count: 31897
list:
- accessibility: Open access
  additionDate: '2026-02-12T16:06:53.794717Z'
  biotoolsCURIE: biotools:vvv2_display
  biotoolsID: vvv2_display
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: fabrice.touzain@anses.fr
    fundrefid: null
    gridid: null
    name: Fabrice Touzain
    note: Dr. in Bioinformatics at ANSES ("Swine virology, innovation and genomics"
      Unit, Bioinformatics Team)
    orcidid: https://orcid.org/0000-0002-1103-2425
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://github.com/ANSES-Ploufragan/vvv2_display
  description: Display SNP proportions (vardict outputs), CDS (vadr annotations) of
    an assembly/genome, coverage depth (samtools depth), in png image and a tsv file,
    filtering results to summarize analyses (alignment, variant calling, annotation).
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: vvv2_display.py -p vadr_pass_annotation.tbl -f vadr_fail_annotation.tbl -s
      vadr_seqstat.txt -n vardict-java_res.vcf -o samtools_depth_out.txt -r signif_snp_annot_res.png
      -u signif_snp_res.tsv -x signif_snp_res.vcf
    input:
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: 'Inputs:

      - tbl pass vadr annotation file

      - tbl fail vadr annotation file

      - seqstat vadr output file

      - vcf vardict-java variant calling results (all)

      - samtools depth text file (coverage depth of an alignment)

      Outputs:

      - png summary file with all info

      - tsv file of indexed significant variant (index showed on png figure)

      - [optional] vcf file of significant variants only'
    operation:
    - term: Base position variability plotting
      uri: http://edamontology.org/operation_0287
    - term: Sequence assembly visualisation
      uri: http://edamontology.org/operation_3184
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
    - data:
        term: Annotated text
        uri: http://edamontology.org/data_3779
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: https://github.com/ANSES-Ploufragan/vvv2_display
  homepage_status: 0
  language:
  - R
  - Python
  lastUpdate: '2026-02-12T16:07:53.280544Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ANSES-Ploufragan/vvv2_display
  - note: Galaxy wrapper
    type:
    - Other
    url: https://toolshed.g2.bx.psu.edu/view/ftouzain/vvv2_display/fcd3aa68bd39
  - note: 'Listing of Galaxy workflow performing all steps:

      - alignment on ref/assembly

      - annotation of ref/assembly

      - coputation of coverage depth

      - vardict variant calling

      - vvv2_display synthesis


      One can be found for each sequencing technology (Illumina SE/Proton, Illumina
      PE, nanopore, pacbio'
    type:
    - Other
    url: https://workflowhub.eu/search?q=vvv2
  maturity: Mature
  name: vvv2_display
  operatingSystem:
  - Linux
  otherID:
  - type: doi
    value: doi:10.3390/v17101385
    version: 0.2.4.0
  owner: fabrice
  publication:
  - doi: 10.3390/v17101385
    metadata: null
    note: published in Viruses journal
    pmcid: PMC12567792
    pmid: '41157655'
    type:
    - Primary
    version: 0.2.4.0
  relation:
  - biotoolsID: ggplot2
    type: uses
  - biotoolsID: pysam
    type: uses
  - biotoolsID: R
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Virology
    uri: http://edamontology.org/topic_0781
  validated: 0
  version:
  - 0.2.5.0
- accessibility: Open access
  additionDate: '2026-02-12T14:54:22.759092Z'
  biotoolsCURIE: biotools:segmentation_evaluation
  biotoolsID: segmentation_evaluation
  collectionID:
  - EUCAIM
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: jose.almeida@research.fchampalimaud.org
    fundrefid: null
    gridid: null
    name: José Guilherme de Almeida
    note: null
    orcidid: https://orcid.org/0000-0002-1887-0157
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Nickolas Papanikolaou
    note: null
    orcidid: https://orcid.org/0000-0003-3298-2072
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: This tool calculates segmentation metrics (Dice score, intersection
    over union, Hausdorff distance, and normalised surface distance) between two sets
    of masks. It can be used to quickly calculate a number of metrics for segmentation
    models.
  documentation:
  - note: null
    type:
    - Quick start guide
    - API documentation
    url: https://github.com/josegcpa/eucaim-metrics/tree/master
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "uv run eval_segmentation \\\n    --pred test_data/predicted/ \\\n    --gt\
      \ test_data/groundtruth/ \\\n    --output test.json \\\n    --n_classes 2 \\\
      \n    --verbose \\\n    --params '{\"normalised_surface_distance\": {\"max_distance\"\
      : 100.0}}'"
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
    note: This is the core command which can be used to calculate image segmentation
      metrics. For more options please run `uv run eval_segmentation --help`
    operation:
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://github.com/josegcpa/eucaim-metrics/tree/master
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-12T15:01:23.363666Z'
  license: CC-BY-4.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/josegcpa/eucaim-metrics/tree/master
  maturity: Emerging
  name: Segmentation evaluation
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: josegcpa
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  - term: MRI
    uri: http://edamontology.org/topic_3444
  validated: 0
  version:
  - v0.1
- accessibility: Open access
  additionDate: '2026-02-12T09:37:33.991999Z'
  biotoolsCURIE: biotools:pathofact2
  biotoolsID: pathofact2
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: luis.delgado@uni.lu
    fundrefid: null
    gridid: null
    name: Luis F. Delgado
    note: null
    orcidid: https://orcid.org/0000-0001-7850-5285
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: julia.ortissunyer@uni.lu
    fundrefid: null
    gridid: null
    name: Júlia Ortís Sunyer
    note: null
    orcidid: https://orcid.org/0000-0002-2714-7067
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: paul.wilmes@uni.lu
    fundrefid: null
    gridid: null
    name: Paul Wilmes
    note: null
    orcidid: https://orcid.org/0000-0002-6478-2924
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: An Integrative Pipeline for Antimicrobial Resistance Genes, Virulence
    Factors, Toxin-associated proteins, and Biosynthetic Gene Clusters Prediction
    in Metagenomes
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format: []
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format: []
    note: null
    operation:
    - term: Antimicrobial resistance prediction
      uri: http://edamontology.org/operation_3482
    - term: Virulence prediction
      uri: http://edamontology.org/operation_3461
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format: []
  homepage: https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2
  homepage_status: 0
  language:
  - Python
  - R
  - Bash
  lastUpdate: '2026-02-12T14:58:55.997656Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2
  - note: null
    type:
    - Repository
    url: https://zenodo.org/records/14192463
  - note: null
    type:
    - Repository
    url: https://zenodo.org/records/17647372
  maturity: null
  name: PathoFact2
  operatingSystem:
  - Linux
  otherID: []
  owner: julia8
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Antimicrobial resistance
    uri: http://edamontology.org/topic_4013
  validated: 0
  version:
  - '2.0'
- accessibility: null
  additionDate: '2026-01-15T11:57:12.274741Z'
  biotoolsCURIE: biotools:motus-db
  biotoolsID: motus-db
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: ssunagawa@ethz.ch
    fundrefid: null
    gridid: null
    name: Shinichi Sunagawa
    note: null
    orcidid: https://orcid.org/0000-0003-3065-0314
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: The mOTUs database provides web-accessible genomic context to taxonomic
    profiling of microbial communities, comprising a large collection of metagenome-assembled
    genomes and isolate genomes from diverse species-level taxonomic units.  It allows
    users to explore and download genomes at various taxonomic levels.
  documentation: []
  download: []
  editPermission:
    authors:
    - vashokan
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Scaffolding
      uri: http://edamontology.org/operation_3216
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    - term: DNA barcoding
      uri: http://edamontology.org/operation_3200
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output: []
  homepage: https://motus-db.org
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-12T14:34:24.708930Z'
  license: null
  link: []
  maturity: null
  name: mOTUs database
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1093/NAR/GKAE1004
    metadata: null
    note: null
    pmcid: PMC11701688
    pmid: '39526369'
    type: []
    version: null
  relation:
  - biotoolsID: motus
    type: usedBy
  - biotoolsID: gtdb
    type: uses
  toolType: []
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Database management
    uri: http://edamontology.org/topic_3489
  - term: Single-cell sequencing
    uri: http://edamontology.org/topic_4028
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  validated: 0
  version: []
- accessibility: null
  additionDate: '2016-02-11T12:02:14Z'
  biotoolsCURIE: biotools:motus
  biotoolsID: motus
  collectionID:
  - de.NBI
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: European Molecular Biology Laboratory (EMBL)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.embl.de/
  - email: null
    fundrefid: null
    gridid: null
    name: HD-HuB
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.hd-hub.de/
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.bork.embl.de/software/mOTU/contact.html
  - email: ssunagawa@ethz.ch
    fundrefid: null
    gridid: null
    name: Shinichi Sunagawa
    note: null
    orcidid: http://orcid.org/0000-0003-3065-0314
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: Metagenomic operational taxonomic units (mOTUs) enable high-accuracy
    taxonomic profiling of known (sequenced) and unknown microorganisms at species-level
    resolution from shotgun metagenomic or metatranscriptomic data. The method clusters
    single-copy phylogenetic marker gene sequences from metagenomes and reference
    genomes into mOTUs to quantify their abundances in meta-omics data with very high
    precision and recall.
  documentation:
  - note: null
    type:
    - General
    url: https://motu-tool.org/
  download:
  - note: null
    type: Biological data
    url: https://motu-tool.org/download.html
    version: null
  - note: null
    type: Source code
    url: https://github.com/motu-tool
    version: null
  - note: MBT:Container
    type: Container file
    url: https://anaconda.org/bioconda/motus
    version: null
  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: FASTQ
        uri: http://edamontology.org/format_1930
    note: Taxonomic profiling from shotgun metagenomes Quality-filtered shotgun metagenomic
      reads A taxonomic profiling matrix with species in rows and samples in columns;
      each entry m_{i,j} indicates the number of reads from sample j mapped to marker
      genes of species i
    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://motu-tool.org/
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2026-02-12T14:33:33.330556Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/motu-tool/mOTUs
  - note: Database for mOTUs profiler
    type:
    - Other
    url: https://motus-db.org/
  maturity: null
  name: Metagenomic operational taxonomic units (mOTUs)
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: hdhub
  publication:
  - doi: 10.1186/s40168-022-01410-z
    metadata: null
    note: null
    pmcid: PMC9721005
    pmid: '36464731'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkae1004
    metadata: null
    note: mOTUs-db paper
    pmcid: PMC11701688
    pmid: '39526369'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: gtdb
    type: uses
  - biotoolsID: motus-db
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 1
  version:
  - 2.5.1
- 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: '2017-08-03T19:02:48Z'
  biotoolsCURIE: biotools:tipp
  biotoolsID: tipp
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: warnow@illinois.edu
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.cs.utexas.edu/users/phylo/
  description: A new marker-based method developed for abundance profiling of metagenomic
    data.  It uses a collection of 30 universal marker genes and bins the fragments
    to the marker genes.  For each set of fragments binned to a marker gene, this
    classifies the fragments by inserting the fragments into the taxonomic tree estimated
    on the marker gene.
  documentation:
  - note: null
    type:
    - General
    url: http://www.cs.utexas.edu/users/phylo/software/sepp/tipp-submission/
  - note: null
    type:
    - General
    url: http://www.cs.utexas.edu/users/phylo/software/sepp/tipp-submission/supplement.pdf
  download: []
  editPermission:
    authors:
    - vashokan
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Community profiling
      uri: http://edamontology.org/operation_3200
    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://github.com/c5shen/TIPP3
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-12T14:19:03.990351Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/tipp-taxon-identification-and-phylogenetic-profiling.html
  - note: github repository
    type:
    - Repository
    url: https://github.com/c5shen/TIPP3
  maturity: null
  name: TIPP
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: mbs_import
  publication:
  - doi: 10.1371/journal.pcbi.1012593
    metadata: null
    note: null
    pmcid: PMC11970662
    pmid: '40184383'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  validated: 1
  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: null
  additionDate: '2026-02-12T14:12:28.254987Z'
  biotoolsCURIE: biotools:gefetch2r
  biotoolsID: gefetch2r
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: GEfetch2R is designed to accelerate users’ downloading and preparation
    of single-cell/bulk RNA-seq datasets from public resources. GEfetch2R supports
    downloading various scRNA-seq data types, including raw data (SRA and ENA), count
    matrix (GEO, UCSC Cell Browser, and PanglaoDB), and processed object (GEO, Zenodo,
    CELLxGENE, and HCA); can access and explore existing scRNA-seq data, load output/downloaded
    count matrices and annotations to R (SeuratObject/DESeqDataSet), extract a subset
    of the SeuratObject based on cell metadata and genes, and merge multiple SeuratObjects
    if applicable; provides format conversions between different scRNA-seq objects,
    including SeuratObject, AnnData, SingleCellExperiment, CellDataSet/cell_data_set,
    and loom.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://showteeth.github.io/GEfetch2R
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-12T14:12:40.533790Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/showteeth/GEfetch2R
  maturity: null
  name: GEfetch2R
  operatingSystem: []
  otherID: []
  owner: yabing
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - 0.7.3
- accessibility: null
  additionDate: '2021-01-18T09:52:08Z'
  biotoolsCURIE: biotools:ganon
  biotoolsID: ganon
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: bernhard.renard@hpi.de
    fundrefid: null
    gridid: null
    name: Bernhard Y Renard
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'ganon is designed to index large sets of genomic reference sequences
    and to classify reads against them efficiently. The tool uses Hierarchical Interleaved
    Bloom Filters as indices based on k-mers with optional minimizers. It was mainly
    developed, but not limited, to the metagenomics classification problem: quickly
    assign sequence fragments to their closest reference among thousands of references.
    After classification, taxonomic or sequence abundances are estimated and reported.'
  documentation: []
  download: []
  editPermission:
    authors:
    - vashokan
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: k-mer counting
      uri: http://edamontology.org/operation_3472
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    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://pirovc.github.io/ganon/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-12T13:50:27.711409Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/pirovc/ganon_benchmark
  maturity: null
  name: Ganon
  operatingSystem: []
  otherID: []
  owner: pirovc
  publication:
  - doi: 10.1093/nargab/lqaf094
    metadata: null
    note: null
    pmcid: PMC12267982
    pmid: '40677913'
    type: []
    version: null
  relation:
  - biotoolsID: gtdb
    type: uses
  toolType:
  - Library
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  validated: 1
  version: []
- accessibility: null
  additionDate: '2026-02-11T06:58:20.948881Z'
  biotoolsCURIE: biotools:protein-small_molecule_docking_service
  biotoolsID: protein-small_molecule_docking_service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Protein-small molecule docking, a pivotal process in drug discovery,
    explores the interactions between proteins and small molecules to identify potential
    drug candidates. CD ComputaBio's advanced computational techniques and expert
    insights allow us to explore and predict the intricate interactions between proteins
    and small molecules, helping you identify promising drug candidates with higher
    precision and efficiency.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/protein-small-molecule-docking-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-11T06:59:51.346028Z'
  license: null
  link: []
  maturity: null
  name: Protein-Small Molecule Docking Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2023-04-20T14:28:02.353577Z'
  biotoolsCURIE: biotools:foldcomp
  biotoolsID: foldcomp
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: martin.steinegger@snu.ac.kr
    fundrefid: null
    gridid: null
    name: Martin Steinegger
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: A library and format for compressing and indexing large protein structure
    sets.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    - term: Protein geometry calculation
      uri: http://edamontology.org/operation_0249
    output: []
  homepage: https://foldcomp.foldseek.com
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-11T06:23:47.889831Z'
  license: MIT
  link: []
  maturity: null
  name: Foldcomp
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: Chan019
  publication:
  - doi: 10.1093/bioinformatics/btad153
    metadata: null
    note: null
    pmcid: PMC10085514
    pmid: '36961332'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Database management
    uri: http://edamontology.org/topic_3489
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-02-09T20:42:59.408390Z'
  biotoolsCURIE: biotools:randmice
  biotoolsID: randmice
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Randmice is an online tool that optimize randomization of animals for
    in vivo experiences by minimizing heterogeneity between groups.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://randmice.com
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-09T20:46:20.459289Z'
  license: null
  link: []
  maturity: Mature
  name: Randmice
  operatingSystem: []
  otherID: []
  owner: sylvain
  publication: []
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Animal study
    uri: http://edamontology.org/topic_3679
  validated: 0
  version:
  - '2.0'
- accessibility: null
  additionDate: '2026-02-05T20:50:33.563257Z'
  biotoolsCURIE: biotools:msnpy
  biotoolsID: msnpy
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: A Python package for processing and annotating multi-stage (MSⁿ) mass
    spectral data
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/computational-metabolomics/msnpy
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-05T20:50:33.567057Z'
  license: null
  link: []
  maturity: null
  name: msnpy
  operatingSystem: []
  otherID: []
  owner: ralf
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-05T20:40:40.977533Z'
  biotoolsCURIE: biotools:dimspy
  biotoolsID: dimspy
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Python package for processing direct-infusion mass spectrometry-based
    metabolomics and lipidomics data
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/computational-metabolomics/dimspy
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-05T20:40:40.981305Z'
  license: null
  link: []
  maturity: null
  name: dimspy
  operatingSystem: []
  otherID: []
  owner: ralf
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- 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: null
  additionDate: '2025-05-15T11:35:23.428773Z'
  biotoolsCURIE: biotools:plantismash
  biotoolsID: plantismash
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: PlantiSMASH is a specialized extension of antiSMASH for the identification
    and analysis of biosynthetic gene clusters (BGCs) in plant genomes. It supports
    advanced plant-specific detection rules and features for comparative genomics,
    visualization, and more.
  documentation:
  - note: null
    type:
    - General
    url: https://plantismash.github.io/documentation/
  download:
  - note: null
    type: Software package
    url: https://github.com/plantismash/plantismash/releases
    version: 2.0-beta4
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://plantismash.bioinformatics.nl/
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-05T15:55:59.835487Z'
  license: AGPL-3.0
  link: []
  maturity: null
  name: plantiSMASH
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: elena0
  publication:
  - doi: 10.1093/nar/gkx305
    metadata:
      abstract: 'Plant specialized metabolites are chemically highly diverse, play
        key roles in host-microbe interactions, have important nutritional value in
        crops and are frequently applied as medicines. It has recently become clear
        that plant biosynthetic pathway-encoding genes are sometimes densely clustered
        in specific genomic loci: Biosynthetic gene clusters (BGCs). Here, we introduce
        plantiSMASH, a versatile online analysis platform that automates the identification
        of candidate plant BGCs. Moreover, it allows integration of transcriptomic
        data to prioritize candidate BGCs based on the coexpression patterns of predicted
        biosynthetic enzyme-coding genes, and facilitates comparative genomic analysis
        to study the evolutionary conservation of each cluster. Applied on 48 high-quality
        plant genomes, plantiSMASH identifies a rich diversity of candidate plant
        BGCs. These results will guide further experimental exploration of the nature
        and dynamics of gene clustering in plant metabolism. Moreover, spurred by
        the continuing decrease in costs of plant genome sequencing, they will allow
        genome mining technologies to be applied to plant natural product discovery.'
      authors:
      - name: Kautsar S.A.
      - name: Suarez Duran H.G.
      - name: Blin K.
      - name: Osbourn A.
      - name: Medema M.H.
      citationCount: 214
      date: '2017-07-03T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'PlantiSMASH: Automated identification, annotation and expression analysis
        of plant biosynthetic gene clusters'
    note: null
    pmcid: PMC5570173
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  validated: 0
  version:
  - 2.0-beta4
- accessibility: Open access
  additionDate: '2016-07-11T10:42:10Z'
  biotoolsCURIE: biotools:3dbionotes
  biotoolsID: 3dbionotes
  collectionID:
  - ELIXIR-ES
  - CNB-CSIC
  - COVID-19
  - INB
  - IMPaCT-ISCIII
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: INB
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-ES
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: cnb.csic.es
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: coss@cnb.csic.es
    fundrefid: null
    gridid: null
    name: Carlos Oscar Sorzano
    note: null
    orcidid: https://orcid.org/0000-0002-9473-283X
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://3dbionotes.cnb.csic.es
  - email: null
    fundrefid: null
    gridid: null
    name: EOSC-Life
    note: 'EOSC Life [INFRAEOSC-04-2018, Proposal: 824087]'
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: CORBEL
    note: CORBEL [INFRADEV-01-2014-1, Proposal 654248]
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: CSIC
    note: CSIC [PIE/COVID-19 number 202020E079]
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Comunidad de Madrid
    note: Comunidad de Madrid through grant CAM [S2017/BMD-3817]
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Spanish Ministry of Science and Innovation
    note: Spanish Ministry of Science and Innovation through projects [SEV 2017-0712,
      FPU-2015/264, PID2019-104757RB-I00/AEI/10.13039/501100011033]
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Instituto de Salud Carlos III
    note: 'Instituto de Salud Carlos III: PT17/0009/0010 [ISCIII-SGEFI/ERDF]'
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole: []
    url: null
  description: Web based application designed to integrate protein structure, protein
    sequence and protein annotations in a unique graphical environment. The current
    version of the application offers a unified, enriched and interactive view of
    EMDB volumes, PDB structures and Uniprot sequences where the protein annotations
    stored in Uniprot, Immune Epitope DB, Phospho Site Plus, BioMuta and dSysMap can
    be explored interactively at sequence and structural level.
  documentation:
  - note: null
    type:
    - General
    url: http://3dbionotes.cnb.csic.es/ws/help
  download: []
  editPermission:
    authors:
    - coss
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Spain
  elixirPlatform:
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: EMDB ID
        uri: http://edamontology.org/data_1146
      format: []
    - data:
        term: PDB ID
        uri: http://edamontology.org/data_1127
      format: []
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    note: Integration of protein structure, protein sequence and protein annotations
      in a unique graphical environment.
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output: []
  homepage: http://3dbionotes.cnb.csic.es/ws
  homepage_status: 0
  language:
  - SQL
  lastUpdate: '2026-02-05T14:26:24.786970Z'
  license: Apache-2.0
  link: []
  maturity: Mature
  name: 3DBIONOTES
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: coss
  publication:
  - doi: 10.1016/j.jsb.2016.02.007
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btx483
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btz118
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btab397
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Data integration and warehousing
    uri: http://edamontology.org/topic_3366
  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  validated: 1
  version:
  - v3
- accessibility: null
  additionDate: '2026-02-05T13:03:47.451732Z'
  biotoolsCURIE: biotools:crabz
  biotoolsID: crabz
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Like pigz, but rust
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/sstadick/crabz
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-05T13:03:47.454691Z'
  license: null
  link: []
  maturity: null
  name: crabz
  operatingSystem: []
  otherID: []
  owner: camlloyd
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- 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: '2017-05-08T10:31:53Z'
  biotoolsCURIE: biotools:fusion
  biotoolsID: fusion
  collectionID:
  - de.NBI
  - Transcriptomics
  - de.NBI-BiGi
  - Proteomics
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: fusion-service@cebitec.uni-bielefeld.de
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.cebitec.uni-bielefeld.de/brf/index.php/fusion
  description: Web application for the integrative analysis of omics data providing
    a collection of new and established tools and visualization methods to support
    researchers in exploring multi-level omics data. The software focuses on data-rich
    high-throughout experiments from transcriptomics, proteomics and/or metabolomics,
    and offers convenient functionality for a) omics data manipulation, b) data analysis,
    c) cluster analysis, d) data visualization.
  documentation:
  - note: null
    type:
    - User manual
    url: https://fusion.cebitec.uni-bielefeld.de/QuickStartGuide.pdf
  download: []
  editPermission:
    authors:
    - proteomics.bio.tools
    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: xlsx
        uri: http://edamontology.org/format_3620
    note: null
    operation:
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    - term: Box-Whisker plot plotting
      uri: http://edamontology.org/operation_2943
    - term: Enrichment analysis
      uri: http://edamontology.org/operation_3501
    - term: Multiple sample visualisation
      uri: http://edamontology.org/operation_3744
    - term: Gene expression correlation
      uri: http://edamontology.org/operation_3463
    - term: Heat map generation
      uri: http://edamontology.org/operation_0531
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Principal component plotting
      uri: http://edamontology.org/operation_2939
    - term: Gene to pathway mapping
      uri: http://edamontology.org/operation_0533
    - term: Pathway or network visualisation
      uri: http://edamontology.org/operation_3083
    - term: Statistical inference
      uri: http://edamontology.org/operation_3658
    - term: Gene expression clustering
      uri: http://edamontology.org/operation_0313
    output: []
  homepage: https://fusion.cebitec.uni-bielefeld.de
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T22:38:42.566746Z'
  license: GPL-3.0
  link: []
  maturity: Emerging
  name: Fusion
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: de.NBI_Service_Team
  publication:
  - doi: 10.2390/biecoll-jib-2016-296
    metadata:
      abstract: 'We present Omics Fusion, a new web-based platform for integrative
        analysis of omics data. Omics Fusion provides a collection of new and established
        tools and visualization methods to support researchers in exploring omics
        data, validating results or understanding how to adjust experiments in order
        to make new discoveries. It is easily extendible and new visualization methods
        are added continuously. It is available for free under: https://fusion.cebitec.uni-bielefeld.de/.'
      authors:
      - name: Brink B.G.
      - name: Seidel A.
      - name: Kleinbolting N.
      - name: Nattkemper T.W.
      - name: Albaum S.P.
      citationCount: 9
      date: '2016-12-18T00:00:00Z'
      journal: Journal of integrative bioinformatics
      title: Omics Fusion - A Platform for Integrative Analysis of Omics Data
    note: null
    pmcid: null
    pmid: '28187412'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Data integration and warehousing
    uri: http://edamontology.org/topic_3366
  - term: Gene regulation
    uri: http://edamontology.org/topic_0204
  - term: Protein expression
    uri: http://edamontology.org/topic_0108
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  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: '2026-02-04T11:00:35.227720Z'
  biotoolsCURIE: biotools:cortoviz
  biotoolsID: cortoviz
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: CORToViz (CORD-19 Topic Visualizer) is a computational method and interactive
    visualization tool designed to explore and analyze the evolution of research topics
    within large text corpora. In the referenced work, it was applied to the COVID-19
    Open Research Dataset (CORD-19), which contains over a million scientific abstracts
    related to the COVID-19 pandemic. CORToViz combines modern machine learning and
    natural language processing techniques to cluster documents, extract temporal
    topic trends, and present results through an interactive dashboard. The dashboard
    supports visualization of topic contents (e.g., with word clouds), time-series
    plots of topic trends over time, and statistical testing to assess significant
    changes in topic prominence within user-selected time windows. While demonstrated
    on CORD-19, the pipeline and visualization components are general and can be adapted
    to other textual datasets with temporal structure.
  documentation: []
  download:
  - note: null
    type: Software package
    url: https://hub.docker.com/r/frinve/cortoviz/
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: http://gmql.eu/cortoviz
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T11:00:41.026549Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://hub.docker.com/r/frinve/cortoviz/
  maturity: null
  name: CORToViz
  operatingSystem: []
  otherID: []
  owner: abernasconi
  publication:
  - doi: 10.1016/j.eswa.2024.124028
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic: []
  validated: 0
  version: []
- 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: null
  additionDate: '2026-02-04T10:08:58.628807Z'
  biotoolsCURIE: biotools:graph-search
  biotoolsID: graph-search
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: GRAPH-SEARCH allows users to explore a network of 130K biomedical entities
    and 48M relations by formulating or adapting graph queries; it produces a bibliography
    of COVID-19-related publications, which are globally ranked; and each publication
    is further associated with the specific parts of the query that it explains, thereby
    allowing the user to understand each aspect of the matching.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/FrInve/graph-search/wiki/
  download:
  - note: null
    type: Software package
    url: https://hub.docker.com/r/frinve/graph-search
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://gmql.eu/graph-search
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T10:09:02.499031Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/FrInve/graph-search/wiki
  maturity: null
  name: GRAPH-SEARCH
  operatingSystem: []
  otherID: []
  owner: abernasconi
  publication:
  - doi: 10.2196/52655
    metadata: null
    note: null
    pmcid: PMC11176882
    pmid: '38814687'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  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: null
  additionDate: '2026-02-04T03:24:52.473123Z'
  biotoolsCURIE: biotools:scipi
  biotoolsID: scipi
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Hepatocyte Ploidy Identification Pipeline on the Stereo-cell Platform
    for Accurate Liver Polyploidy Classification via Fluorescence Staining and Deep
    Learning Tools
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/JeffLuo9/Hep_Ploidy_protocol
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T03:26:06.350767Z'
  license: null
  link: []
  maturity: null
  name: SCIPI
  operatingSystem: []
  otherID: []
  owner: jiahui
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T02:24:49.967847Z'
  biotoolsCURIE: biotools:guacamole
  biotoolsID: guacamole
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Detects and corrects GC bias in metagenomic libraries
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/CIbiv/guaCAMOLE
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T02:24:49.969863Z'
  license: null
  link: []
  maturity: null
  name: GuaCAMOLE
  operatingSystem: []
  otherID: []
  owner: florian
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T01:48:29.964334Z'
  biotoolsCURIE: biotools:smintegration
  biotoolsID: smintegration
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: SMIntegration is an innovative open-source platform for integrated
    analysis of spatial transcriptomics and metabolomics data. It integrates spatial
    pattern recognition, differential comparison, network construction, and functional
    annotation into a unified workflow. Designed to address key challenges in spatial
    multi-omics correlation analysis, SMIntegration enables researchers to explore
    gene-metabolite co-regulation mechanisms through an intuitive web interface, revealing
    spatial heterogeneity in tissue development and disease progression.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://metax.genomics.cn/app/smintegration
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T01:48:29.966207Z'
  license: null
  link: []
  maturity: null
  name: SMIntegration
  operatingSystem: []
  otherID: []
  owner: haoke
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - '1.0'
- accessibility: null
  additionDate: '2026-02-04T01:21:28.611408Z'
  biotoolsCURIE: biotools:hopsworks_chef
  biotoolsID: hopsworks_chef
  collectionID:
  - Unverified
  - IHEN
  - HEAP
  confidence_flag: null
  cost: null
  credit:
  - email: roxana.martinez@ki.se
    fundrefid: null
    gridid: null
    name: HEAP
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: Chef Cookbook for Hopsworks, providing automation scripts for deployment
    and configuration.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/HEAP-EXPOSOME/hopsworks-chef
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T01:21:28.613392Z'
  license: null
  link: []
  maturity: null
  name: hopsworks-chef
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T01:21:16.133156Z'
  biotoolsCURIE: biotools:metagenomics_ml
  biotoolsID: metagenomics_ml
  collectionID:
  - Unverified
  - IHEN
  - HEAP
  confidence_flag: null
  cost: null
  credit:
  - email: roxana.martinez@ki.se
    fundrefid: null
    gridid: null
    name: HEAP
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: ML-based sequence classification pipeline for metagenomics data.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/HEAP-EXPOSOME/metagenomics-ML
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T01:21:16.135430Z'
  license: null
  link: []
  maturity: null
  name: metagenomics-ML
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T01:21:04.370412Z'
  biotoolsCURIE: biotools:heap_exposome_demo
  biotoolsID: heap_exposome_demo
  collectionID:
  - Unverified
  - IHEN
  - HEAP
  confidence_flag: null
  cost: null
  credit:
  - email: roxana.martinez@ki.se
    fundrefid: null
    gridid: null
    name: HEAP
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: Chemical exposome pipeline with a sample dataset. The Docker container
    includes all dependencies, which can be run in RStudio or installed via Docker.
    R scripts process the dataset, producing output data and an HTML report.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/HEAP-EXPOSOME/exposome-demo
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T01:21:04.372560Z'
  license: null
  link: []
  maturity: null
  name: HEAP exposome demo
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T01:20:40.952325Z'
  biotoolsCURIE: biotools:heap_streaming_demo
  biotoolsID: heap_streaming_demo
  collectionID:
  - Unverified
  - IHEN
  - HEAP
  confidence_flag: null
  cost: null
  credit:
  - email: roxana.martinez@ki.se
    fundrefid: null
    gridid: null
    name: HEAP
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: Streaming tutorial notebooks for PPG data. Demonstrates producing and
    consuming streaming data from an external Kafka topic into Hopsworks using dummy
    PPG data. Requires a Kafka cluster and a pre-created topic.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/HEAP-EXPOSOME/streaming-demo
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T01:20:40.954643Z'
  license: null
  link: []
  maturity: null
  name: HEAP streaming demo
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T01:20:25.653675Z'
  biotoolsCURIE: biotools:fair_data_self_assessment_service
  biotoolsID: fair_data_self_assessment_service
  collectionID:
  - Unverified
  - IHEN
  - HEAP
  confidence_flag: null
  cost: null
  credit:
  - email: roxana.martinez@ki.se
    fundrefid: null
    gridid: null
    name: HEAP
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: The Self Assessment Service (SAS) is an online questionnaire guiding
    researchers on how Findable, Accessible, Interoperable and Reusable (FAIR) their
    data is.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://heap.bibbox.org/surveys/?s=XC8YLX8W8R
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T01:20:25.655691Z'
  license: null
  link: []
  maturity: null
  name: FAIR data self-assessment service
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T01:20:11.704347Z'
  biotoolsCURIE: biotools:bibbox
  biotoolsID: bibbox
  collectionID:
  - Unverified
  - IHEN
  - HEAP
  confidence_flag: null
  cost: null
  credit:
  - email: roxana.martinez@ki.se
    fundrefid: null
    gridid: null
    name: HEAP
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: The BIBBOX allows researchers to publish their data and associated
    data management software (Apps) in a FAIR manner, by incorporating a FAIR Data
    Point into the Apps. The architecture is modular and flexible, enabling integration
    with existing open-source software and publication in the App Store.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/bibbox
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T01:20:11.709239Z'
  license: null
  link: []
  maturity: null
  name: BIBBOX
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T00:57:35.249500Z'
  biotoolsCURIE: biotools:spatial_agent_based_modeling_urban_health_interventions
  biotoolsID: spatial_agent_based_modeling_urban_health_interventions
  collectionID:
  - Unverified
  - EXPANSE
  - IHEN
  confidence_flag: null
  cost: null
  credit:
  - email: t.s.sonnenschein@uu.nl
    fundrefid: null
    gridid: null
    name: Tabea Sonnenschein
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: expanse@uu.nl
    fundrefid: null
    gridid: null
    name: EXPANSE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: Repository containing methods and models for urban health interventions,
    including spatial synthetic population generation (GenSynthPop), routing setup
    with OSRM, environmental spatial layer preparation, NLP knowledge extraction,
    and GAMA agent-based simulation models.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/TabeaSonnenschein/Spatial-Agent-based-Modeling-of-Urban-Health-Interventions
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:57:35.255232Z'
  license: null
  link: []
  maturity: null
  name: Spatial Agent-based Modeling of Urban Health Interventions
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T00:56:31.885816Z'
  biotoolsCURIE: biotools:gensynthpop
  biotoolsID: gensynthpop
  collectionID:
  - Unverified
  - EXPANSE
  - IHEN
  confidence_flag: null
  cost: null
  credit:
  - email: t.s.sonnenschein@uu.nl
    fundrefid: null
    gridid: null
    name: Tabea Sonnenschein
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: expanse@uu.nl
    fundrefid: null
    gridid: null
    name: EXPANSE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: Sample-free tool to construct synthetic populations from mixed-aggregation
    contingency tables. Prepares stratified census datasets, generates conditional
    propensities, combines with spatial marginals, and validates generated populations
    for simulations such as agent-based models.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/TabeaSonnenschein/GenSynthPop
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:56:31.887941Z'
  license: null
  link: []
  maturity: null
  name: GenSynthPop
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T00:56:20.148531Z'
  biotoolsCURIE: biotools:cellautdisp
  biotoolsID: cellautdisp
  collectionID:
  - Unverified
  - IHEN
  - EXPANSE
  confidence_flag: null
  cost: null
  credit:
  - email: t.s.sonnenschein@uu.nl
    fundrefid: null
    gridid: null
    name: Tabea Sonnenschein
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: expanse@uu.nl
    fundrefid: null
    gridid: null
    name: EXPANSE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: Python package for dispersion modeling of traffic-related NO2, including
    hourly and monthly calculations, model calibration, and a genetic algorithm for
    calibration. Supports cellular automata dispersion modeling with adjustable parameters.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/TabeaSonnenschein/CellAutDisp
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:56:20.150784Z'
  license: null
  link: []
  maturity: null
  name: CellAutDisp
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T00:56:03.219737Z'
  biotoolsCURIE: biotools:urbhealth_abm
  biotoolsID: urbhealth_abm
  collectionID:
  - Unverified
  - IHEN
  - EXPANSE
  confidence_flag: null
  cost: null
  credit:
  - email: t.s.sonnenschein@uu.nl
    fundrefid: null
    gridid: null
    name: Tabea Sonnenschein
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: expanse@uu.nl
    fundrefid: null
    gridid: null
    name: EXPANSE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: An Agent-Based Model (ABM) simulating individual-level activity schedules,
    mobility choices, traffic, air pollution, and exposure to air pollution and transport-related
    physical activity under different urban scenarios.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/TabeaSonnenschein/UrbHealth-ABM
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:56:03.223237Z'
  license: null
  link: []
  maturity: null
  name: 'UrbHealth-ABM: Urban Health Scenario Agent-based Model'
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T00:55:34.163174Z'
  biotoolsCURIE: biotools:expanseeker
  biotoolsID: expanseeker
  collectionID:
  - Unverified
  - IHEN
  - EXPANSE
  confidence_flag: null
  cost: null
  credit:
  - email: expanse@uu.nl
    fundrefid: null
    gridid: null
    name: EXPANSE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: Expanseeker is the official app of the Urban Labs study within the
    EXPANSE project. It engages users in Challenges and Activities to help researchers
    collect exposome data and understand the relationship between the exposome and
    health.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://play.google.com/store/apps/details?id=com.GamesForHealth.Expanse
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:55:34.165389Z'
  license: null
  link: []
  maturity: null
  name: Expanseeker
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Restricted access
  additionDate: '2025-03-17T14:01:59.601345Z'
  biotoolsCURIE: biotools:exposome_maps
  biotoolsID: exposome_maps
  collectionID:
  - EXPANSE
  - EHEN
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: R.C.H.Vermeulen@uu.nl
    fundrefid: null
    gridid: null
    name: Roel Vermeulen
    note: null
    orcidid: https://orcid.org/0000-0003-4082-8163
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: z.s.r.m.boudewijns@uu.nl
    fundrefid: null
    gridid: null
    name: Zimbo Boudewijns
    note: null
    orcidid: https://orcid.org/0000-0002-9383-9571
    rorid: null
    typeEntity: null
    typeRole:
    - Maintainer
    url: null
  - email: l.q.roga@uu.nl
    fundrefid: null
    gridid: null
    name: Lloyd Roga
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  description: 'Exposome Maps is a data catalogue of geospatially resolved datasets
    on environmental exposure estimates. It contains more than 20,000 datasets on
    several Exposome dimensions including Physico-Chemical Environment, Built Environment,
    Food Environment, and Social Environment. It provides harmonized data collections
    across Europe for following environmental factors: PM10, PM2.5, NO2, O3, Temperature,
    Ultra Violet Radiation, Road Traffic Noise, Urbanicity, NDVI (Normalized Difference
    Vegetation Index ), MSAVI (Modified Soil Adjusted Vegetation Index), Green spaces,
    Blue spaces, Imperviousness, Light at night, Walkability Index.'
  documentation:
  - note: Description of Environmental variables available through Exposome Maps
    type:
    - User manual
    url: https://surfdrive.surf.nl/files/index.php/s/uqUORDrd428H2F9
  - note: Exposome-NL data platform Data Access and Publication Policy
    type:
    - Terms of use
    url: https://surfdrive.surf.nl/files/index.php/s/fI0Gmuu5O1MJAI9
  download: []
  editPermission:
    authors:
    - hkucukali
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://exposome.uu.nl/
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:46:44.590787Z'
  license: Other
  link:
  - note: Project information page
    type:
    - Other
    url: https://expanseproject.eu/
  maturity: Mature
  name: Exposome Maps
  operatingSystem: []
  otherID: []
  owner: Channel2291
  publication:
  - doi: 10.1126/science.aay3164
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1097/EE9.0000000000000162
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  - term: Environmental sciences
    uri: http://edamontology.org/topic_3855
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-03T23:14:10.223819Z'
  biotoolsCURIE: biotools:sharp-r
  biotoolsID: sharp-r
  collectionID:
  - LongITools
  - Unverified
  - EXPANSE
  - IHEN
  confidence_flag: null
  cost: null
  credit:
  - email: barbara.bodinier@gmail.com
    fundrefid: null
    gridid: null
    name: Barbara Bodinier
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: teija.juola@oulu.fi
    fundrefid: null
    gridid: null
    name: LongITools
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: An R package providing a unified framework for stability-enhanced variable
    selection, graphical modelling, and clustering using resampling-based approaches.
    In stability selection and consensus clustering, resampling techniques are used
    to enhance the reliability of the results. In this package, hyper-parameters are
    calibrated by maximising model stability, which is measured under the null hypothesis
    that all selection (or co-membership) probabilities are identical. Functions are
    readily implemented for the use of LASSO regression, sparse PCA, sparse (group)
    PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning
    around medoids, K means or Gaussian mixture models in consensus clustering.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://cran.r-project.org/web/packages/sharp/index.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:45:04.049849Z'
  license: null
  link: []
  maturity: null
  name: 'sharp: Stability-enHanced Approaches using Resampling Procedures'
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T00:35:46.144285Z'
  biotoolsCURIE: biotools:working_life_expectancy_and_working_years_lost
  biotoolsID: working_life_expectancy_and_working_years_lost
  collectionID:
  - Unverified
  - IHEN
  - EPHOR
  confidence_flag: null
  cost: null
  credit:
  - email: eelco.kuijpers@tno.nl
    fundrefid: null
    gridid: null
    name: EPHOR
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: Calculates working life expectancy (WLE) and working years lost (WYL),
    including healthy working life expectancy (HWLE), based on cumulative labor market
    attachment and health status.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.we-expose.eu/tool-on-calculating-the-working-life-expectancy-and-working-years-lost
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:35:46.146687Z'
  license: null
  link: []
  maturity: null
  name: Calculation of the working life expectancy and working years lost
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T00:34:37.175666Z'
  biotoolsCURIE: biotools:ephorhia
  biotoolsID: ephorhia
  collectionID:
  - Unverified
  - EPHOR
  - IHEN
  confidence_flag: null
  cost: null
  credit:
  - email: eelco.kuijpers@tno.nl
    fundrefid: null
    gridid: null
    name: EPHOR
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: A Stata program for flexible simulation studies on occupational exposures,
    allowing users to define custom parameters and replicate intervention scenarios
    from EPHOR analyses.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.we-expose.eu/open-access-stata-statistical-package-program-ephorhia2019
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:34:37.178401Z'
  license: null
  link: []
  maturity: null
  name: ephorhia
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T00:33:51.163186Z'
  biotoolsCURIE: biotools:disease_multiple_exposure_hierarchical_penalization_models
  biotoolsID: disease_multiple_exposure_hierarchical_penalization_models
  collectionID:
  - Unverified
  - IHEN
  - EPHOR
  confidence_flag: null
  cost: null
  credit:
  - email: eelco.kuijpers@tno.nl
    fundrefid: null
    gridid: null
    name: EPHOR
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: Hierarchical and penalization models developed for agnostic exploration
    of exposure-disease associations, applied to lung cancer risk in pooled case-control
    populations. Includes sample code on GitHub.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/cb-ge/ephor_wp4_agnostic_models
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:33:51.165530Z'
  license: null
  link: []
  maturity: null
  name: Disease multiple exposure hierarchical and penalization models
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T00:31:27.401743Z'
  biotoolsCURIE: biotools:multiple_exposures_response
  biotoolsID: multiple_exposures_response
  collectionID:
  - Unverified
  - IHEN
  - EPHOR
  confidence_flag: null
  cost: null
  credit:
  - email: w.wan@uu.nl
    fundrefid: null
    gridid: null
    name: Wenxin Wan
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: eelco.kuijpers@tno.nl
    fundrefid: null
    gridid: null
    name: EPHOR
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: A suite of statistical approaches for multiple exposure-response modelling
    in the working-life exposome context, guiding analyses of combined occupational
    and non-occupational risk factors.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/Wenxin-Wan/ephor_wp4_method_tutorial
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:31:27.404506Z'
  license: null
  link: []
  maturity: null
  name: Multiple exposures-response (MER)
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T00:29:49.187393Z'
  biotoolsCURIE: biotools:eurojem
  biotoolsID: eurojem
  collectionID:
  - Unverified
  - IHEN
  - EPHOR
  confidence_flag: null
  cost: null
  credit:
  - email: eurojem@ki.se
    fundrefid: null
    gridid: null
    name: EuroJEM
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Primary contact
    url: null
  - email: eelco.kuijpers@tno.nl
    fundrefid: null
    gridid: null
    name: EPHOR
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: EuroJEM is a comprehensive job-exposure matrix instrument providing
    harmonized occupational exposure data across Europe for systematic evaluation
    where individual-level data is unavailable.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://ki.se/en/imm/eurojem
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:29:49.189225Z'
  license: null
  link: []
  maturity: null
  name: EuroJEM
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T00:29:17.402450Z'
  biotoolsCURIE: biotools:inventory_of_occupational_exposure_tools
  biotoolsID: inventory_of_occupational_exposure_tools
  collectionID:
  - Unverified
  - IHEN
  - EPHOR
  confidence_flag: null
  cost: null
  credit:
  - email: s.peters@uu.nl
    fundrefid: null
    gridid: null
    name: Susan Peters
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: michelle.turner@isglobal.org
    fundrefid: null
    gridid: null
    name: Michelle C Turner
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: svetlana.solovieva@ttl.fi
    fundrefid: null
    gridid: null
    name: Svetlana Solovieva
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: eelco.kuijpers@tno.nl
    fundrefid: null
    gridid: null
    name: EPHOR
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: Provides a meta-data inventory of existing occupational exposure information
    and tools, including job-exposure matrices, exposure databases, and occupational
    coding systems, to facilitate harmonization and research replication.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://occupationalexposuretools.net/
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:29:17.404465Z'
  license: null
  link: []
  maturity: null
  name: Inventory of Occupational Exposure Tools
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-04T00:28:41.678903Z'
  biotoolsCURIE: biotools:isco08_to_isco88
  biotoolsID: isco08_to_isco88
  collectionID:
  - Unverified
  - IHEN
  - EPHOR
  confidence_flag: null
  cost: null
  credit:
  - email: eelco.kuijpers@tno.nl
    fundrefid: null
    gridid: null
    name: EPHOR
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: null
  description: This tool converts job codes from ISCO-08 to ISCO-88, allowing users
    to upload a CSV file and receive a translated output with corrected occupational
    codes.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://diamonds.tno.nl/shiny/ephor/diamonds/
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:28:41.680635Z'
  license: null
  link: []
  maturity: null
  name: 'Automatic job code crosswalking tool: ISCO-08 to ISCO-88'
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
next: ?page=2
previous: null
