadata: null
    note: This is the publication about the nf-core framework
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.12688/f1000research.16665.2
    metadata: null
    note: This is the publication about the nf-core framework
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.1038/s41587-020-0439-x
    metadata:
      abstract: ''
      authors:
      - name: Ewels P.A.
      - name: Peltzer A.
      - name: Fillinger S.
      - name: Patel H.
      - name: Alneberg J.
      - name: Wilm A.
      - name: Garcia M.U.
      - name: Di Tommaso P.
      - name: Nahnsen S.
      citationCount: 935
      date: '2020-03-01T00:00:00Z'
      journal: Nature Biotechnology
      title: The nf-core framework for community-curated bioinformatics pipelines
    note: This is the publication about the nf-core framework
    pmcid: null
    pmid: '32055031'
    type:
    - Other
    version: null
  relation:
  - biotoolsID: caw
    type: isNewVersionOf
  - biotoolsID: nf-core-sarek
    type: hasNewVersion
  toolType:
  - Command-line tool
  - Workflow
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  validated: 1
  version:
  - 2.0.0
  - 2.1.0
  - 2.2.0
  - 2.2.1
  - 2.2.2
  - '2.3'
  - 2.3.FIX1
- accessibility: null
  additionDate: '2025-05-29T08:55:46.088021Z'
  biotoolsCURIE: biotools:denoising-inhomogeneity_correction_tool
  biotoolsID: denoising-inhomogeneity_correction_tool
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: matias_fernandez@iislafe.es
    fundrefid: null
    gridid: null
    name: Matias Fernandez-Paton
    note: null
    orcidid: https://orcid.org/0000-0001-9374-1411
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Documentor
    - Support
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Documentor
    - Support
    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: 'The tool is designed to perform a customisable image pre-processing
    to reduce noise and inhomogeneity field effect, thus improving image quality and
    reproducibility of radiomics features. This tool consists of two independent steps:
    one for denoising using one of the 5 integrated filters (Bilateral Filter, Anisotropic
    Diffusion Filter (ADF), Curvature Flow Filter (CFF), SUSAN and Non Local Means
    (NLM)), and another for the ANTs N4 and another for the ANT''s N4 bias correction
    filter. The parameter configuration of this tool has been optimised for TW1, T2W,
    DWI and DCE sequences in neuroblastoma (NB) and paediatric brain tumours, but
    it can also be configured with some of their parameters using a JSON parameter
    configuration file.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/wYJ7Fttnk6Dp7gc
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/oseiKoeFZqwoRCA
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=HkHqFGXGEbo&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=9
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: docker run -it --rm --name container_name -v "<input_path>:/input" -v "<output_path>:/output"
      -v "<config_path>:/config" harbor.eucaim.cancerimage.eu/processing-tools/denoising_inhomogeneity_correction_tool:1.1.0
      --config /config/config.json
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processin-tools/denoising_inhomogeneity_correction_tool:1.1.0
      --paths /input/Dataset/Patient_1/Study/T1W /input/Dataset/Patient_2/Study/T2W
      --output /output --series_number 2000 --series_description_suffix "_harmonized"
      --denoising adf --conductance 0.5 --iterations 3 --time_step 0.0625 --n4 --bspline_size
      50 --n4_iterations 50 30 --shrink_factor 2
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-04T15:33:01.249605Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: null
  name: Denoising-Inhomogeneity Correction Tool (EUCAIM-SW-015_T-01-01-015)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: casopon
  publication:
  - doi: 10.1007/s10278-021-00512-8
    metadata: null
    note: null
    pmcid: PMC8554919
    pmid: '34505958'
    type:
    - Primary
    version: null
  - doi: 10.1186/s41747-020-00150-9
    metadata: null
    note: null
    pmcid: PMC7125275
    pmid: '32246291'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  validated: 0
  version:
  - 1.1.0
- accessibility: null
  additionDate: '2026-02-04T10:55:57.317793Z'
  biotoolsCURIE: biotools:recombinhunt
  biotoolsID: recombinhunt
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: RecombinHunt is a data-driven computational tool developed for detecting
    and characterizing recombinant viral genomes — sequences formed by combining genetic
    material from two (or more) different viral lineages. It uses statistical analyses
    of mutations in viral genome sequences to identify contributing parental lineages
    and the positions (breakpoints) where recombination occurred, doing so with high
    specificity and sensitivity and relatively fast performance compared with other
    methods. Originally applied to SARS-CoV-2 and shown to also work with viruses
    like monkeypox, it helps improve genomic surveillance of evolving viruses and
    can support early warning systems for future pandemics.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://doi.org/10.5281/zenodo.8123832
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T10:56:03.581236Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/tomalf2/recombinhunt-cov
  maturity: null
  name: RecombinHunt
  operatingSystem: []
  otherID: []
  owner: abernasconi
  publication:
  - doi: 10.1038/s41467-024-47464-5
    metadata: null
    note: null
    pmcid: PMC11024102
    pmid: '38632281'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-02-04T10:02:52.405439Z'
  biotoolsCURIE: biotools:fluwarning
  biotoolsID: fluwarning
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: FluWarning is a computational early-warning system to detect early
    genetic signals in influenza A viruses that may indicate a risk of cross-species
    transmission (“spillover”) and potential epidemic or pandemic events.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/DEIB-GECO/flu-warning-system/blob/main/README.md
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://doi.org/10.5281/zenodo.15498406
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-04T10:03:01.978429Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://doi.org/10.5281/zenodo.15498406
  - note: null
    type:
    - Repository
    url: https://github.com/DEIB-GECO/flu-warning-system
  maturity: null
  name: FluWarning
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: abernasconi
  publication:
  - doi: 10.1126/sciadv.adz7312
    metadata: null
    note: null
    pmcid: PMC12551695
    pmid: '41134898'
    type: []
    version: '2'
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Informatics
    uri: http://edamontology.org/topic_0605
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  validated: 0
  version:
  - '2'
- accessibility: Open access (with restrictions)
  additionDate: '2025-11-25T09:58:37.569343Z'
  biotoolsCURIE: biotools:ml_model_for_mr_series_categorisation
  biotoolsID: ml_model_for_mr_series_categorisation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: gibi230@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: armago@alumni.uv.es
    fundrefid: null
    gridid: null
    name: Armando Gomis-Maya
    note: null
    orcidid: https://orcid.org/0000-0002-9527-8093
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: A tool based on artificial intelligence that is able to perform a categorisation
    of MRI series by using standardized DICOM tags. The categorisation includes the
    type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W,
    DCE, ...), the presence of fat suppression and the detection of non-relevant /
    junk series (e.g. localizers, calibrations, screenshots...).
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/rpm56rD5FfXAHyb
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/8r3CzyQXrd7ERFp
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=gudDCiuJIf8&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=11
  download: []
  editPermission:
    authors:
    - casopon
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
      \ \\\n  -v \"<output_path>:/output\" \\\n  harbor.eucaim.cancerimage.eu/processing-tools/ml_model_for_mr_series_categorisation:<version>\
      \ \\\n  --config-string \"{'output_name': 'classification_results.json'}\""
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Classification
      uri: http://edamontology.org/operation_2990
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-03T12:02:23.334589Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: ML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication:
  - doi: 10.1186/s40537-025-01086-w
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  - term: Data acquisition
    uri: http://edamontology.org/topic_3077
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T09:19:51.404419Z'
  biotoolsCURIE: biotools:mr-based_dipg_tumour_detection_and_segmentation
  biotoolsID: mr-based_dipg_tumour_detection_and_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: matias_fernandez@iislafe.es
    fundrefid: null
    gridid: null
    name: Matias Fernandez-Paton
    note: null
    orcidid: https://orcid.org/0000-0001-9374-1411
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Support
    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
    gridid: null
    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Documentor
    - Support
    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: The tool performs an automatic segmentation of the possible DIPG tumours
    on MR images. DIPG (Diffuse Intrinsic Pontine Glioma), or more recently, DMG (Diffuse
    Midline Glioma) is a H3 K27M–mutant pediatric brainstem cancer detected in T1W
    and Flair/T2-weighted magnetic resonance images. The tool includes a complete
    workflow from DICOM images to DICOM seg tumoral masks.
  documentation:
  - note: null
    type:
    - General
    url: https://link.springer.com/article/10.1007/s10278-025-01557-9
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/5CL2H8tyMDzFHex
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=f3DPS56z6oI&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=36
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input \\\n  -v /path/to/output:/output\
      \ \\\nharbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest\
      \ \\\n  --series-selector /input/config/series.csv"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input -v /path/to/output:/output\
      \ harbor.eucaim.cancerimage.eu/processing-tools/mr-based_dipg_tumour_detection_and_segmentation:latest\
      \ \\\n  --json-args '{\"dataset_id\":\"DS1\",\"patient_id\":\"P1\",\"study_id\"\
      :\"S1\",\"sequences\":{\"T1w\":\"/input/DICOM/DS1/P1/S1/T1\",\"FLAIR\":\"/input/DICOM/DS1/P1/S1/FLAIR\"\
      }}'"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-03T11:45:32.223088Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: MR-based DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: casopon
  publication:
  - doi: 10.1007/s10278-025-01557-9
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  validated: 0
  version:
  - 2.0.0
- accessibility: null
  additionDate: '2019-06-20T14:18:28Z'
  biotoolsCURIE: biotools:decompTumor2Sig
  biotoolsID: decompTumor2Sig
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: r.piro@fu-berlin.de
    fundrefid: null
    gridid: null
    name: Prof. Dr. Rosario M. Piro
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: null
  description: R package for identification of mutational signatures active in individual
    tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type
    or Shiraishi-type signatures, thus quantifying the contribution of the corresponding
    mutational processes to the somatic mutations identified in the tumor.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/rmpiro/decompTumor2Sig/blob/master/decompTumor2Sig-manual.pdf
  download:
  - note: null
    type: Downloads page
    url: http://rmpiro.net/index.html#downloads
    version: null
  editPermission:
    authors:
    - ELIXIR-ITA-POLIMI
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Parsing
      uri: http://edamontology.org/operation_1812
    output: []
  homepage: http://rmpiro.net/decompTumor2Sig/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-02-02T08:12:42.981321Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/rmpiro/decompTumor2Sig/issues
  - note: null
    type:
    - Repository
    url: https://github.com/rmpiro/decompTumor2Sig
  - note: null
    type:
    - Software catalogue
    url: https://bioconductor.org/packages/release/bioc/html/decompTumor2Sig.html
  maturity: Mature
  name: decompTumor2Sig
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: Ruta
  publication:
  - doi: 10.1186/s12859-019-2688-6
    metadata:
      abstract: '© 2019 The Author(s).Background: The somatic mutations found in a
        tumor have in most cases been caused by multiple mutational processes such
        as those related to extrinsic carcinogens like cigarette smoke, and those
        related to intrinsic processes like age-related spontaneous deamination of
        5-methylcytosine. The effect of such mutational processes can be modeled by
        mutational signatures, of which two different conceptualizations exist: the
        model introduced by Alexandrov et al., Nature 500:415-421, 2013, and the model
        introduced by Shiraishi et al., PLoS Genetics 11(12):e1005657, 2015. The initial
        identification and definition of mutational signatures requires large sets
        of tumor samples. Results: Here, we present decompTumor2Sig, an easy to use
        R package that can decompose an individual tumor genome into a given set of
        Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution
        of the corresponding mutational processes to the somatic mutations identified
        in the tumor. Until now, such tools were available only for Alexandrov signatures.
        We demonstrate the correctness and usefulness of our approach with three test
        cases, using somatic mutations from 21 breast cancer genomes, from 435 tumor
        genomes of ten different tumor entities, and from simulated tumor genomes,
        respectively. Conclusions: The decompTumor2Sig package is freely available
        and has been accepted for inclusion in Bioconductor.'
      authors:
      - name: Kruger S.
      - name: Piro R.M.
      citationCount: 8
      date: '2019-04-18T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'DecompTumor2Sig: Identification of mutational signatures active in individual
        tumors'
    note: null
    pmcid: PMC6472187
    pmid: '30999866'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - 2.0.0
- accessibility: Open access
  additionDate: '2019-08-09T13:06:36Z'
  biotoolsCURIE: biotools:DrugComb
  biotoolsID: DrugComb
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: jing.tang@helsinki.fi
    fundrefid: null
    gridid: null
    name: Jing Tang
    note: null
    orcidid: https://orcid.org/0000-0001-7480-7710
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: 'The data portal for drug combination and monotherapy sensitivity screenings.

    [v1.5] DrugComb update: a more comprehensive drug sensitivity data repository
    and analysis portal. https://doi.org/10.1093/nar/gkab438

    [v1.4] DrugComb: an integrative cancer drug combination data portal. https://doi.org/10.1093/nar/gkz337'
  documentation:
  - note: null
    type:
    - General
    url: https://researchportal.helsinki.fi/en/datasets/drugcomb/
  - note: null
    type:
    - User manual
    url: https://researchportal.helsinki.fi/en/datasets/drugcomb/
  download:
  - note: https://zenodo.org/records/11102665
    type: Downloads page
    url: https://zenodo.org/records/11102665
    version: 1.4 summary
  - note: https://zenodo.org/records/15235991
    type: Downloads page
    url: https://zenodo.org/records/15235991
    version: 1.5 summary
  - note: https://zenodo.org/records/18449193
    type: Downloads page
    url: https://doi.org/10.5281/zenodo.18449193
    version: 1.4 raw
  editPermission:
    authors:
    - jtang920
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://researchportal.helsinki.fi/en/datasets/drugcomb/
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-01T17:44:46.966665Z'
  license: Unlicense
  link:
  - note: alternative links
    type:
    - Repository
    url: https://researchportal.helsinki.fi/en/datasets/drugcomb/
  - note: null
    type:
    - Social media
    url: https://twitter.com/DrugComb
  maturity: Mature
  name: DrugComb
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: jtang920
  publication:
  - doi: 10.1093/NAR/GKZ337
    metadata: null
    note: null
    pmcid: PMC6602441
    pmid: '31066443'
    type:
    - Primary
    version: '1.4'
  - doi: 10.1093/nar/gkab438
    metadata: null
    note: null
    pmcid: PMC8218202
    pmid: '34060634'
    type: []
    version: '1.5'
  relation:
  - biotoolsID: synergyfinder
    type: uses
  toolType:
  - Web application
  - Database portal
  topic:
  - term: Informatics
    uri: http://edamontology.org/topic_0605
  - term: Drug metabolism
    uri: http://edamontology.org/topic_3375
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  validated: 1
  version:
  - '1.5'
- accessibility: Open access
  additionDate: '2026-01-30T11:47:35.909206Z'
  biotoolsCURIE: biotools:cineca-hpc
  biotoolsID: cineca-hpc
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: s.gioiosa@cineca.it
    fundrefid: null
    gridid: null
    name: Silvia Gioiosa
    note: null
    orcidid: https://orcid.org/0000-0003-1302-8320
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Primary contact
    url: https://www.hpc.cineca.it/our-activities/domains/hpc-for-bioinformatics/
  description: 'HPC@CINECA provides high-performance computing resources for Elixir
    members to support large-scale processing and analysis of High-Throughput Sequencing
    (HTS) data. The service operates on a continuous open-call basis, with approved
    projects receiving a 1-year allocation that includes 50,000 CPU hours and 1 TB
    of storage by default, with the possibility to request additional resources. Proposals
    are evaluated by a scientific committee, with feedback typically provided within
    seven working days.


    From 2025, a pilot program enables the analysis of GDPR-protected sensitive data
    for up to two projects per year (maximum one per user or institution, first-come
    first-served). Projects involving non-sensitive data are unlimited and may be
    submitted at any time.'
  documentation:
  - note: null
    type:
    - Other
    url: https://link.springer.com/article/10.1186/s12859-020-03565-8
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Galaxy
  elixirNode:
  - Italy
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Service management
      uri: http://edamontology.org/operation_3760
    output: []
  homepage: https://docs.google.com/forms/d/e/1FAIpQLSchmLCugIShXAneQmTgbM5SlPLDdZH0KCIECk0R9Tm6GTDcNw/viewform
  homepage_status: 0
  language:
  - Bash
  lastUpdate: '2026-01-30T12:10:29.923314Z'
  license: Not licensed
  link:
  - note: null
    type:
    - Service
    url: https://docs.google.com/forms/d/e/1FAIpQLSchmLCugIShXAneQmTgbM5SlPLDdZH0KCIECk0R9Tm6GTDcNw/viewform
  maturity: Legacy
  name: ELIXIR-CINECA-HPC
  operatingSystem:
  - Linux
  otherID: []
  owner: silvia9
  publication:
  - doi: 10.1186/s12859-020-03565-8
    metadata: null
    note: null
    pmcid: PMC7446135
    pmid: '32838759'
    type:
    - Primary
    version: null
  - doi: 10.1186/s40537-024-01047-9
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Usage
    version: null
  relation:
  - biotoolsID: kraken2
    type: uses
  - biotoolsID: annovar
    type: uses
  - biotoolsID: tophat2
    type: uses
  - biotoolsID: bowtie
    type: uses
  - biotoolsID: bowtie2
    type: uses
  - biotoolsID: hisat2
    type: uses
  - biotoolsID: vep
    type: uses
  - biotoolsID: gatk
    type: uses
  - biotoolsID: snakemake
    type: uses
  - biotoolsID: samtools
    type: uses
  - biotoolsID: R
    type: uses
  - biotoolsID: biopython
    type: uses
  - biotoolsID: hpc-reditools
    type: uses
  - biotoolsID: reditools
    type: uses
  - biotoolsID: tabix
    type: uses
  - biotoolsID: cutadapt
    type: uses
  - biotoolsID: fastqc
    type: uses
  - biotoolsID: multiqc
    type: uses
  - biotoolsID: trimmomatic
    type: uses
  - biotoolsID: htseqcount
    type: uses
  - biotoolsID: deseq2
    type: uses
  - biotoolsID: plink
    type: uses
  - biotoolsID: majiq-spel
    type: uses
  - biotoolsID: stringtie
    type: uses
  - biotoolsID: bcftools
    type: uses
  - biotoolsID: limma
    type: uses
  - biotoolsID: bedtools
    type: uses
  - biotoolsID: alphafold2
    type: uses
  - biotoolsID: blast
    type: uses
  - biotoolsID: bwa-mem2
    type: uses
  - biotoolsID: cufflinks
    type: uses
  - biotoolsID: wgsim
    type: uses
  - biotoolsID: jellyfish
    type: uses
  - biotoolsID: freebayes
    type: uses
  - biotoolsID: seqtk
    type: uses
  - biotoolsID: sra
    type: uses
  - biotoolsID: varscan
    type: uses
  - biotoolsID: star
    type: uses
  - biotoolsID: vcftools
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - '5'
- accessibility: null
  additionDate: '2026-01-28T08:45:35.923304Z'
  biotoolsCURIE: biotools:unexakorea_dataset
  biotoolsID: unexakorea_dataset
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: 'This Investigationevaluated the in vivo maintenance effect of a sustained-release
    vitamin formulation developed using the proprietary coating technology of unexakorea
    Inc. In a mouse model, the formulation demonstrated a stable plasma concentration
    for approximately 10–12 hours after administration.

    These findings suggest that the sustained-release formulation may serve as a promising
    alternative

    to conventional high-absorption formulations, offering improved physiological
    stability and reduced

    adverse effects associated with excessive absorption


    sustained-release, plasma concentration, Lipid Encapsulation Material'
  documentation: []
  download:
  - note: Comparison Invivo vs limited range fitting
    type: Other
    url: https://drive.google.com/drive/folders/1-gEfIhJuctGxGXa8Kz7-yPiTKhateOx1?usp=drive_link
    version: v1
  - note: figure set
    type: Other
    url: https://drive.google.com/drive/folders/1s0dQ1G9P1TMOPGYqUvjnM2N5kI91I1rR?usp=drive_link
    version: v1
  - note: Full range fitting
    type: Other
    url: https://drive.google.com/drive/folders/1hUwIsDJNHGZ1dmVXZpiL-R6Cp8Pp-9mZ?usp=drive_link
    version: v1
  - note: limited range fitting
    type: Other
    url: https://drive.google.com/drive/folders/1OqrEQHPgTasUcrlkdrCOR1TQQ4lcGc3o?usp=drive_link
    version: v1
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://unexakorea.com
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-30T06:45:59.591871Z'
  license: null
  link: []
  maturity: null
  name: unexakorea dataset
  operatingSystem: []
  otherID: []
  owner: unexakorea
  publication:
  - doi: 10.26434/chemrxiv-2025-2jq7b
    metadata: null
    note: Optimizing Pharmacokinetic Persistence of Functional Agents Through Next-Generation
      Sustained-Release Formulations
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: v1
  relation: []
  toolType: []
  topic:
  - term: Bioengineering
    uri: http://edamontology.org/topic_3398
  - term: Chemical biology
    uri: http://edamontology.org/topic_3369
  validated: 0
  version: []
- 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/14916843
    version: v6.0
  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: GFF3
        uri: http://edamontology.org/format_1975
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - 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: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
    - 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: '2026-01-29T12:11:19.042627Z'
  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: null
    note: null
    pmcid: PMC8743544
    pmid: '34739369'
    type:
    - Primary
    version: '1.1'
  - doi: 10.1093/nar/gkaf335
    metadata: null
    note: null
    pmcid: PMC12230652
    pmid: '40271661'
    type:
    - Primary
    version: null
  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:
  - Web application
  - Command-line tool
  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:
  - v1.12.0
- accessibility: null
  additionDate: '2026-01-15T18:19:41.098465Z'
  biotoolsCURIE: biotools:meteor
  biotoolsID: meteor
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Meteor is a plateform for quantitative metagenomics profiling of complex
    ecosystems. Meteor relies on genes catalogue to perform species-level taxonomic
    profiling (Bacteria, Archaea and Eukaryotes), functional analysis and strain-level
    population structure inference.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format: []
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
  homepage: https://github.com/metagenopolis/meteor
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-26T10:57:22.600550Z'
  license: null
  link: []
  maturity: null
  name: meteor
  operatingSystem: []
  otherID: []
  owner: vashokan
  publication:
  - doi: 10.1186/s40168-025-02249-w
    metadata: null
    note: null
    pmcid: PMC12590682
    pmid: '41199348'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-06-18T16:24:28.343068Z'
  biotoolsCURIE: biotools:centrifuger
  biotoolsID: centrifuger
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: Li.Song@dartmouth.edu
    fundrefid: null
    gridid: null
    name: Li Song
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ben Langmead
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Lossless compression of microbial genomes for efficient and accurate
    metagenomic sequence classification.
  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: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
  homepage: https://github.com/mourisl/centrifuger
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-01-26T10:46:40.835466Z'
  license: MIT
  link: []
  maturity: null
  name: Centrifuger
  operatingSystem: []
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1186/s13059-024-03244-4
    metadata: null
    note: null
    pmcid: PMC11046777
    pmid: '38664753'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Script
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Metagenomic sequencing
    uri: http://edamontology.org/topic_3837
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  validated: 0
  version: []
- accessibility: null
  additionDate: '2021-01-18T12:30:59Z'
  biotoolsCURIE: biotools:macse
  biotoolsID: macse
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: ranwez@supagro.fr
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'Aligning Protein-Coding Nucleotide Sequences with MACSE.


    MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop
    Codons.


    A wide range of molecular analyses relies on multiple sequence alignments (MSA).


    MACSE aligns coding NT sequences with respect to their AA translation while allowing
    NT sequences to contain multiple frameshifts and or stop codons.'
  documentation: []
  download:
  - note: Pipelines source code
    type: Source code
    url: https://github.com/ranwez/MACSE_V2_PIPELINES
    version: null
  editPermission:
    authors:
    - ranwez
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Global alignment
      uri: http://edamontology.org/operation_0496
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    - term: Frameshift detection
      uri: http://edamontology.org/operation_0265
    - term: Sequence trimming
      uri: http://edamontology.org/operation_3192
    output: []
  homepage: https://bioweb.supagro.inra.fr/macse/
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T16:37:52.513457Z'
  license: null
  link: []
  maturity: null
  name: MACSE
  operatingSystem: []
  otherID: []
  owner: Niclaskn
  publication:
  - doi: 10.1007/978-1-0716-1036-7_4
    metadata:
      abstract: '© 2021, Springer Science+Business Media, LLC, part of Springer Nature.Most
        genomic and evolutionary comparative analyses rely on accurate multiple sequence
        alignments. With their underlying codon structure, protein-coding nucleotide
        sequences pose a specific challenge for multiple sequence alignment. Multiple
        Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program
        that provided the first automatic solution for aligning protein-coding gene
        datasets containing both functional and nonfunctional sequences (pseudogenes).
        Through its unique features, reliable codon alignments can be built in the
        presence of frameshifts and stop codons suitable for subsequent analysis of
        selection based on the ratio of nonsynonymous to synonymous substitutions.
        Here we offer a practical overview and guidelines on the use of MACSE v2.
        This major update of the initial algorithm now comes with a graphical interface
        providing user-friendly access to different subprograms to handle multiple
        alignments of protein-coding sequences. We also present new pipelines based
        on MACSE v2 subprograms to handle large datasets and distributed as Singularity
        containers. MACSE and associated pipelines are available at: https://bioweb.supagro.inra.fr/macse/.'
      authors:
      - name: Ranwez V.
      - name: Chantret N.
      - name: Delsuc F.
      citationCount: 1
      date: '2021-01-01T00:00:00Z'
      journal: Methods in Molecular Biology
      title: Aligning Protein-Coding Nucleotide Sequences with MACSE
    note: null
    pmcid: null
    pmid: '33289886'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Molecular evolution
    uri: http://edamontology.org/topic_3945
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: Protein expression
    uri: http://edamontology.org/topic_0108
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:53.048754Z'
  biotoolsCURIE: biotools:annotatability
  biotoolsID: annotatability
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: barak.raveh@mail.huji.ac.il
    fundrefid: null
    gridid: null
    name: Barak Raveh
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: mor.nitzan@mail.huji.ac.il
    fundrefid: null
    gridid: null
    name: Mor Nitzan
    note: null
    orcidid: https://orcid.org/0000-0003-0074-9196
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Annotatability is a framework for analyzing the dynamics of deep neural
    network training on single-cell and spatial omics data to identify annotation
    mismatches and characterize biological data structure. It develops a signal-aware
    graph embedding method for downstream analysis.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Dimensionality reduction
      uri: http://edamontology.org/operation_3935
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    output: []
  homepage: https://github.com/nitzanlab/Annotatability
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T12:22:53.050870Z'
  license: null
  link: []
  maturity: null
  name: Annotatability
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S43588-024-00721-5
    metadata: null
    note: null
    pmcid: PMC11659171
    pmid: '39633094'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Multiomics
    uri: http://edamontology.org/topic_4021
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:50.782749Z'
  biotoolsCURIE: biotools:italicc_galapagoense_italic
  biotoolsID: italicc_galapagoense_italic
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Interactive Tree Of Life is an online tool for displaying, annotating,
    and managing phylogenetic trees. It allows users to manage and visualize trees
    directly in the browser, and annotate them with various datasets.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Phylogenetic tree visualisation
      uri: http://edamontology.org/operation_0567
    - term: Virtual PCR
      uri: http://edamontology.org/operation_0307
    - term: Phylogenetic inference
      uri: http://edamontology.org/operation_0323
    - term: Phylogenetic tree editing
      uri: http://edamontology.org/operation_0326
    - term: Phylogenetic tree annotation
      uri: http://edamontology.org/operation_0558
    output: []
  homepage: https://itol.embl.de/
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T12:22:50.784927Z'
  license: null
  link: []
  maturity: null
  name: Interactive Tree Of Life
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.21203/RS.3.RS-5657151/V1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Cladistics
    uri: http://edamontology.org/topic_3944
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:47.114327Z'
  biotoolsCURIE: biotools:fair_data_cube
  biotoolsID: fair_data_cube
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: XiaoFeng.Liao@radboudumc.nl
    fundrefid: null
    gridid: null
    name: Xiaofeng Liao
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: Peter-Bram.tHoen@radboudumc.nl
    fundrefid: null
    gridid: null
    name: Peter A. C. ’t Hoen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: The FAIR Data Cube (FDCube) is an infrastructure component of the Netherlands
    X-omics initiative designed to facilitate the reuse of multi-omics data by making
    it FAIR and enabling integration across different data layers while ensuring data
    security and privacy.
  documentation: []
  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: Data deposition
      uri: http://edamontology.org/operation_3431
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output: []
  homepage: https://github.com/Xomics/FAIRDataCube/wiki
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T12:22:47.116470Z'
  license: null
  link: []
  maturity: null
  name: FAIR Data Cube (FDCube)
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1186/S13326-024-00321-2
    metadata: null
    note: null
    pmcid: PMC11681678
    pmid: '39732721'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Multiomics
    uri: http://edamontology.org/topic_4021
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  - term: Cybersecurity
    uri: http://edamontology.org/topic_4045
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:44.915914Z'
  biotoolsCURIE: biotools:exmo
  biotoolsID: exmo
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: juanm.ruso@usc.es
    fundrefid: null
    gridid: null
    name: Juan M. Ruso
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: bairong.shen@scu.edu.cn
    fundrefid: null
    gridid: null
    name: Bairong Shen
    note: null
    orcidid: https://orcid.org/0000-0003-2899-1531
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: EXMO (Exercise Medicine Ontology) is a reference ontology for individualized
    exercise prescriptions, providing a structured vocabulary of physical activity,
    health status, and exercise prescription terms.  It aims to support personalized
    exercise recommendations and integrate with databases and recommendation systems.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Ontology visualisation
      uri: http://edamontology.org/operation_3559
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output: []
  homepage: https://github.com/DarkKnight0-0/exmo
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T12:22:44.918122Z'
  license: null
  link: []
  maturity: null
  name: EXMO - Exercise Medicine Ontology
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S41597-024-04217-9
    metadata: null
    note: null
    pmcid: PMC11655637
    pmid: '39695140'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Personalised medicine
    uri: http://edamontology.org/topic_3577
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  - term: Cardiology
    uri: http://edamontology.org/topic_3335
  - term: Physics
    uri: http://edamontology.org/topic_3318
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:40.762690Z'
  biotoolsCURIE: biotools:morphosource
  biotoolsID: morphosource
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: salmecija@amnh.org
    fundrefid: null
    gridid: null
    name: Sergio Almécija
    note: null
    orcidid: https://orcid.org/0000-0003-1373-1497
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: MorphoSource is a platform for housing and sharing 3D morphological
    data of primate specimens, facilitating collaborative research in phenomics. It
    provides a repository for digitized specimens from various institutions and enables
    researchers to access and analyze morphological data.
  documentation: []
  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: Quantification
      uri: http://edamontology.org/operation_3799
    - term: Data digitisation
      uri: http://edamontology.org/operation_4043
    output: []
  homepage: https://www.morphosource.org/
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T12:22:40.764503Z'
  license: null
  link: []
  maturity: null
  name: MorphoSource
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S41597-024-04261-5
    metadata: null
    note: null
    pmcid: PMC11655552
    pmid: '39695181'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Zoology
    uri: http://edamontology.org/topic_3500
  - term: Phenomics
    uri: http://edamontology.org/topic_3298
  - term: Tomography
    uri: http://edamontology.org/topic_3452
  - term: Sample collections
    uri: http://edamontology.org/topic_3277
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:30.478977Z'
  biotoolsCURIE: biotools:pathsingle
  biotoolsID: pathsingle
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: dani.livne@yahoo.com
    fundrefid: null
    gridid: null
    name: Dani Livne
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: PathSingle is a Python-based pathway analysis tool designed for single-cell
    data analysis, employing a graph-based algorithm for classifying cellular states.
    The tool is open-source, extensible, and computationally efficient, facilitating
    the identification of molecular drivers within cellular contexts.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Pathway analysis
      uri: http://edamontology.org/operation_3928
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    - term: Dimensionality reduction
      uri: http://edamontology.org/operation_3935
    output: []
  homepage: https://github.com/zurkin1/PathSingle
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-01-15T12:22:30.481672Z'
  license: MIT
  link: []
  maturity: null
  name: PathSingle
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1186/S13040-024-00416-7
    metadata: null
    note: null
    pmcid: PMC11668091
    pmid: '39716187'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:29.421922Z'
  biotoolsCURIE: biotools:mhcquant2
  biotoolsID: mhcquant2
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: MHCquant2 is a Nextflow-based pipeline for identifying and quantifying
    HLA-presented peptides from immunopeptidomics mass spectrometry data. It leverages
    OpenMS tools and peptide property predictors to improve peptide identifications
    and facilitate tumor antigen discovery.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Chromatographic alignment
      uri: http://edamontology.org/operation_3628
    - term: Peptide immunogenicity prediction
      uri: http://edamontology.org/operation_0252
    - term: Protein identification
      uri: http://edamontology.org/operation_3767
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    - term: Peptide identification
      uri: http://edamontology.org/operation_3631
    output: []
  homepage: https://nf-co.re/mhcquant/2.6.0
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T12:22:29.423978Z'
  license: null
  link: []
  maturity: null
  name: MHCquant2
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.21203/RS.3.RS-5560023/V1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Immunoproteins and antigens
    uri: http://edamontology.org/topic_2830
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:21.651247Z'
  biotoolsCURIE: biotools:jecfa
  biotoolsID: jecfa
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: ileana.baldi@unipd.it
    fundrefid: null
    gridid: null
    name: Ileana Baldi
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: The JECFA Data Retriever is an R package and associated workflow that
    automates the retrieval of key identifiers and toxicological data from the Joint
    FAO/WHO Expert Committee on Food Additives (JECFA) database via web scraping.
    It provides a reproducible pipeline for accessing and processing JECFA data, facilitating
    more efficient research.
  documentation: []
  download:
  - note: null
    type: Container file
    url: https://hub.docker.com/repository/docker/corradolanera/jecfa
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Phasing
      uri: http://edamontology.org/operation_3454
    output: []
  homepage: https://ubesp-dctv.github.io/jecfa/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-01-15T12:22:21.653255Z'
  license: null
  link: []
  maturity: null
  name: JECFA Data Retriever
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S41597-024-04294-W
    metadata: null
    note: null
    pmcid: PMC11682307
    pmid: '39732706'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Toxicology
    uri: http://edamontology.org/topic_2840
  - term: Chemical biology
    uri: http://edamontology.org/topic_3369
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:15.335509Z'
  biotoolsCURIE: biotools:preytouch
  biotoolsID: preytouch
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: sheinmark@tauex.tau.ac.il
    fundrefid: null
    gridid: null
    name: Mark Shein-Idelson
    note: null
    orcidid: https://orcid.org/0000-0001-8132-2826
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: PreyTouch is a touchscreen-based closed-loop system for studying predator-prey
    interactions, enabling flexible prey control, accurate monitoring of predator
    strikes, and automated rewarding. It provides a platform for long-term experiments
    and allows for the study of predator-prey dynamics and learning.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output: []
  homepage: https://github.com/EvolutionaryNeuralCodingLab/PreyTouch
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T12:22:15.337762Z'
  license: null
  link: []
  maturity: null
  name: PreyTouch
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S42003-024-07345-5
    metadata: null
    note: null
    pmcid: PMC11659303
    pmid: '39702825'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Neurobiology
    uri: http://edamontology.org/topic_3304
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Zoology
    uri: http://edamontology.org/topic_3500
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Cybersecurity
    uri: http://edamontology.org/topic_4045
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:06.591190Z'
  biotoolsCURIE: biotools:nico
  biotoolsID: nico
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: dominic.gruen@uni-wuerzburg.de
    fundrefid: null
    gridid: null
    name: Dominic Grün
    note: null
    orcidid: https://orcid.org/0000-0002-3364-5898
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: NiCo is a computational framework that integrates single-cell resolution
    spatial transcriptomics with matched single-cell RNA-sequencing data to infer
    the influence of the spatial niche on the cell state.  It identifies extrinsic
    drivers of cell state modulation by niche covariation analysis.
  documentation:
  - note: null
    type:
    - User manual
    url: https://nico-sc-sp.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    - term: Peptide immunogenicity prediction
      uri: http://edamontology.org/operation_0252
    - term: Deisotoping
      uri: http://edamontology.org/operation_3629
    output: []
  homepage: https://pypi.org/project/nico-sc-sp/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-01-15T12:22:06.593021Z'
  license: null
  link: []
  maturity: null
  name: NiCo
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S41467-024-54973-W
    metadata: null
    note: null
    pmcid: PMC11621405
    pmid: '39639035'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Immunoproteins and antigens
    uri: http://edamontology.org/topic_2830
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:21:55.855426Z'
  biotoolsCURIE: biotools:bebe
  biotoolsID: bebe
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: benjamin@earthspecies.org
    fundrefid: null
    gridid: null
    name: Benjamin Hoffman
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: BEBE is a benchmark for computational analysis of animal behavior using
    bio-logger data, providing datasets, modeling tasks, and evaluation metrics to
    facilitate machine learning-based analysis of animal behavior.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output: []
  homepage: https://github.com/earthspecies/BEBE
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T12:21:55.857386Z'
  license: null
  link: []
  maturity: null
  name: BEBE (Bio-logger Ethogram Benchmark)
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1186/S40462-024-00511-8
    metadata: null
    note: null
    pmcid: PMC11654173
    pmid: '39695785'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Zoology
    uri: http://edamontology.org/topic_3500
  - term: RNA immunoprecipitation
    uri: http://edamontology.org/topic_3794
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:21:52.873116Z'
  biotoolsCURIE: biotools:lcrannotationsdb
  biotoolsID: lcrannotationsdb
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: joannazl@ibb.waw.pl
    fundrefid: null
    gridid: null
    name: Joanna Ziemska-Legiecka
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: aleksandra.gruca@polsl.pl
    fundrefid: null
    gridid: null
    name: Aleksandra Gruca
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: greenb@ibb.waw.pl
    fundrefid: null
    gridid: null
    name: Marcin Grynberg
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: LCRAnnotationsDB is a database storing functional and structural annotations
    for Low Complexity Regions (LCRs) in proteins. It consolidates knowledge about
    LCRs, categorizes redundant annotations, and links them to Gene Ontology terms,
    accessible programmatically via a REST API.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://lcrannotdb.lcr-lab.org/api/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Text annotation
      uri: http://edamontology.org/operation_3778
    - term: Protein structure assignment
      uri: http://edamontology.org/operation_0320
    output: []
  homepage: https://lcrannotdb.lcr-lab.org/
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T12:21:52.875687Z'
  license: null
  link:
  - note: null
    type:
    - Helpdesk
    url: https://lcrannotdb.lcr-lab.org/contact/
  maturity: null
  name: LCRAnnotationsDB
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1186/S12864-024-10960-5
    metadata: null
    note: null
    pmcid: PMC11674544
    pmid: '39731018'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Database management
    uri: http://edamontology.org/topic_3489
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:21:43.226578Z'
  biotoolsCURIE: biotools:surtvep
  biotoolsID: surtvep
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Kevin He
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: surtvep is an R package designed for estimating time-varying effects
    in Cox non-proportional hazards models, addressing computational challenges associated
    with large-scale time-to-event data.
  documentation: []
  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: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    output: []
  homepage: https://um-kevinhe.github.io/surtvep/articles/surtvep.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T12:21:43.228682Z'
  license: null
  link:
  - note: null
    type:
    - Other
    url: https://um-kevinhe.github.io/surtvep/index.html
  maturity: null
  name: surtvep
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.21105/JOSS.05688
    metadata: null
    note: null
    pmcid: PMC11664633
    pmid: '39717690'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  - term: Public health and epidemiology
    uri: http://edamontology.org/topic_3305
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:21:39.846737Z'
  biotoolsCURIE: biotools:dnea
  biotoolsID: dnea
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: akarnovs@med.umich.edu
    fundrefid: null
    gridid: null
    name: Alla Karnovsky
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: gmichail@ufl.edu
    fundrefid: null
    gridid: null
    name: George Michailidis
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: DNEA is an R package for fast and versatile data-driven network analysis
    of metabolomics data, enabling identification of differentially enriched metabolic
    modules. It builds upon the Filigree tool and provides a more flexible and powerful
    implementation for analyzing large metabolomics datasets.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Network visualisation
      uri: http://edamontology.org/operation_3925
    - term: Natural product identification
      uri: http://edamontology.org/operation_3803
    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    - term: Pathway analysis
      uri: http://edamontology.org/operation_3928
    output: []
  homepage: http://www.github.com/Karnovsky-Lab/DNEA/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-01-15T12:21:39.848626Z'
  license: null
  link: []
  maturity: null
  name: DNEA
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1186/S12859-024-05994-1
    metadata: null
    note: null
    pmcid: PMC11657348
    pmid: '39695921'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Endocrinology and metabolism
    uri: http://edamontology.org/topic_3407
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:21:36.404512Z'
  biotoolsCURIE: biotools:piikun
  biotoolsID: piikun
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: jsukumaran@sdsu.edu
    fundrefid: null
    gridid: null
    name: Jeet Sukumaran
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Piikun is a Python package for analyzing and visualizing species delimitation
    models using information theoretic frameworks. It calculates the Variation of
    Information (VI) criterion and provides true metric functions for comparing these
    models.
  documentation: []
  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: Dimensionality reduction
      uri: http://edamontology.org/operation_3935
    - term: Clustering
      uri: http://edamontology.org/operation_3432
    output: []
  homepage: https://github.com/jeetsukumaran/piikun
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-01-15T12:21:36.406739Z'
  license: MIT
  link: []
  maturity: null
  name: Piikun
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1186/S12859-024-05997-Y
    metadata: null
    note: null
    pmcid: PMC11657818
    pmid: '39695946'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:21:23.946250Z'
  biotoolsCURIE: biotools:pheno-ranker
  biotoolsID: pheno-ranker
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: manuel.rueda@cnag.eu
    fundrefid: null
    gridid: null
    name: Manuel Rueda
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Pheno-Ranker is an open-source toolkit for comparing phenotypic data
    stored in GA4GH standards, enabling individual-level comparisons and statistical
    significance analysis. It supports various data formats and provides a command-line
    tool and a web-based user interface for interactive analysis.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    - term: Scatter plot plotting
      uri: http://edamontology.org/operation_2940
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output: []
  homepage: https://pheno-ranker.cnag.eu
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-01-15T12:21:23.949311Z'
  license: null
  link: []
  maturity: null
  name: Pheno-Ranker
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1186/S12859-024-05993-2
    metadata: null
    note: null
    pmcid: PMC11616229
    pmid: '39633268'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Natural language processing
    uri: http://edamontology.org/topic_0218
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Biobank
    uri: http://edamontology.org/topic_3337
  - term: Mathematics
    uri: http://edamontology.org/topic_3315
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:58:26.147458Z'
  biotoolsCURIE: biotools:scregclust
  biotoolsID: scregclust
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: sven.nelander@igp.uu.se
    fundrefid: null
    gridid: null
    name: Sven Nelander
    note: null
    orcidid: https://orcid.org/0000-0003-1758-1262
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: scregclust is an R package that reconstructs cellular regulatory programs
    from single-cell RNA sequencing (scRNA-seq) data, facilitating the exploration
    of regulatory programs underlying cell plasticity and identifying critical regulators
    in nervous system cancers.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene regulatory network analysis
      uri: http://edamontology.org/operation_1781
    - term: Gene regulatory network prediction
      uri: http://edamontology.org/operation_2437
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    output: []
  homepage: https://github.com/scmethods/scregclust
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-01-15T11:58:26.149617Z'
  license: null
  link: []
  maturity: null
  name: scregclust
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S41467-024-53954-3
    metadata: null
    note: null
    pmcid: PMC11549355
    pmid: '39516198'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Pharmacology
    uri: http://edamontology.org/topic_0202
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: Gene regulation
    uri: http://edamontology.org/topic_0204
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:58:20.128202Z'
  biotoolsCURIE: biotools:cluster_randomised_trials
  biotoolsID: cluster_randomised_trials
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: c.l.chan@qmul.ac.uk
    fundrefid: null
    gridid: null
    name: Claire L. Chan
    note: null
    orcidid: https://orcid.org/0000-0002-0821-4068
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: The Cluster Randomised Trials Stepped Wedge website provides resources
    and information related to cluster randomised trials and stepped wedge designs,
    aiming to promote high-quality research in these methodologies. It offers a collection
    of links to relevant papers and announcements related to the field.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Clustering
      uri: http://edamontology.org/operation_3432
    output: []
  homepage: https://clusterrandomisedtrials.qmul.ac.uk/
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:58:20.130503Z'
  license: null
  link: []
  maturity: null
  name: Cluster Randomised Trials Stepped Wedge
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1186/S13063-024-08597-6
    metadata: null
    note: null
    pmcid: PMC11542435
    pmid: '39506853'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: Medicine
    uri: http://edamontology.org/topic_3303
  - term: Human biology
    uri: http://edamontology.org/topic_2815
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:58:16.698952Z'
  biotoolsCURIE: biotools:mice
  biotoolsID: mice
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: michael.p.camilleri@ed.ac.uk
    fundrefid: null
    gridid: null
    name: Michael P. J. Camilleri
    note: null
    orcidid: https://orcid.org/0000-0002-8619-3231
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Mice-N-Mates is a software resource providing tools for studying mouse
    behaviour in home-cage environments, including automated classification using
    the Activity Labelling Module (ALM) and modeling using a Global Behaviour Model
    (GBM). The resource also provides training datasets (ABODe and IMADGE).
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    output: []
  homepage: https://github.com/michael-camilleri/Mice-N-Mates
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:58:16.700997Z'
  license: null
  link: []
  maturity: null
  name: Mice-N-Mates
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1007/S11263-024-02118-3
    metadata: null
    note: null
    pmcid: PMC11568001
    pmid: '39554493'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Mouse clinic
    uri: http://edamontology.org/topic_3338
  - term: Data acquisition
    uri: http://edamontology.org/topic_3077
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:58:13.073364Z'
  biotoolsCURIE: biotools:scimilarity
  biotoolsID: scimilarity
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: heimberg@gene.com
    fundrefid: null
    gridid: null
    name: Graham Heimberg
    note: null
    orcidid: https://orcid.org/0009-0002-6493-5721
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: kaminker@gene.com
    fundrefid: null
    gridid: null
    name: Josh Kaminker
    note: null
    orcidid: https://orcid.org/0000-0001-5067-9275
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: vanderheiden.jason@gene.com
    fundrefid: null
    gridid: null
    name: Jason A. Vander Heiden
    note: null
    orcidid: https://orcid.org/0000-0002-1474-310X
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: regev.aviv@gene.com
    fundrefid: null
    gridid: null
    name: Aviv Regev
    note: null
    orcidid: https://orcid.org/0000-0003-3293-3158
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: SCimilarity is a metric-learning framework for scalable search of similar
    human cells within single-cell RNA sequencing atlases. It learns a unified representation
    enabling rapid queries for cells with similar transcriptional profiles.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: DNA vaccine design
      uri: http://edamontology.org/operation_0560
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Database search
      uri: http://edamontology.org/operation_2421
    output: []
  homepage: https://github.com/Genentech/scimilarity
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:58:13.075465Z'
  license: null
  link: []
  maturity: null
  name: SCimilarity
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S41586-024-08411-Y
    metadata: null
    note: null
    pmcid: PMC11864978
    pmid: '39566551'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Immunology
    uri: http://edamontology.org/topic_0804
  - term: Single-cell sequencing
    uri: http://edamontology.org/topic_4028
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:58:09.439863Z'
  biotoolsCURIE: biotools:celldetail
  biotoolsID: celldetail
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: tanja.schuster@uni-ulm.de
    fundrefid: null
    gridid: null
    name: Tanja Schuster
    note: null
    orcidid: https://orcid.org/0009-0000-2691-4570
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: hartmut.geiger@uni-ulm.de
    fundrefid: null
    gridid: null
    name: Hartmut Geiger
    note: null
    orcidid: https://orcid.org/0000-0002-5794-5430
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: CellDetail is an open-source 3D-cell-image analysis platform used to
    quantitatively determine the spatial distribution of components within cells,
    particularly focusing on polarity proteins and Septin networks.  It uses a dipole
    moment-based algorithm and has been used to analyze hematopoietic stem cells and
    human fibroblasts.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    - term: Protein dipole moment calculation
      uri: http://edamontology.org/operation_0386
    output: []
  homepage: https://github.com/xyq91/CellDetail-TS
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:58:09.442184Z'
  license: null
  link: []
  maturity: null
  name: CellDetail
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S41467-024-54638-8
    metadata: null
    note: null
    pmcid: PMC11599593
    pmid: '39592623'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Biophysics
    uri: http://edamontology.org/topic_3306
  - term: Pharmacology
    uri: http://edamontology.org/topic_0202
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:57:52.428935Z'
  biotoolsCURIE: biotools:cylinter
  biotoolsID: cylinter
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: gregory_baker2@hms.harvard.edu
    fundrefid: null
    gridid: null
    name: Gregory J. Baker
    note: null
    orcidid: https://orcid.org/0000-0002-5196-3961
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: peter_sorger@hms.harvard.edu
    fundrefid: null
    gridid: null
    name: Peter K. Sorger
    note: null
    orcidid: https://orcid.org/0000-0002-3364-1838
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: CyLinter is a software tool for quality control in single-cell analysis
    of high-plex tissue profiles, designed to identify and remove noisy data points
    in multiplex images corrupted by artifacts. It allows users to work with both
    pixel-level and single-cell data.
  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
    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    - term: Validation
      uri: http://edamontology.org/operation_2428
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    output: []
  homepage: https://labsyspharm.github.io/cylinter/
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:57:52.431148Z'
  license: null
  link: []
  maturity: null
  name: CyLinter
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S41592-024-02328-0
    metadata: null
    note: null
    pmcid: PMC11621021
    pmid: '39478175'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Cytometry
    uri: http://edamontology.org/topic_3934
  - term: Single-cell sequencing
    uri: http://edamontology.org/topic_4028
  - term: Preclinical and clinical studies
    uri: http://edamontology.org/topic_3379
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:57:47.587035Z'
  biotoolsCURIE: biotools:pyprobound
  biotoolsID: pyprobound
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: hjb2004@columbia.edu
    fundrefid: null
    gridid: null
    name: Harmen J. Bussemaker
    note: null
    orcidid: https://orcid.org/0000-0002-7274-5277
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: PyProBound is a software resource for benchmarking and building DNA
    binding affinity models, particularly focused on allele-specific transcription
    factor binding data. It facilitates de novo inference of high-quality models and
    motif discovery.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Transcription factor binding site prediction
      uri: http://edamontology.org/operation_0445
    - term: Sequence motif discovery
      uri: http://edamontology.org/operation_0238
    - term: Peak calling
      uri: http://edamontology.org/operation_3222
    output: []
  homepage: https://pyprobound.readthedocs.io
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:57:47.590483Z'
  license: null
  link: []
  maturity: null
  name: PyProBound
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1186/S13059-024-03424-2
    metadata: null
    note: null
    pmcid: PMC11529166
    pmid: '39482734'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: ChIP-seq
    uri: http://edamontology.org/topic_3169
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: Biophysics
    uri: http://edamontology.org/topic_3306
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:57:46.286765Z'
  biotoolsCURIE: biotools:scstatedynamics
  biotoolsID: scstatedynamics
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: jianhuayao@tencent.com
    fundrefid: null
    gridid: null
    name: Jianhua Yao
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: jgu@tsinghua.edu.cn
    fundrefid: null
    gridid: null
    name: Jin Gu
    note: null
    orcidid: https://orcid.org/0000-0003-3968-8036
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: scStateDynamics is a computational method for deciphering drug-responsive
    tumor cell state dynamics by modeling single-cell level expression changes. It
    infers cell state dynamics and identifies common drug effects by modeling gene
    expression changes and has been validated on simulated and lineage tracing data.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    - term: Expression profile clustering
      uri: http://edamontology.org/operation_0313
    output: []
  homepage: http://lifeome.net/software/scStateDynamics/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-01-15T11:57:46.288950Z'
  license: MIT
  link: []
  maturity: null
  name: scStateDynamics
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1186/S13059-024-03436-Y
    metadata: null
    note: null
    pmcid: PMC11583649
    pmid: '39574111'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Single-cell sequencing
    uri: http://edamontology.org/topic_4028
  - term: Mathematics
    uri: http://edamontology.org/topic_3315
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:57:43.846260Z'
  biotoolsCURIE: biotools:abds
  biotoolsID: abds
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: yuewang@vt.edu
    fundrefid: null
    gridid: null
    name: Yue Wang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: ABDS is an R tool suite designed for analyzing biologically diverse
    samples, specifically addressing challenges with missing data imputation, signature
    gene detection, and differential pattern visualization. It provides tools for
    mechanistic imputation, group-wise testing, and heatmap visualization.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    - term: Imputation
      uri: http://edamontology.org/operation_3557
    - term: Multiple sample visualisation
      uri: http://edamontology.org/operation_3744
    output: []
  homepage: https://github.com/niccolodpdu/ABDS
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-01-15T11:57:43.848985Z'
  license: null
  link: []
  maturity: null
  name: ABDS
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.21203/RS.3.RS-4419408/V1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1038/S41598-024-78076-0
    metadata: null
    note: null
    pmcid: PMC11569126
    pmid: '39550430'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Biomarkers
    uri: http://edamontology.org/topic_3360
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Sample collections
    uri: http://edamontology.org/topic_3277
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:57:40.561421Z'
  biotoolsCURIE: biotools:chrysalis
  biotoolsID: chrysalis
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: peter.turos@unibe.ch
    fundrefid: null
    gridid: null
    name: Demeter Túrós
    note: null
    orcidid: https://orcid.org/0000-0001-5783-5314
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: sven.rottenberg@unibe.ch
    fundrefid: null
    gridid: null
    name: Sven Rottenberg
    note: null
    orcidid: https://orcid.org/0000-0003-2044-9844
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: alberto.valdeolivas_urbelz@roche.com
    fundrefid: null
    gridid: null
    name: Alberto Valdeolivas
    note: null
    orcidid: https://orcid.org/0000-0001-5482-9023
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Chrysalis is a computational method that uncovers tissue compartments
    in spatial transcriptomics data using archetypal analysis without external reference
    data. It offers a unique visualisation approach for characterising tissue and
    identifying distinct cellular niches.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    - term: Deisotoping
      uri: http://edamontology.org/operation_3629
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Dimensionality reduction
      uri: http://edamontology.org/operation_3935
    output: []
  homepage: https://chrysalis.readthedocs.io
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:57:40.563749Z'
  license: null
  link: []
  maturity: null
  name: Chrysalis
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S42003-024-07165-7
    metadata: null
    note: null
    pmcid: PMC11569261
    pmid: '39550461'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Zoology
    uri: http://edamontology.org/topic_3500
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:57:39.354046Z'
  biotoolsCURIE: biotools:calicost
  biotoolsID: calicost
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: lding@wustl.edu
    fundrefid: null
    gridid: null
    name: Li Ding
    note: null
    orcidid: https://orcid.org/0000-0003-1517-2975
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: braphael@princeton.edu
    fundrefid: null
    gridid: null
    name: Benjamin J. Raphael
    note: null
    orcidid: https://orcid.org/0000-0003-1274-048X
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: CalicoST is a software tool that infers allele-specific copy number
    aberrations and reconstructs spatial tumor evolution from spatially resolved transcriptomics
    data. It improves upon existing methods by identifying key CNA classes and achieving
    an accuracy of 86% in analysis of tumor data.
  documentation: []
  download: []
  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
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Ancestral reconstruction
      uri: http://edamontology.org/operation_3745
    output: []
  homepage: https://github.com/raphael-group/CalicoST/
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:57:39.356078Z'
  license: null
  link: []
  maturity: null
  name: CalicoST
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S41592-024-02438-9
    metadata: null
    note: null
    pmcid: PMC11621028
    pmid: '39478176'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Physics
    uri: http://edamontology.org/topic_3318
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:57:36.876931Z'
  biotoolsCURIE: biotools:rnasselem
  biotoolsID: rnasselem
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: mkazanov@gmail.com
    fundrefid: null
    gridid: null
    name: Marat D. Kazanov
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: RNAsselem is a Python package for analyzing RNA secondary structure
    elements in viral genomes, enabling the recognition of common patterns and the
    generation of descriptive statistics. The tool is described in a recent publication
    and is openly available on GitHub.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: RNA secondary structure prediction
      uri: http://edamontology.org/operation_0278
    - term: RNA secondary structure alignment
      uri: http://edamontology.org/operation_0502
    - term: Protein secondary structure comparison
      uri: http://edamontology.org/operation_2488
    - term: RNA structure covariance model generation
      uri: http://edamontology.org/operation_3469
    output: []
  homepage: http://github.com/KazanovLab/RNAsselem
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-01-15T11:57:36.879172Z'
  license: null
  link: []
  maturity: null
  name: RNAsselem
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S41598-024-80240-5
    metadata: null
    note: null
    pmcid: PMC11577020
    pmid: '39562668'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: RNA
    uri: http://edamontology.org/topic_0099
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Protein secondary structure
    uri: http://edamontology.org/topic_3542
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:57:25.196126Z'
  biotoolsCURIE: biotools:amphibian_genomics_consortium
  biotoolsID: amphibian_genomics_consortium
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: tiffany.kosch@gmail.com
    fundrefid: null
    gridid: null
    name: Tiffany A. Kosch
    note: null
    orcidid: https://orcid.org/0000-0001-5158-5748
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: torressanchez.maria@gmail.com
    fundrefid: null
    gridid: null
    name: María Torres-Sánchez
    note: null
    orcidid: https://orcid.org/0000-0001-8484-9279
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: The Amphibian Genomics Consortium (AGC) is an international initiative
    focused on advancing genomic resources for amphibian research and conservation.
    It brings together researchers to improve understanding of amphibian biology and
    facilitate genomic studies.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Expression analysis
      uri: http://edamontology.org/operation_2495
    - term: Scaffolding
      uri: http://edamontology.org/operation_3216
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    output: []
  homepage: https://mvs.unimelb.edu.au/amphibian-genomics-consortium
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:57:25.198152Z'
  license: null
  link: []
  maturity: null
  name: Amphibian Genomics Consortium (AGC)
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1186/S12864-024-10899-7
    metadata: null
    note: null
    pmcid: PMC11529218
    pmid: '39487448'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:57:21.742690Z'
  biotoolsCURIE: biotools:onix
  biotoolsID: onix
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: voigtsj@janelia.hhmi.org
    fundrefid: null
    gridid: null
    name: Jakob Voigts
    note: null
    orcidid: https://orcid.org/0000-0002-5174-7214
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: ONIX is an open-source data acquisition system designed for recording
    neural activity in freely behaving animals. It minimizes behavioral impact through
    a thin tether and enables long-duration recordings with high throughput and low
    latency.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Neurite measurement
      uri: http://edamontology.org/operation_3450
    output: []
  homepage: https://open-ephys.github.io/onix-docs
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:57:21.744753Z'
  license: null
  link: []
  maturity: null
  name: ONIX
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S41592-024-02521-1
    metadata: null
    note: null
    pmcid: PMC11725498
    pmid: '39528678'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Neurobiology
    uri: http://edamontology.org/topic_3304
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Zoology
    uri: http://edamontology.org/topic_3500
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:57:09.895166Z'
  biotoolsCURIE: biotools:gasidn
  biotoolsID: gasidn
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: yhchen@ujn.edu.cn
    fundrefid: null
    gridid: null
    name: Yuehui Chen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: GASIDN is a computational model for identifying sub-Golgi proteins
    using multi-scale feature fusion, combining protein sequence and contact map information
    derived from AlphaFold2. It achieves high accuracy and has been applied to other
    organelle protein identification.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Small molecule design
      uri: http://edamontology.org/operation_4009
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    - term: Protein secondary structure prediction
      uri: http://edamontology.org/operation_0267
    - term: Protein identification
      uri: http://edamontology.org/operation_3767
    output: []
  homepage: https://github.com/SJNNNN/GASIDN
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:57:09.897482Z'
  license: null
  link: []
  maturity: null
  name: GASIDN
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1186/S12864-024-10954-3
    metadata: null
    note: null
    pmcid: PMC11526662
    pmid: '39478465'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Pathology
    uri: http://edamontology.org/topic_0634
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:57:07.457998Z'
  biotoolsCURIE: biotools:sssdb
  biotoolsID: sssdb
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: SSSDb is a database providing coarse-grained representations of biomolecular
    structures, specifically focusing on CATH protein domains. It offers a resource
    of surface and shape representations to aid in applications like database docking
    studies and simulations.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Phasing
      uri: http://edamontology.org/operation_3454
    - term: Backbone modelling
      uri: http://edamontology.org/operation_0479
    - term: Simulation analysis
      uri: http://edamontology.org/operation_0244
    - term: Molecular dynamics
      uri: http://edamontology.org/operation_2476
    - term: Molecular docking
      uri: http://edamontology.org/operation_0478
    output: []
  homepage: https://www.sssdb.nbrkarampudi.org/
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:57:07.460035Z'
  license: null
  link: []
  maturity: null
  name: SSSDb
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.21203/RS.3.RS-5310952/V1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  - term: Protein structural motifs and surfaces
    uri: http://edamontology.org/topic_0166
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Molecular dynamics
    uri: http://edamontology.org/topic_0176
  validated: 0
  version: []
next: ?page=2
previous: null
