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    via sequence and genomic annotation statistics, to benchmarking CLIP-seq peak
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  topic:
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- accessibility: null
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  description: HyPPI classifies a protein-protein complex based on its interaction
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    upon dissociation of the protein-protein complex. Transient protein-protein complexes
    are stable in the complexed as well as in the monomeric form, depending on the
    necessary function of the complex. Crystal artifacts have no biological function
    and are artificially formed during the crystallization process. The discrimination
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    note: Probability score for interface classification
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  lastUpdate: '2026-05-22T09:20:50.341489Z'
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  description: 'Stress Knowledge Map:  A compilation of knowledge on mechanisms underlying
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  biotoolsCURIE: biotools:jamda
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    orcidid: null
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  description: JAMDA enables the preparation of individual protein structures and
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    Alternatively, users can also provide externally prepared ligand conformers.
  documentation:
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  download:
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      format:
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    - data:
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  link:
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  maturity: Mature
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  biotoolsCURIE: biotools:dogsite3
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  description: DoGSite3 was developed for predicting robust and reliable small molecule
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    to its predecessor, it shows increased robustness through comprehensive parameter
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  documentation:
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  download:
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  topic:
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  - term: Drug discovery
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- accessibility: null
  additionDate: '2016-11-21T10:33:07Z'
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  description: DoGSiteScorer is a grid-based automated pocket detection and analysis
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    of the predicted (sub-)pockets, are calculated. Per default, a simple druggability
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    be.
  documentation:
  - note: null
    type:
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  description: A tool that checks the clinical metadata quality (validity, completeness),
    the integrity between images and clinical metadata provided as well as their accuracy,  the
    de-identification protocol applied, and existence of annotation together with
    the consistency between the images and the annotation files and informs the user
    on corrective actions prior to data upload.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://drive.eucaim.cancerimage.eu/s/tdK9tHCiKQXbgW5
  - note: null
    type:
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    url: https://drive.eucaim.cancerimage.eu/s/LfsFZYDbmXpstHL
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  homepage: https://www.mdpi.com/2939712
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  language:
  - Python
  - R
  lastUpdate: '2026-05-21T00:40:40.168342Z'
  license: Proprietary
  link:
  - note: Link to the Harbor image
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    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicqt/info-tab
  - note: Link to the temporary license of the tool
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    url: https://drive.google.com/drive/folders/15HotbC4RnBXe83lzWEnOQZksB0pZa1JY
  maturity: Mature
  name: Data Integration Quality Check Tool (DIQCT)
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  owner: authEucaim
  publication:
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    metadata: null
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  - doi: 10.1109/EMBC48229.2022.9871018
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  toolType:
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  topic:
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-28T23:55:08.439649Z'
  biotoolsCURIE: biotools:dicom_image_similarity-duplicate_checker
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  description: 'Automatically detects duplicate and near-duplicate DICOM image series
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    analysis, SHA-based pixel hashing, and image similarity metrics (SSIM, cosine,
    MAD) to identify exact copies, re-exported series, and near-identical acquisitions.
    All findings are reported for human expert review — no files are modified or deleted
    automatically.


    For scenarios requiring strict, image-level deduplication based on pixel content,
    fully agnostic to metadata changes, consider using [https://bio.tools/image_duplicate_check_tool]'
  documentation:
  - note: null
    type:
    - General
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  language:
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  lastUpdate: '2026-05-21T00:27:06.913860Z'
  license: Apache-2.0
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  owner: difoto
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  topic:
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    uri: http://edamontology.org/topic_3572
  validated: 0
  version:
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- accessibility: null
  additionDate: '2026-05-20T09:31:45.052360Z'
  biotoolsCURIE: biotools:gc_derivatization
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  confidence_flag: null
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    name: Wudimir Rojas
    note: null
    orcidid: https://orcid.org/0000-0001-7036-9987
    rorid: null
    typeEntity: Person
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    url: https://github.com/wverastegui
  - email: null
    fundrefid: null
    gridid: null
    name: Helge Hecht
    note: null
    orcidid: https://orcid.org/0000-0001-6744-996X
    rorid: null
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    url: https://github.com/hechth
  - email: GalaxyToolsDevelopmentandDeployment@space.muni.cz
    fundrefid: null
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    name: RECETOX MUNI
    note: null
    orcidid: null
    rorid: null
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    url: https://www.recetox.muni.cz/
  description: 'In silico derivatization for GC.


    The GC-derivatization tool converts carbonyl groups to C═N-OCH3 (MeOX) and transforms
    acidic protons into -Si(CH3)3 (TMS). Key functionalities include checking for
    specific groups, removing derivatization groups, and adding derivatization groups
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  lastUpdate: '2026-05-20T09:31:45.054565Z'
  license: null
  link:
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  maturity: null
  name: gc_derivatization
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  owner: aniehues
  publication:
  - doi: 10.1021/acs.analchem.7b01010
    metadata: null
    note: null
    pmcid: null
    pmid: '28520403'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  - Command-line tool
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  validated: 0
  version:
  - 1.0.1
- accessibility: Open access
  additionDate: '2026-05-19T13:51:52.767136Z'
  biotoolsCURIE: biotools:minigraph
  biotoolsID: minigraph
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: Minigraph is a sequence-to-graph mapper and graph constructor. For
    graph generation, it aligns a query sequence against a sequence graph and incrementally
    augments an existing graph with long query subsequences diverged from the graph.
  documentation:
  - note: null
    type:
    - General
    url: https://lh3.github.io/minigraph/
  download: []
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  function:
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    input: []
    note: null
    operation:
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    output: []
  homepage: https://github.com/lh3/minigraph
  homepage_status: 0
  language:
  - C
  - JavaScript
  lastUpdate: '2026-05-20T09:16:39.920961Z'
  license: MIT
  link: []
  maturity: null
  name: minigraph
  operatingSystem:
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  otherID: []
  owner: anitamnd
  publication: []
  relation: []
  toolType:
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  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-05-20T09:15:46.569943Z'
  biotoolsCURIE: biotools:snpfreq
  biotoolsID: snpfreq
  collectionID: []
  confidence_flag: null
  cost: null
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  description: "snpFreq significant SNPs in case-control data. \n\nThis tool performs\
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    \ environment and Fisher''s exact test to identify SNPs with a significant difference\
    \ in the allele frequencies between the two groups.  R''s \"qvalue\" package is\
    \ used to correct for multiple testing."
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  function:
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    input:
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        term: Count matrix
        uri: http://edamontology.org/data_3917
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: null
    operation:
    - term: SNP detection
      uri: http://edamontology.org/operation_0484
    output:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format:
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        uri: http://edamontology.org/format_2330
  homepage: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2026-05-20T09:15:46.574506Z'
  license: null
  link:
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    type:
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  name: snpfreq
  operatingSystem: []
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  owner: aniehues
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  relation: []
  toolType:
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  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2026-05-20T08:59:02.212508Z'
  biotoolsCURIE: biotools:snp-sites
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  confidence_flag: null
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  description: Finds SNP sites from a multi-FASTA alignment file.
  documentation:
  - note: null
    type:
    - General
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  download: []
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  function:
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        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
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      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: VCF
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    note: null
    operation:
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      format:
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      - term: FASTA-aln
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      - term: VCF
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  homepage_status: 0
  language:
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  lastUpdate: '2026-05-20T08:59:02.214591Z'
  license: GPL-3.0
  link:
  - note: null
    type:
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  maturity: null
  name: SNP-sites
  operatingSystem:
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  otherID: []
  owner: aniehues
  publication:
  - doi: 10.1099/mgen.0.000056
    metadata: null
    note: null
    pmcid: PMC5320690
    pmid: '28348851'
    type:
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    version: null
  relation: []
  toolType:
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  topic:
  - term: Genomics
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  - term: DNA polymorphism
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  validated: 0
  version:
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- accessibility: null
  additionDate: '2026-05-20T06:55:26.498806Z'
  biotoolsCURIE: biotools:nanoporedb
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  description: NanoporeDB is an open-access structural database dedicated to the exploration,
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    gateways in biological membranes and form the basis of many advanced biosensing
    and sequencing technologies. This platform integrates large-scale structure-guided
    mining and deep learning-based modeling using AlphaFold-Multimer and AlphaFold3
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    includes detailed information on membrane embedding, pore geometry annotation,
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    Through an interactive 3D visualization interface and quantitative parameters
    such as tilt angle, insertion depth, and pore geometry, NanoporeDB enables researchers
    to explore nanopore diversity, discover novel scaffolds, and accelerate innovation
    in molecular sensing, precision diagnostics, and synthetic biology.
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  function:
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    input: []
    note: null
    operation:
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    output: []
  homepage: https://db.genomics.cn/nanopore
  homepage_status: 0
  language: []
  lastUpdate: '2026-05-20T07:52:15.982715Z'
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  maturity: null
  name: NanoporeDB
  operatingSystem: []
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  owner: Yuqian
  publication: []
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  toolType: []
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-05-20T07:48:09.421627Z'
  biotoolsCURIE: biotools:np-likeness
  biotoolsID: np-likeness
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: kalai@ebi.ac.uk
    fundrefid: null
    gridid: null
    name: Kalai Vanii Jayaseelan
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
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    note: null
    orcidid: null
    rorid: null
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    url: null
  - email: null
    fundrefid: null
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    name: Pablo Moreno
    note: null
    orcidid: null
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  - email: null
    fundrefid: null
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  - email: christoph.steinbeck@uni-jena.de
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    note: null
    orcidid: null
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    typeRole: []
    url: null
  description: 'Natural Product-likeness calculator v-2.1 : calculates natural product-likeness
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  homepage: https://github.com/vcnainala/NP-Likeness
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  license: LGPL-2.0-or-later
  link: []
  maturity: null
  name: NP-Likeness
  operatingSystem: []
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  owner: aniehues
  publication:
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    metadata: null
    note: null
    pmcid: PMC3436723
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    type:
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    version: null
  - doi: 10.1021/ci700286x
    metadata: null
    note: null
    pmcid: null
    pmid: '18034468'
    type:
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  relation: []
  toolType:
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  topic:
  - term: Small molecules
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- accessibility: null
  additionDate: '2026-05-20T07:09:58.565680Z'
  biotoolsCURIE: biotools:generate_count_matrix
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  credit:
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    gridid: null
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    note: null
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    rorid: null
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  description: "Tool to generate a count matrix for expression data in Galaxy. \n\n\
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  - note: null
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  function:
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      \             [--version] [--log LOG_FILE]\n                             COUNT_FILE\
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      format: []
    note: null
    operation:
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  language:
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  lastUpdate: '2026-05-20T07:09:58.567963Z'
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  maturity: null
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  topic:
  - term: Transcriptomics
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  validated: 0
  version:
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- accessibility: null
  additionDate: '2026-05-20T05:53:56.575576Z'
  biotoolsCURIE: biotools:nanosv
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  description: NanoSV is a software package that can be used to identify structural
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    Nanopore Technologies’ MinION, GridION or PromethION instruments, or Pacific Biosciences
    RSII or Sequel sequencers.
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  function:
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    input:
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      format:
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    note: null
    operation:
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      format:
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  homepage_status: 0
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  lastUpdate: '2026-05-20T05:53:56.577944Z'
  license: MIT
  link: []
  maturity: null
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  - Linux
  otherID: []
  owner: veitveit11
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    metadata: null
    note: null
    pmcid: PMC5673902
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  relation: []
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  topic:
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  - term: Long-read sequencing
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  validated: 0
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- accessibility: null
  additionDate: '2026-05-20T05:39:16.046772Z'
  biotoolsCURIE: biotools:s3segmenter
  biotoolsID: s3segmenter
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  confidence_flag: null
  cost: Free of charge
  credit: []
  description: S3segmenter is a Matlab-based set of functions that generates single
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  elixir_badge: 0
  function:
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    input:
    - data:
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      format:
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    - data:
        term: Map data
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    note: null
    operation:
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  homepage_status: 0
  language:
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  lastUpdate: '2026-05-20T05:39:16.048628Z'
  license: Not licensed
  link: []
  maturity: Mature
  name: s3segmenter
  operatingSystem:
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  - Linux
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  description: The electron density score for individual atoms (EDIA) quantifies the
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  description: Three-dimensional protein structures play a vital role in drug design.
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  description: LifeSoaks was designed to find solvent channels in macromolecular structures
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    PID=https://doi.org/10.5281/zenodo.20181900'
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next: ?page=2
previous: null
