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    metadata: null
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  - doi: 10.1109/ISBI56570.2024.10635469
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  toolType:
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  - Web application
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  topic:
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  validated: 0
  version:
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    name: Nathalie Reuter
    note: null
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    - Developer
    url: http://www.cbu.uib.no/reuter/
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    typeRole:
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    name: Department of Molecular Biology, University of Bergen, Norway
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    name: Computational Biology Unit, Department of Informatics, University of Bergen,
      Norway
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  description: WEBnm@ provides quick, automated computation and analysis of low-frequency
    normal modes for protein structures.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: http://apps.cbu.uib.no/webnma3/howto/single
  - note: null
    type:
    - FAQ
    url: http://apps.cbu.uib.no/webnma3/qanda
  - note: null
    type:
    - General
    - Citation instructions
    url: http://apps.cbu.uib.no/webnma3/about
  download: []
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  function:
  - cmd: null
    input:
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        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: Constructs elastic network model from alpha carbon coordinates of the protein,
      and computes properties to describe large scale conformations. Computes normal
      modes, fluctuation profiles, inter-residue correlations, conformational overlap
      analysis and vector field representations. Structural amino acid profiles, and
      normal mode characteristics describing protein motion, visualized in plots and
      decorated structure visualizations. White space delimited tabular data for normal
      modes and the provided plots
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Protein flexibility and motion analysis
      uri: http://edamontology.org/operation_0244
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PDF
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    - data:
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      format:
      - term: Textual format
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  - cmd: null
    input:
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        term: Structure alignment
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        uri: http://edamontology.org/format_2200
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: Performs comparative analysis of the normal modes of protein structures.
      Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner
      Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins
      to be compared. Multiple protein structures Heatmaps, dendrograms and structural
      amino acid profiles for visual comparison of structural similarity. White space
      delimited tabular data for the provided plots
    operation:
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      uri: http://edamontology.org/operation_2487
    - term: Visualisation
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    output:
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        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Structural profile
        uri: http://edamontology.org/data_0889
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://apps.cbu.uib.no/webnma
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-03-11T08:56:55.566213Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    - Issue tracker
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  - note: Helpdesk and support for ELIXIR Norway services.
    type:
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    url: https://elixir.no/helpdesk
  maturity: Mature
  name: WEBnma
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  - Windows
  - Mac
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  owner: UiB
  publication:
  - doi: 10.1186/s12859-014-0427-6
    metadata:
      abstract: 'Background: Normal mode analysis (NMA) using elastic network models
        is a reliable and cost-effective computational method to characterise protein
        flexibility and by extension, their dynamics. Further insight into the dynamics-function
        relationship can be gained by comparing protein motions between protein homologs
        and functional classifications. This can be achieved by comparing normal modes
        obtained from sets of evolutionary related proteins. Results: We have developed
        an automated tool for comparative NMA of a set of pre-aligned protein structures.
        The user can submit a sequence alignment in the FASTA format and the corresponding
        coordinate files in the Protein Data Bank (PDB) format. The computed normalised
        squared atomic fluctuations and atomic deformation energies of the submitted
        structures can be easily compared on graphs provided by the web user interface.
        The web server provides pairwise comparison of the dynamics of all proteins
        included in the submitted set using two measures: the Root Mean Squared Inner
        Product and the Bhattacharyya Coefficient. The Comparative Analysis has been
        implemented on our web server for NMA, WEBnmat, which also provides recently
        upgraded functionality for NMA of single protein structures. This includes
        new visualisations of protein motion, visualisation of inter-residue correlations
        and the analysis of conformational change using the. In addition, programmatic
        access to WEBnmat is now available through a SOAP-based web service. WEBnmat
        is available at. Conclusion: WEBnmat v2.0 is an online tool offering unique
        capability for comparative NMA on multiple protein structures. Along with
        a convenient web interface, powerful computing resources, and several methods
        for mode analyses, WEBnmat facilitates the assessment of protein flexibility
        within protein families and superfamilies. These analyses can give a good
        view of how the structures move and how the flexibility is conserved over
        the different structures.'
      authors:
      - name: Tiwari S.P.
      - name: Fuglebakk E.
      - name: Hollup S.M.
      - name: Skjaerven L.
      - name: Cragnolini T.
      - name: Grindhaug S.H.
      - name: Tekle K.M.
      - name: Reuter N.
      citationCount: 87
      date: '2014-12-30T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'WEBnmat v2.0: Web server and services for comparing protein flexibility'
    note: null
    pmcid: PMC4339738
    pmid: '25547242'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1186/1471-2105-6-52
    metadata:
      abstract: 'Background: Normal mode analysis (NMA) has become the method of choice
        to investigate the slowest motions in macromolecular systems. NMA is especially
        useful for large biomolecular assemblies, such as transmembrane channels or
        virus capsids. NMA relies on the hypothesis that the vibrational normal modes
        having the lowest frequencies (also named soft modes) describe the largest
        movements in a protein and are the ones that are functionally relevant. Results:
        We developed a web-based server to perform normal modes calculations and different
        types of analyses. Starting from a structure file provided by the user in
        the PDB format, the server calculates the normal modes and subsequently offers
        the user a series of automated calculations; normalized squared atomic displacements,
        vector field representation and animation of the first six vibrational modes.
        Each analysis is performed independently from the others and results can be
        visualized using only a web browser. No additional plug-in or software is
        required. For users who would like to analyze the results with their favorite
        software, raw results can also be downloaded. The application is available
        on http://www.bioinfo.no/tools/normalmodes. We present here the underlying
        theory, the application architecture and an illustration of its features using
        a large transmembrane protein as an example. Conclusion: We built an efficient
        and modular web application for normal mode analysis of proteins. Non specialists
        can easily and rapidly evaluate the degree of flexibility of multi-domain
        protein assemblies and characterize the large amplitude movements of their
        domains. © 2005 Hollup et al; licensee BioMed Central Ltd.'
      authors:
      - name: Hollup S.M.
      - name: Salensminde G.
      - name: Reuter N.
      citationCount: 105
      date: '2005-03-11T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'WEBnm@: A web application for normal mode analyses of proteins'
    note: null
    pmcid: PMC1274249
    pmid: '15762993'
    type:
    - Primary
    version: '1.0'
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    type: uses
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  toolType:
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  - Suite
  topic:
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    uri: http://edamontology.org/topic_2814
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  validated: 1
  version:
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    note: null
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    rorid: null
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    url: https://www.qmritools.com/
  description: QMRITools is a collection of tools for quantitative muscle MRI analysis,
    enabling the assessment of neuromuscular disorders and conditions. The software
    utilizes various MRI sequences and processing pipelines to generate metrics for
    comparative evaluation.
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    note: null
    operation:
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    - term: Standardisation and normalisation
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  publication:
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    metadata: null
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    type:
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  - doi: 10.1002/jmri.23608
    metadata: null
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    metadata: null
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    pmid: '20725932'
    type:
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  - doi: 10.1002/nbm.4119
    metadata: null
    note: null
    pmcid: null
    pmid: '31313867'
    type:
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    version: null
  relation: []
  toolType: []
  topic:
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    uri: http://edamontology.org/topic_3444
  - term: Endocrinology and metabolism
    uri: http://edamontology.org/topic_3407
  - term: Pathology
    uri: http://edamontology.org/topic_0634
  - term: Preclinical and clinical studies
    uri: http://edamontology.org/topic_3379
  validated: 0
  version: []
- accessibility: Open access
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  confidence_flag: tool
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Charles Girardot
    note: Head of MODIS team at EMBL Heidelberg
    orcidid: https://orcid.org/0000-0003-4301-3920
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    url: null
  - email: null
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    name: Jelle Scholtalbers
    note: Former MODIS team member, now working as a freelance (LabRise solutions)
    orcidid: https://orcid.org/0000-0002-6090-2482
    rorid: null
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  description: Lab Integrated Data (LabID) is an open-source web-based platform for
    research data management in life science institutes, featuring sample and dataset
    management, an inventory management system and an electronic lab notebook. LabID
    allows recording extensive experimental information about the provenance of data
    (samples, reagents, instrument, protocols, assay parameters) and is designed to
    help individual scientists, research groups and core facilities better manage,
    annotate and share their research according to FAIR principles.
  documentation:
  - note: Main documentation including installation instructions and training
    type:
    - General
    url: https://grp-gbcs.embl-community.io/labid-user-docs/
  - note: Test server for e.g LabID and trainings
    type:
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    url: https://labid-demo.embl.de/
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  license: MIT
  link:
  - note: Open source repositories for the LabID subprojects (UI, Server, Command
      Line Interface, Library)
    type:
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    url: https://gitlab.com/lab-integrated-data
  - note: Channel for questions from externals
    type:
    - Discussion forum
    url: https://labintegrateddata.slack.com/
  - note: Website of the MODIS team behind LabID
    type:
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    url: https://www.embl.org/groups/modis/
  maturity: Mature
  name: Lab Integrated Data (LabID)
  operatingSystem: []
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  owner: laurent_s._v.
  publication: []
  relation: []
  toolType:
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  - Command-line tool
  topic:
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    uri: http://edamontology.org/topic_3070
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-27T17:39:14.144907Z'
  biotoolsCURIE: biotools:random_number_lab
  biotoolsID: random_number_lab
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  confidence_flag: null
  cost: Free of charge
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    fundrefid: null
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    name: Thomas Amthor
    note: null
    orcidid: https://orcid.org/0000-0002-1456-6131
    rorid: null
    typeEntity: Person
    typeRole:
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    - Maintainer
    url: null
  description: An interactive set of tools including randomization of data (even stratified
    random sampling) and random assignments for studies, generation of random numbers
    following specific probability distributions, generation of random and quasi-random
    point distributions and sampling patterns, noise in one or two dimensions with
    adjustable spectral properties, random walks and Lévy flights. Own data tables
    can be provided for random sampling in a privacy-friendly way, as data processing
    takes place directly in the browser and no data is transferred to anywhere else.
    The Random Number Lab also offers some educational material and worksheets and
    can be used for scientific and educational purposes.
  documentation: []
  download: []
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  function:
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    note: Generation of sequences of random numbers or elements, spatial point patterns,
      random walks
    operation:
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      uri: http://edamontology.org/operation_0364
    output: []
  - cmd: null
    input: []
    note: Visualization of random distributions and random processes
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  - cmd: null
    input: []
    note: Randomization and permutation of data in a privacy-preserving way
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output: []
  homepage: https://randomnumberlab.org
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2026-02-27T18:10:10.460700Z'
  license: null
  link: []
  maturity: Mature
  name: Random Number Lab
  operatingSystem:
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  - iOS
  - Mac
  - Android
  - Windows
  otherID:
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    value: RRID:SCR_028010
    version: null
  owner: thomas9
  publication: []
  relation: []
  toolType:
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  topic:
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Experimental design and studies
    uri: http://edamontology.org/topic_3678
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2021-05-06T06:18:52Z'
  biotoolsCURIE: biotools:pangenome-blast
  biotoolsID: pangenome-blast
  collectionID: []
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  cost: Free of charge
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    name: Bielefeld University
    note: null
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    url: https://www.uni-bielefeld.de/
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    name: Genome Informatics
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    url: https://gi.cebitec.uni-bielefeld.de/
  - email: plast-service@cebitec.uni-bielefeld.de
    fundrefid: null
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    note: null
    orcidid: https://orcid.org/0000-0003-0744-7078
    rorid: null
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  description: PLAST is a heuristical method to search for highest scoring local alignments
    between a DNA sequence query and a graphical pangenome. It takes as input a plain
    DNA sequence and a pangenome which may either be a set of (multiple) FASTA or
    FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs
    statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard
    output format. Alignments are calculated based on a "seed-and-extend approach"
    while traversing the sequence graph. Biologically meaningful alignments are filtered
    by using an alignment statistic explicitly developed for sequence-to-graph alignments
    involving graphical pangenomes.
  documentation:
  - note: null
    type:
    - General
    url: https://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.md
  download: []
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    authors: []
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  function:
  - cmd: PLAST Search -i pangenomeGraphCommonFilePrefix -q fileContainingOneQueryPerLine
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: unambiguous pure nucleotide
        uri: http://edamontology.org/format_1211
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: GFA 1
        uri: http://edamontology.org/format_3975
      - term: Binary format
        uri: http://edamontology.org/format_2333
    note: "In order to search for alignments within the pangenome graph, \nA pangenome\
      \ graph used to search for alignments consists of (1) a file in GFA format containing\
      \ all sequences of the graph, (2) a binary file produced by the tool itself\
      \ or the software \"Bifrost\" and (3) a program-specific index data structure\
      \ in binary format."
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: BLAST results
        uri: http://edamontology.org/format_1333
  - cmd: PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fasta
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: If a pangenome graph already exists and only an index has to be built, FASTA/FASTQ
      files are not needed.
    operation:
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    output:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: GFA 1
        uri: http://edamontology.org/format_3975
      - term: Binary format
        uri: http://edamontology.org/format_2333
  homepage: https://github.com/tischulz1/plast
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-02-26T11:22:02.485629Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.ub.uni-bielefeld.de/gi/plast
  - note: null
    type:
    - Mirror
    url: https://github.com/tischulz1/plast
  maturity: Mature
  name: PLAST
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: tizian
  publication:
  - doi: 10.1093/bioinformatics/btab077
    metadata:
      abstract: 'Motivation: Increasing amounts of individual genomes sequenced per
        species motivate the usage of pangenomic approaches. Pangenomes may be represented
        as graphical structures, e.g. compacted colored de Bruijn graphs, which offer
        a low memory usage and facilitate reference-free sequence comparisons. While
        sequence-to-graph mapping to graphical pangenomes has been studied for some
        time, no local alignment search tool in the vein of BLAST has been proposed
        yet. Results: We present a new heuristic method to find maximum scoring local
        alignments of a DNA query sequence to a pangenome represented as a compacted
        colored de Bruijn graph. Our approach additionally allows a comparison of
        similarity among sequences within the pangenome. We show that local alignment
        scores follow an exponential-tail distribution similar to BLAST scores, and
        we discuss how to estimate its parameters to separate local alignments representing
        sequence homology from spurious findings. An implementation of our method
        is presented, and its performance and usability are shown. Our approach scales
        sublinearly in running time and memory usage with respect to the number of
        genomes under consideration. This is an advantage over classical methods that
        do not make use of sequence similarity within the pangenome.'
      authors:
      - name: Schulz T.
      - name: Wittler R.
      - name: Rahmann S.
      - name: Hach F.
      - name: Stoye J.
      citationCount: 6
      date: '2021-08-15T00:00:00Z'
      journal: Bioinformatics
      title: Detecting high-scoring local alignments in pangenome graphs
    note: null
    pmcid: PMC8388040
    pmid: '33532821'
    type:
    - Primary
    - Method
    - Benchmarking study
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 0.0.1-0.2.0
- accessibility: Restricted access
  additionDate: '2026-02-23T13:56:07.187145Z'
  biotoolsCURIE: biotools:HelixInsight
  biotoolsID: HelixInsight
  collectionID: []
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  cost: Commercial
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    fundrefid: null
    gridid: null
    name: Helena Bioinformatics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Developer
    url: https://helena.bio
  description: AI-powered variant interpretation platform for clinical genetics laboratories.
    Automates ACMG/AMP 2015 classification using Bayesian point-based framework (Tavtigian
    et al. 2018) with BayesDel ClinGen SVI-calibrated thresholds (Pejaver et al. 2022).
    Integrates 8 reference databases (gnomAD v4.1, ClinVar, dbNSFP 4.9c, SpliceAI,
    gnomAD Constraint, HPO, ClinGen, Ensembl VEP) for comprehensive variant annotation.
    Supports HPO-based phenotype matching with semantic similarity scoring, automated
    biomedical literature mining across 2M+ PubMed publications, and structured clinical
    report generation. Delivers full clinical interpretation of whole genome sequencing
    (WGS) in under 15 minutes. EU-hosted on dedicated infrastructure in Helsinki,
    Finland (GDPR-compliant).
  documentation:
  - note: null
    type:
    - General
    url: https://helixinsight.bio/docs
  - note: null
    type:
    - API documentation
    url: https://helixinsight.bio/docs/getting-started
  - note: null
    type:
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    url: https://helixinsight.bio/how-it-works
  - note: null
    type:
    - Terms of use
    url: https://helixinsight.bio/terms
  - note: Privacy policy
    type:
    - Other
    url: https://helixinsight.bio/privacy
  download: []
  editPermission:
    authors: []
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: null
    operation:
    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    output:
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format: []
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format: []
    - data:
        term: Disease report
        uri: http://edamontology.org/data_1622
      format: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genetic variation analysis
      uri: http://edamontology.org/operation_3197
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Literature search
      uri: http://edamontology.org/operation_0305
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output: []
  homepage: https://helixinsight.bio
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-24T22:17:23.859555Z'
  license: Proprietary
  link: []
  maturity: Emerging
  name: Helix Insight
  operatingSystem:
  - Linux
  otherID: []
  owner: helenabio
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Human genetics
    uri: http://edamontology.org/topic_3574
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  validated: 0
  version:
  - '3.5'
- accessibility: Open access
  additionDate: '2025-06-25T13:31:29.384393Z'
  biotoolsCURIE: biotools:fantasiav2
  biotoolsID: fantasiav2
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: fmpercan@upo.es
    fundrefid: null
    gridid: null
    name: Francisco Miguel Pérez Canales
    note: Programmer
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    - Support
    - Provider
    url: http://www.bioinfocb.es/
  - email: a.rojas.m@csic.es
    fundrefid: null
    gridid: null
    name: Ana M Rojas Mendoza
    note: Scientific concept and functionalities
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Contributor
    - Documentor
    - Support
    url: http://www.bioinfocb.es/
  - email: rosa.fernandez@ibe.upf-csic.es
    fundrefid: null
    gridid: null
    name: Rosa Fernandez
    note: Scientific concept and functionalities
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    - Documentor
    url: https://www.metazomics.com/
  - email: fraruimot@alum.us.es
    fundrefid: null
    gridid: null
    name: Francisco J. Ruiz Mota
    note: Junior developer
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: http://www.bioinfocb.es/
  - email: gemma.martinez@ibe.upf-csic.es
    fundrefid: null
    gridid: null
    name: Gemma Martinez Redondo
    note: Contributed  as developer of the first version of FANTASIA V1
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    url: https://www.metazomics.com/
  - email: adomrod4@upo.es
    fundrefid: null
    gridid: null
    name: Alex Dominguez Rodriguez
    note: Implemented the LITE version of FANTASIA
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    - Maintainer
    - Documentor
    url: http://www.bioinfocb.es/
  description: FANTASIA (Functional ANnoTAtion based on embedding space SImilArity)
    is a pipeline for protein annotating via GO term transference using the embedding
    space. FANTASIA’s latest developments include additional protein language models
    and provide enhanced functionalities.
  documentation:
  - note: Full documetnation with user cases, benchmarking, and cluster implementations
    type:
    - General
    url: https://fantasia.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors: []
    type: group
  elixirCommunity:
  - 3D-BioInfo
  - Proteomics
  elixirNode:
  - Spain
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene functional annotation
      uri: http://edamontology.org/operation_3672
    output: []
  homepage: https://github.com/CBBIO/
  homepage_status: 0
  language:
  - Python
  - SQL
  lastUpdate: '2026-02-22T21:19:22.986918Z'
  license: MIT
  link:
  - note: Main repository contains documentation  from latest version
    type:
    - Repository
    url: https://github.com/CBBIO/FANTASIA
  - note: Main repository contains documentation  from linitial version based on Bioembeddings
      implementation.
    type:
    - Repository
    url: https://github.com/MetazoaPhylogenomicsLab/FANTASIA
  - note: Recommended tool for the Earth Biogenome Project
    type:
    - Software catalogue
    url: https://www.earthbiogenome.org/report-on-annotation-recommended-tools
  - note: This is the LITE version of FANTASIA for a quick and custom annotation
    type:
    - Software catalogue
    url: https://github.com/CBBIO/FANTASIA-Lite
  - note: This is a repository for FANTASIA-LITE available in Elixir France
    type:
    - Repository
    url: https://gitlab.com/ifb-elixirfr/cluster/tools/-/tree/master/tools/fantasia/0.1.0?ref_type=heads
  maturity: Mature
  name: FANTASIA
  operatingSystem:
  - Linux
  otherID: []
  owner: arojas
  publication:
  - doi: 10.1093/nargab/lqae078
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Usage
    version: null
  - doi: 10.1007/978-1-0716-4623-6_8
    metadata: null
    note: This protocol describes the use of the first version of FANTASIA
    pmcid: null
    pmid: '40601255'
    type:
    - Method
    version: 2.8.0
  - doi: 10.1038/s42003-025-08651-2
    metadata: null
    note: Application of FANTASIA to annotate 24 million of genes of 1000 animal species
    pmcid: PMC12354702
    pmid: '40813894'
    type:
    - Primary
    version: '4.0'
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Molecular evolution
    uri: http://edamontology.org/topic_3945
  - term: Natural language processing
    uri: http://edamontology.org/topic_0218
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  - term: Open science
    uri: http://edamontology.org/topic_4010
  validated: 0
  version:
  - '4.0'
  - LITE
- accessibility: Open access
  additionDate: '2026-02-19T07:51:45.702608Z'
  biotoolsCURIE: biotools:poly_pipeline
  biotoolsID: poly_pipeline
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: pccrvl@gmail.com
    fundrefid: null
    gridid: null
    name: Pedro Cristovão Carvalho
    note: Main developer of the pipeline
    orcidid: https://orcid.org/0000-0001-9242-6911
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    - Maintainer
    - Provider
    - Support
    url: https://cafinvest.com.br/resume.php
  description: A data analysis pipeline for Spatial Transcriptomics data tailored
    to polyploid organisms.
  documentation:
  - note: Github Documentation
    type:
    - User manual
    url: https://github.com/capuccino26/POLY_PIPELINE#poly_pipeline
  download:
  - note: Github Release
    type: Source code
    url: https://github.com/capuccino26/POLY_PIPELINE/releases/tag/v1.0.0
    version: v1.0.0
  editPermission:
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    type: private
  elixirCommunity:
  - Plant Sciences
  elixirNode: []
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: ANALYSIS=1
    input:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format: []
    note: Clustering of GEF files.
    operation:
    - term: Expression profile clustering
      uri: http://edamontology.org/operation_0313
    output:
    - data:
        term: Clustered expression profiles
        uri: http://edamontology.org/data_3768
      format: []
  - cmd: ANALYSIS=3
    input:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format: []
    note: Generation of Nodes and Edges.
    operation:
    - term: Network visualisation
      uri: http://edamontology.org/operation_3925
    output:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format: []
  - cmd: ANALYSIS=0
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
    note: Data converter.
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
  - cmd: ANALYSIS=1
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
    note: Generation of count matrix.
    operation:
    - term: RNA-Seq quantification
      uri: http://edamontology.org/operation_3800
    output:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format: []
  - cmd: ANALYSIS=1
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
    note: Filtering of GEF files.
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
  homepage: https://github.com/capuccino26/POLY_PIPELINE
  homepage_status: 0
  language:
  - R
  - Bash
  - Python
  lastUpdate: '2026-02-19T08:19:12.181956Z'
  license: MIT
  link:
  - note: Github Repository
    type:
    - Repository
    url: https://github.com/capuccino26/POLY_PIPELINE
  - note: Zenodo Insert
    type:
    - Other
    url: https://zenodo.org/records/18655692
  maturity: Mature
  name: Poly Pipeline
  operatingSystem:
  - Linux
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.18655692
    version: v1.0.0
  owner: pedro
  publication:
  - doi: 10.5281/zenodo.18655692
    metadata: null
    note: Zenodo Insertion
    pmcid: null
    pmid: null
    type:
    - Other
    version: v1.0.0
  relation: []
  toolType:
  - Command-line tool
  - Script
  topic:
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version:
  - v1.0.0
- accessibility: null
  additionDate: '2016-08-13T19:15:03Z'
  biotoolsCURIE: biotools:grnsight
  biotoolsID: grnsight
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Ngoc Kim Ngan Tran
    note: null
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    typeRole:
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    url: null
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    fundrefid: null
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    name: Cecilia Zaragoza
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    fundrefid: null
    gridid: null
    name: A’Kaia Phelps
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    typeRole:
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    url: null
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    fundrefid: null
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    typeRole:
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    fundrefid: null
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    fundrefid: null
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    fundrefid: null
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    name: NSF award 0921038; LMU Rains Research Assistant Program; LMU Summer Undergraduate
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    fundrefid: null
    gridid: null
    name: John David N. Dionisio
    note: null
    orcidid: https://orcid.org/0000-0001-8655-4693
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Web application and service for visualizing small- to medium-scale
    models of gene regulatory networks. It automatically lays out either an unweighted
    or weighted network graph based on an Excel input spreadsheet containing an adjacency
    matrix where regulators are named in the columns and target genes in the rows.
    It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges
    and has general applicability.
  documentation:
  - note: null
    type:
    - General
    url: http://dondi.github.io/GRNsight/documentation.html
  download:
  - note: null
    type: Source code
    url: https://github.com/dondi/GRNsight/archive/refs/heads/main.zip
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: GRNsight automatically lays out a network graph based on an Excel input
      spreadsheet containing an adjacency matrix where regulators are named in the
      columns and target genes in the rows. When a user uploads a spreadsheet with
      an unweighted adjacency matrix, GRNsight automatically lays out the graph using
      black lines and pointed arrowheads.  When a user uploads a spreadsheet with
      a weighted adjacency matrix, GRNsight uses pointed and blunt arrowheads, and
      colors the edges and adjusts their thicknesses based on the sign (positive for
      activation or negative for repression) and magnitude of the weight parameter.
      Nodes are rectangular and support gene labels of up to 12 characters.  The edges
      are arcs, which become straight lines when the nodes are close together.  Self-regulatory
      edges are indicated by a loop on the lower-right side of a node. Visualizations
      can be modified by sliders that adjust D3.js's force graph layout parameters
      and through manual node dragging.
    operation:
    - term: Gene regulatory network analysis
      uri: http://edamontology.org/operation_1781
    - term: Pathway or network visualisation
      uri: http://edamontology.org/operation_3083
    output: []
  homepage: http://dondi.github.io/GRNsight/
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2026-02-17T08:19:18.244542Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/dondi/GRNsight
  maturity: Mature
  name: GRNsight
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: dondi@lmu.edu
  publication:
  - doi: 10.7717/peerj-cs.85
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.5281/zenodo.7411630
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Gene regulation
    uri: http://edamontology.org/topic_0204
  validated: 1
  version:
  - 7.4.1
- accessibility: Open access (with restrictions)
  additionDate: '2025-04-15T17:42:40.968987Z'
  biotoolsCURIE: biotools:dicom_file_integrity_checker_by_gibi230
  biotoolsID: dicom_file_integrity_checker_by_gibi230
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: gibi230@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
    gridid: null
    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Documentor
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: 'The tool performs a DICOM quality check in terms of correct number
    of files per sequence, corrupted files, precise directory hierarchy, separated
    dynamic series merging them, interest series filtering/selection by specific series
    description lists and diffusion sequence identification by b-values. It applies
    the desired changes to the dataset and generates a report containing information
    about the selected sequences, corrupted files, missing files and merged files.


    Status: Deployed'
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/LAKqSQZY4Bjqz5W
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/EEqjraK574HrwMf
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=oUebkjLYeSs&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=3
  download:
  - note: EUCAIM user needed
    type: Container file
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab
    version: 2.1.0
  editPermission:
    authors:
    - casopon
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
      \ \\\n  -v \"<output_path>:/output\" \\\n  -v \"<config_path>:/config\" \\\n\
      \  harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_file_integrity_checker:latest"
    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: xlsx
        uri: http://edamontology.org/format_3620
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: For Data Holders (ingestion-tools)
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output:
    - 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: HTML
        uri: http://edamontology.org/format_2331
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: JSON
        uri: http://edamontology.org/format_3464
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
      \ \\\n  -v \"<output_path>:/output\" \\\n  harbor.eucaim.cancerimage.eu/processing-tools/dicom_file_integrity_checker:latest\
      \ \\\n  /app/entrypoint.sh --config-string \"{'QA': {'sequence_selection': ['ALL'],\
      \ 'modality_selection': ['ALL'], 'input_directory': 'dataset_id'}}\""
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: For Data Users (processing-tools)
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output:
    - 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: HTML
        uri: http://edamontology.org/format_2331
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-16T17:32:26.457200Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  - note: Link to EUCAIM's Harbor for Data Holders
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab
  - note: Link to EUCAIM's Harbor for Data Users
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/dicom_file_integrity_checker/artifacts-tab
  maturity: Mature
  name: DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  - term: Data acquisition
    uri: http://edamontology.org/topic_3077
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
  - 2.0.0
  - 2.1.0
  - 2.1.1
- 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: null
  additionDate: '2019-06-20T14:18:28Z'
  biotoolsCURIE: biotools:decompTumor2Sig
  biotoolsID: decompTumor2Sig
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: r.piro@fu-berlin.de
    fundrefid: null
    gridid: null
    name: Prof. Dr. Rosario M. Piro
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: null
  description: R package for identification of mutational signatures active in individual
    tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type
    or Shiraishi-type signatures, thus quantifying the contribution of the corresponding
    mutational processes to the somatic mutations identified in the tumor.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/rmpiro/decompTumor2Sig/blob/master/decompTumor2Sig-manual.pdf
  download:
  - note: null
    type: Downloads page
    url: http://rmpiro.net/index.html#downloads
    version: null
  editPermission:
    authors:
    - ELIXIR-ITA-POLIMI
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Parsing
      uri: http://edamontology.org/operation_1812
    output: []
  homepage: http://rmpiro.net/decompTumor2Sig/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-02-12T13:42:21.288130Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/rmpiro/decompTumor2Sig/issues
  - note: null
    type:
    - Repository
    url: https://github.com/rmpiro/decompTumor2Sig
  - note: null
    type:
    - Software catalogue
    url: https://bioconductor.org/packages/release/bioc/html/decompTumor2Sig.html
  maturity: Mature
  name: decompTumor2Sig
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: rosario7
  publication:
  - doi: 10.1186/s12859-019-2688-6
    metadata:
      abstract: '© 2019 The Author(s).Background: The somatic mutations found in a
        tumor have in most cases been caused by multiple mutational processes such
        as those related to extrinsic carcinogens like cigarette smoke, and those
        related to intrinsic processes like age-related spontaneous deamination of
        5-methylcytosine. The effect of such mutational processes can be modeled by
        mutational signatures, of which two different conceptualizations exist: the
        model introduced by Alexandrov et al., Nature 500:415-421, 2013, and the model
        introduced by Shiraishi et al., PLoS Genetics 11(12):e1005657, 2015. The initial
        identification and definition of mutational signatures requires large sets
        of tumor samples. Results: Here, we present decompTumor2Sig, an easy to use
        R package that can decompose an individual tumor genome into a given set of
        Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution
        of the corresponding mutational processes to the somatic mutations identified
        in the tumor. Until now, such tools were available only for Alexandrov signatures.
        We demonstrate the correctness and usefulness of our approach with three test
        cases, using somatic mutations from 21 breast cancer genomes, from 435 tumor
        genomes of ten different tumor entities, and from simulated tumor genomes,
        respectively. Conclusions: The decompTumor2Sig package is freely available
        and has been accepted for inclusion in Bioconductor.'
      authors:
      - name: Kruger S.
      - name: Piro R.M.
      citationCount: 8
      date: '2019-04-18T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'DecompTumor2Sig: Identification of mutational signatures active in individual
        tumors'
    note: null
    pmcid: PMC6472187
    pmid: '30999866'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - 2.0.0
- accessibility: Open access
  additionDate: '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
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  description: 'The tool is designed to perform a customisable image pre-processing
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  description: A CLI tool for detecting duplicate DICOM images by analyzing pixel
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  description: 'The tool is designed to perform radiomics harmonization on large and
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  description: This preprocessing tool is design for 2D digital mammograms in DICOM  format.
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    note: Command Arguments
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/2d_digital_mammography_harmonization/artifacts-tab
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  name: 2D Digital Mammography Harmonization (EUCAIM-SW-046_T-01-03-008)
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  owner: pedromiguel_martinez_HULAFE
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  topic:
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  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
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  description: A tool based on artificial intelligence that is able to perform a categorisation
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  description: "Tool that aims to validate visually the chronological order and logical\
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  description: The tool performs by deep learning an automatic segmentation of the
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  description: 'The tool performs an automatic segmentation of the possible glioblastoma
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  function:
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  description: The tool performs an automatic segmentation of the possible DIPG tumours
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  description: 'This tool is specifically designed and validated for automated detection
    and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images
    (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs
    in NIFTI or DICOM SEG.


    TRAINING & VALIDATION COHORTS:


    Initial Development (Veiga-Canuto 2022):

    -Training: 106 patients, 5-fold CV (median DSC 0.965 ± 0.018).

    -Internal validation: 26 patients (median DSC 0.918 ± 0.067).

    -Sources: La Fe (Spain), SIOPEN HR-NBL1/LINES, St. Anna (Austria), Pisa (Italy).

    -Mean age: 37.6 ± 39.3 months.

    -Median tumor volume: 116,518 mm³.


    External Validation (Veiga-Canuto 2023):

    -300 patients, 535 independent T2 MRI scans (486 at diagnosis, 49 post-chemotherapy).

    -Performance: median DSC 0.997 (0.944–1.000), 94% successful detection.

    -Sources: 12 European countries (HR-NBL1/SIOPEN 119, LINES/SIOPEN 107, German
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    -Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105),
    Canon (3).'
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  description: A comprehensive collection of the fungal ribosomal RNA Internal Transcribed
    Spacer 1 (ITS1) sequences aimed at supporting metagenomic surveys of fungal environmental
    communities.
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  description: D-GENIES – for Dot plot large Genomes in an Interactive, Efficient
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    url: https://github.com/asvarvara/MitSorter/blob/main/README.md
  download: []
  editPermission:
    authors:
    - sharonnatasha.cox
    type: group
  elixirCommunity:
  - Federated Human Data
  elixirNode:
  - Italy
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://github.com/asvarvara/MitSorter
  homepage_status: 0
  language:
  - Python
  - Shell
  lastUpdate: '2025-12-15T11:29:47.221679Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/asvarvara/MitSorter
  maturity: Emerging
  name: MitSorter
  operatingSystem:
  - Linux
  otherID: []
  owner: asvarvara
  publication:
  - doi: 10.1093/bioadv/vbaf135
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-01-01T00:00:00Z'
      journal: Bioinformatics Advances
      title: 'MitSorter: a standalone tool for accurate discrimination of mtDNA and
        NuMT ONT reads based on differential methylation'
    note: null
    pmcid: PMC12275464
    pmid: '40688360'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Workflow
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  validated: 0
  version: []
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