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  description: RMSX + Flipbook is a molecular dynamics analysis and visualization
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    trajectories. It computes per-residue motion metrics and produces color- and thickness-encoded
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  cost: null
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    fundrefid: null
    gridid: null
    name: Anne S Meyer
    note: null
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    rorid: null
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    url: null
  description: Conserved Unique Peptide Patterns (CUPP) is a approach for sequence
    analysis employing conserved peptide patterns for determination of similarities
    between proteins. CUPP performs unsupervised clustering of proteins for formation
    of protein groups and can be used for fast annotation of enzyme protein family,
    subfamily and EC function of carbohydrate-active enzymes.
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  function:
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    input: []
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    - term: Phylogenetic tree annotation
      uri: http://edamontology.org/operation_0558
    - term: Deposition
      uri: http://edamontology.org/operation_3431
    output: []
  homepage: https://cupp.info
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-26T14:13:04.866330Z'
  license: null
  link: []
  maturity: null
  name: CUPP
  operatingSystem: []
  otherID: []
  owner: Fanrrz
  publication:
  - doi: 10.1093/NAR/GKAA375
    metadata:
      abstract: © The Author(s) 2020. Published by Oxford University Press on behalf
        of Nucleic Acids Research.The CUPP platform includes a web server for functional
        annotation and sub-grouping of carbohydrate active enzymes (CAZymes) based
        on a novel peptide-based similarity assessment algorithm, i.e. protein grouping
        according to Conserved Unique Peptide Patterns (CUPP). This online platform
        is open to all users and there is no login requirement. The web server allows
        the user to perform genome-based annotation of carbohydrate active enzymes
        to CAZy families, CAZy subfamilies, CUPP groups and EC numbers (function)
        via assessment of peptide-motifs by CUPP. The web server is intended for functional
        annotation assessment of the CAZy inventory of prokaryotic and eukaryotic
        organisms from genomic DNA (up to 30MB compressed) or directly from amino
        acid sequences (up to 10MB compressed). The custom query sequences are assessed
        using the CUPP annotation algorithm, and the outcome is displayed in interactive
        summary result pages of CAZymes. The results displayed allow for inspection
        of members of the individual CUPP groups and include information about experimentally
        characterized members. The web server and the other resources on the CUPP
        platform can be accessed from https://cupp.info.
      authors:
      - name: Barrett K.
      - name: Hunt C.J.
      - name: Lange L.
      - name: Meyer A.S.
      citationCount: 4
      date: '2020-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'Conserved unique peptide patterns (CUPP) online platform: Peptide-based
        functional annotation of carbohydrate active enzymes'
    note: null
    pmcid: PMC7319580
    pmid: '32406917'
    type: []
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Carbohydrates
    uri: http://edamontology.org/topic_0152
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Enzymes
    uri: http://edamontology.org/topic_0821
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: DNA
    uri: http://edamontology.org/topic_0654
  validated: 0
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2026-02-26T12:47:29.542367Z'
  biotoolsCURIE: biotools:inflexa
  biotoolsID: inflexa
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    note: null
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    typeEntity: null
    typeRole:
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    url: null
  description: Inflexa is a semi-autonomous analysis agent for multi-omics, cheminformatics,
    and imaging data. It reads the literature, generates hypotheses from both published
    work and the dataset, runs multiple analytical methods per step, compares results,
    and traces every finding back to source. The agent tests more hypotheses than
    manual analysis typically covers, including ones that weren't pre-specified. Every
    checkpoint is reviewable. Every result links to the input data, code version,
    and parameters that produced it. Reports include publication-ready figures, reproducible
    code, and full audit trails. Accepts RNA-seq counts, proteomics tables, VCF files,
    metabolomics peak lists, compound screens, imaging data, and more.
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  function:
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    operation:
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      uri: http://edamontology.org/operation_2945
    output: []
  homepage: https://inflexa.ai
  homepage_status: 0
  language:
  - Python
  - TypeScript
  - Go
  lastUpdate: '2026-02-26T13:03:10.946329Z'
  license: Proprietary
  link:
  - note: Fluoxetine in H460 Lung Cancer (Re-analysis of GSE200209)
    type:
    - Other
    url: https://public.inflexa.ai/GSE200209/fluoxetine-er-stress-nsclc
  - note: Pharmacogenomic Drug Screen in Mouse Cerebrocortical Cultures (Re-analysis
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    type:
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    url: https://public.inflexa.ai/GSE110256/pharmacogenomic-mouse-cerebrocortical-cultures
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      Inflammation (Re-analysis of GSE282861)
    type:
    - Other
    url: https://public.inflexa.ai/GSE282861/il-33-il-4ra-blockade-hdm-airway-inflammation
  - note: How Genetic Ancestry Shapes Breast Cancer Biology (Re-analysis of Roelands
      et al. 2021 (npj Breast Cancer) )
    type:
    - Other
    url: https://public.inflexa.ai/33558495/breast-cancer-african-arab-european-ancestry
  - note: ATG7 Deficiency Reshapes Microglia Biology in Alzheimer’s Disease (Re-analysis
      of GSE286094 / GSE286095)
    type:
    - Other
    url: https://public.inflexa.ai/GSE286094-GSE286095/atg7-deficiency-reshapes-microglia-biology-alzheimers-disease
  - note: Atopic Dermatitis Transcriptome Under Dupilumab and Cyclosporine (Re-analysis
      of GSE157194)
    type:
    - Other
    url: https://public.inflexa.ai/GSE157194/atopic-dermatitis-dupilumab-cyclosporine
  maturity: null
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  - Linux
  - Mac
  otherID: []
  owner: radu.tanasa
  publication: []
  relation: []
  toolType:
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  - Web application
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Cheminformatics
    uri: http://edamontology.org/topic_2258
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Natural language processing
    uri: http://edamontology.org/topic_0218
  - term: Omics
    uri: http://edamontology.org/topic_3391
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2021-05-06T06:18:52Z'
  biotoolsCURIE: biotools:pangenome-blast
  biotoolsID: pangenome-blast
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Bielefeld University
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uni-bielefeld.de/
  - email: null
    fundrefid: null
    gridid: null
    name: Genome Informatics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://gi.cebitec.uni-bielefeld.de/
  - email: plast-service@cebitec.uni-bielefeld.de
    fundrefid: null
    gridid: null
    name: Tizian Schulz
    note: null
    orcidid: https://orcid.org/0000-0003-0744-7078
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  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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  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: Open access
  additionDate: '2016-12-19T14:29:34Z'
  biotoolsCURIE: biotools:cuffcompare
  biotoolsID: cuffcompare
  collectionID:
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  - galaxyPasteur
  confidence_flag: null
  cost: null
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    fundrefid: null
    gridid: null
    name: Galaxy Support Team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Compare assembled transcripts to a reference annotation and track Cufflinks
    transcripts across multiple experiments.
  documentation:
  - note: null
    type:
    - General
    url: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/
  download: []
  editPermission:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: GFF3
        uri: http://edamontology.org/format_1975
      - term: GTF
        uri: http://edamontology.org/format_2306
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: GTF
        uri: http://edamontology.org/format_2306
  homepage: http://cole-trapnell-lab.github.io/cufflinks/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-02-26T11:14:58.790920Z'
  license: null
  link:
  - note: null
    type:
    - Galaxy service
    url: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/cuffcompare/cuffcompare/2.2.1.0
  maturity: Mature
  name: cuffcompare
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: hmenager
  publication:
  - doi: 10.1038/nbt.1621
    metadata: null
    note: null
    pmcid: PMC3146043
    pmid: '20436464'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkw343
    metadata: null
    note: null
    pmcid: PMC4987906
    pmid: '27137889'
    type:
    - Other
    version: null
  - doi: 10.7490/f1000research.1114334.1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - 2.2.1.0
- 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:
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  otherID:
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  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: Open access
  additionDate: '2021-04-21T22:48:24Z'
  biotoolsCURIE: biotools:open-cravat
  biotoolsID: open-cravat
  collectionID:
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  - Rare disease
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    gridid: null
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    note: null
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    typeEntity: null
    typeRole: []
    url: null
  - email: null
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    rorid: null
    typeEntity: null
    typeRole: []
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  - email: null
    fundrefid: null
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    name: Kyle Moad
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Rachel Karchin
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
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  description: OpenCRAVAT is a new open source, scalable decision support system to
    support variant and gene prioritization. It offers a dynamic GUI, allowing users
    to easily, download tools from an extensive resource catalog, create customized
    pipelines, run jobs at speeds that exceed current variant annotation API services,
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    from similar tools by the amount and diversity of data resources and computational
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    open and modular to maximize community and developer involvement, and as a result
    the catalog is being actively developed and growing larger every month.
  documentation:
  - note: null
    type:
    - General
    - API documentation
    - Installation instructions
    - Quick start guide
    - User manual
    url: https://docs.opencravat.org/en/latest/index.html
  download:
  - note: null
    type: Downloads page
    url: https://github.com/KarchinLab/open-cravat/releases/
    version: null
  - note: null
    type: Container file
    url: https://hub.docker.com/r/karchinlab/opencravat
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  editPermission:
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    type: group
  elixirCommunity: []
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  function:
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    input:
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        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
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        uri: http://edamontology.org/format_3016
    note: 'Additional input formats include: list of dbSNP rsIDs, HGVS annotation,
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      Output is also in text, excel, and a SQLite database. The SQLIte database format
      can be loaded into `oc gui` as an interactive web application'
    operation:
    - term: Variant calling
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    - term: SNP annotation
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    - term: Variant effect prediction
      uri: http://edamontology.org/operation_0331
    - term: Genetic variation analysis
      uri: http://edamontology.org/operation_3197
    - term: Gene functional annotation
      uri: http://edamontology.org/operation_3672
    - term: Variant prioritisation
      uri: http://edamontology.org/operation_3226
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: https://opencravat.org
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-18T22:04:46.355009Z'
  license: MIT
  link:
  - note: Web server for running the current version of OpenCRAVAT without needing
      a local installation.
    type:
    - Service
    url: https://run.opencravat.org/
  - note: null
    type:
    - Repository
    url: https://github.com/KarchinLab/open-cravat
  - note: Catalogue of modules for OpenCRAVAT, including annotators, variant effect
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    type:
    - Software catalogue
    url: https://run.opencravat.org/submit/nocache/index.html
  maturity: Mature
  name: open-cravat
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: rachel2
  publication:
  - doi: 10.1200/cci.19.00132
    metadata: null
    note: null
    pmcid: PMC7113103
    pmid: '32228266'
    type: []
    version: null
  relation: []
  toolType:
  - Web API
  - Web application
  - Command-line tool
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Structural variation
    uri: http://edamontology.org/topic_3175
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Exome sequencing
    uri: http://edamontology.org/topic_3676
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  validated: 0
  version:
  - 2.16.0
  - 2.17.0
- accessibility: Open access
  additionDate: '2026-02-17T16:37:44.602133Z'
  biotoolsCURIE: biotools:hierarchical_matrix_layout_and_annotation_software_himalayas
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  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: A Python framework for post hoc enrichment-based annotation of hierarchically
    clustered matrices across biological and non-biological domains.
  documentation:
  - note: null
    type:
    - User manual
    url: https://himalayas-base.github.io/himalayas-docs/
  download:
  - note: null
    type: Software package
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  editPermission:
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  function:
  - cmd: null
    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_3432
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Enrichment analysis
      uri: http://edamontology.org/operation_3501
    output: []
  homepage: https://github.com/himalayas-base/himalayas
  homepage_status: 0
  language:
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  lastUpdate: '2026-02-17T16:41:20.656177Z'
  license: BSD-3-Clause
  link: []
  maturity: Mature
  name: Hierarchical Matrix Layout and Annotation Software (HiMaLAYAS)
  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: ira
  publication:
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    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Function analysis
    uri: http://edamontology.org/topic_1775
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Bioinformatics
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  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-02-17T16:25:26.383789Z'
  biotoolsCURIE: biotools:regional_inference_of_significant_kinships_risk
  biotoolsID: regional_inference_of_significant_kinships_risk
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  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: A scalable Python tool for biological network annotation and visualization.
  documentation:
  - note: null
    type:
    - User manual
    url: https://riskportal.github.io/risk-docs/
  download:
  - note: null
    type: Software package
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  function:
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    input: []
    note: null
    operation:
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    output: []
  - cmd: null
    input: []
    note: null
    operation:
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    output: []
  - cmd: null
    input: []
    note: null
    operation:
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    output: []
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    input: []
    note: null
    operation:
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  homepage: https://github.com/riskportal/risk
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  language:
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  lastUpdate: '2026-02-17T16:31:30.082840Z'
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  link: []
  maturity: Mature
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  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: ira
  publication:
  - doi: 10.1093/bioinformatics/btaf669
    metadata: null
    note: null
    pmcid: PMC12766918
    pmid: '41423796'
    type:
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    version: null
  relation: []
  toolType:
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  topic:
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  - term: Computational biology
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  - term: Systems biology
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- accessibility: Open access
  additionDate: '2017-07-20T18:33:51Z'
  biotoolsCURIE: biotools:wikipathways
  biotoolsID: wikipathways
  collectionID:
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  - Rare Disease
  - BIGCAT-UM
  - RD-connect
  confidence_flag: null
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    gridid: null
    name: Martina Kutmon
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    rorid: null
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    typeRole:
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  - email: null
    fundrefid: null
    gridid: null
    name: Egon Willighagen
    note: null
    orcidid: https://orcid.org/0000-0001-7542-0286
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: apico@gladstone.ucsf.edu
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    note: null
    orcidid: null
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    typeEntity: Person
    typeRole:
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  description: WikiPathways is a database of biological pathways maintained by and
    for the scientific community.
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    type:
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    url: https://www.wikipathways.org/index.php/WikiPathways
  - note: null
    type:
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  download:
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  function:
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    input:
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    note: getPathway
    operation:
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    - term: Data retrieval
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    output:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: XML
        uri: http://edamontology.org/format_2332
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  homepage_status: 0
  language:
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  lastUpdate: '2026-02-17T12:05:57.404853Z'
  license: Apache-2.0
  link:
  - note: GitHub Organization
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    - Repository
    url: https://github.com/wikipathways/
  - note: null
    type:
    - Social media
    url: https://fosstodon.org/@wikipathways
  maturity: Mature
  name: WikiPathways
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: ChrisEvelo
  publication:
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    metadata: null
    note: null
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    type:
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    note: null
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    pmid: '33211851'
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    metadata: null
    note: null
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    metadata: null
    note: null
    pmcid: PMC10767877
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    type: uses
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  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 1
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- accessibility: Open access
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  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Chris Burge
    note: null
    orcidid: null
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  description: A tool for predicting the locations and exon-intron structures of genes
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  - note: null
    type:
    - General
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    note: null
    operation:
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  publication:
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    metadata:
      abstract: We introduce a general probabilistic model of the gene structure of
        human genomic sequences which incorporates descriptions of the basic transcriptional,
        translational and splicing signals, as well as length distributions and compositional
        features of exons, introns and intergenic regions. Distinct sets of model
        parameters are derived to account for the many substantial differences in
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        of the human genome. in addition, new models of the donor and acceptor splice
        signals are described which capture potentially important dependencies between
        signal positions. The model is applied to the problem of gene identification
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        DNA strands. GENSCAN is shown to have substantially higher accuracy than existing
        methods when tested on standardized sets of human and vertebrate genes, with
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        fairly accurately the reliability of each predicted exon. Consistently high
        levels of accuracy are observed for sequences of differing C + G content and
        for distinct groups of vertebrates.
      authors:
      - name: Burge C.
      - name: Karlin S.
      citationCount: 2866
      date: '1997-04-25T00:00:00Z'
      journal: Journal of Molecular Biology
      title: Prediction of complete gene structures in human genomic DNA
    note: null
    pmcid: null
    pmid: '9149143'
    type:
    - Primary
    version: null
  relation: []
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  topic:
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    uri: http://edamontology.org/topic_3512
  - term: Gene structure
    uri: http://edamontology.org/topic_0114
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Genomics
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  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2017-03-24T09:34:05Z'
  biotoolsCURIE: biotools:vista
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    gridid: null
    name: Vista Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: Comprehensive suite of programs and databases for comparative analysis
    of genomic sequences. There are two ways of using VISTA - you can submit your
    own sequences and alignments for analysis (VISTA servers) or examine pre-computed
    whole-genome alignments of different species.
  documentation:
  - note: null
    type:
    - General
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  download: []
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  - cmd: null
    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_0491
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    - term: Global alignment
      uri: http://edamontology.org/operation_0496
    output: []
  homepage: http://genome.lbl.gov/vista/index.shtml
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2026-02-17T10:10:39.922919Z'
  license: null
  link: []
  maturity: Mature
  name: VISTA
  operatingSystem:
  - Linux
  - Windows
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  publication:
  - doi: 10.1093/bioinformatics/btg459
    metadata:
      abstract: 'Motivation: The power of multi-sequence comparison for biological
        discovery is well established. The need for new capabilities to visualize
        and compare cross-species alignment data is intensified by the growing number
        of genomic sequence datasets being generated for an ever-increasing number
        of organisms. To be efficient these visualization algorithms must support
        the ability to accommodate consistently a wide range of evolutionary distances
        in a comparison framework based upon phylogenetic relationships. Results:
        We have developed Phylo-VISTA, an interactive tool for analyzing multiple
        alignments by visualizing a similarity measure for multiple DNA sequences.
        The complexity of visual presentation is effectively organized using a framework
        based upon interspecies phylogenetic relationships. The phylogenetic organization
        supports rapid, user-guided interspecies comparison. To aid in navigation
        through large sequence datasets, Phylo-VISTA leverages concepts from VISTA
        that provide a user with the ability to select and view data at varying resolutions.
        The combination of multiresolution data visualization and analysis, combined
        with the phylogenetic framework for interspecies comparison, produces a highly
        flexible and powerful tool for visual data analysis of multiple sequence alignments.
        © Oxford University Press 2004; all rights reserved.'
      authors:
      - name: Shah N.
      - name: Couronne O.
      - name: Pennacchio L.A.
      - name: Brudno M.
      - name: Batzoglou S.
      - name: Bethel E.W.
      - name: Rubin E.M.
      - name: Hamann B.
      - name: Dubchak I.
      citationCount: 34
      date: '2004-03-22T00:00:00Z'
      journal: Bioinformatics
      title: 'Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments'
    note: null
    pmcid: null
    pmid: '15033870'
    type: []
    version: null
  - doi: 10.1093/nar/gkm279
    metadata:
      abstract: The VISTA portal for comparative genomics is designed to give biomedical
        scientists a unified set of tools to lead them from the raw DNA sequences
        through the alignment and annotation to the visualization of the results.
        The VISTA portal also hosts the alignments of a number of genomes computed
        by our group, allowing users to study the regions of their interest without
        having to manually download the individual sequences. Here we describe various
        algorithmic and functional improvements implemented in the VISTA portal over
        the last 2 years. The VISTA Portal is accessible at http://genome.lbl.gov/vista.
        © 2007 The Author(s).
      authors:
      - name: Brudno M.
      - name: Poliakov A.
      - name: Minovitsky S.
      - name: Ratnere I.
      - name: Dubchak I.
      citationCount: 26
      date: '2007-07-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: Multiple whole genome alignments and novel biomedical applications at
        the VISTA portal
    note: null
    pmcid: PMC1933192
    pmid: '17488840'
    type: []
    version: null
  - doi: 10.1093/bioinformatics/btg1005
    metadata:
      abstract: 'Motivation: To compare entire genomes from different species, biologists
        increasingly need alignment methods that are efficient enough to handle long
        sequences, and accurate enough to correctly align the conserved biological
        features between distant species. The two main classes of pain/vise alignments
        are global alignment, where one string is transformed into the other, and
        local alignment, where all locations of similarity between the two strings
        are returned. Global alignments are less prone to demonstrating false homology
        as each letter of one sequence is constrained to being aligned to only one
        letter of the other. Local alignments, on the other hand, can cope with rearrangements
        between non-syntenic, orthologous sequences by identifying similar regions
        in sequences; this, however, comes at the expense of a higher false positive
        rate due to the inability of local aligners to take into account overall conservation
        maps. Results: In this paper we introduce the notion of glocal alignment,
        a combination of global and local methods, where one creates a map that transforms
        one sequence into the other while allowing for rearrangement events. We present
        Shuffle-LAGAN, a glocal alignment algorithm that is based on the CHAOS local
        alignment algorithm and the LAGAN global aligner, and is able to align long
        genomic sequences. To test Shuffle-LAGAN we split the mouse genome into BAC-sized
        pieces, and aligned these pieces to the human genome. We demonstrate that
        Shuffle-LAGAN compares favorably in terms of sensitivity and specificity with
        standard local and global aligners. From the alignments we conclude that about
        9% of human/mouse homology may be attributed to small rearrangements, 63%
        of which are duplications. Availability: Our systems, supplemental information,
        and the alignment of the human and mouse genomes using Shuffle-LAGAN are available
        at http://lagan.stanford.edu/glocal. © Oxford University Press 2003; all rights
        reserved.'
      authors:
      - name: Brudno M.
      - name: Malde S.
      - name: Poliakov A.
      - name: Do C.B.
      - name: Couronne O.
      - name: Dubchak I.
      - name: Batzoglou S.
      citationCount: 238
      date: '2003-12-01T00:00:00Z'
      journal: Bioinformatics
      title: 'Glocal alignment: Finding rearrangements during alignment'
    note: null
    pmcid: null
    pmid: '12855437'
    type: []
    version: null
  - doi: 10.1093/bioinformatics/16.11.1046
    metadata:
      abstract: VISTA is a program for visualizing global DNA sequence alignments
        of arbitrary length. It has a clean output, allowing for easy identification
        of similarity, and is easily configurable, enabling the visualization of alignments
        of various lengths at different levels of resolution. It is currently available
        on the web, thus allowing for easy access by all researchers.
      authors:
      - name: Mayor C.
      - name: Brudno M.
      - name: Schwartz J.R.
      - name: Poliakov A.
      - name: Rubin E.M.
      - name: Frazer K.A.
      - name: Pachter L.S.
      - name: Dubchak I.
      citationCount: 736
      date: '2000-01-01T00:00:00Z'
      journal: Bioinformatics
      title: 'Vista: Visualizing global DNA sequence alignments of arbitrary length'
    note: null
    pmcid: null
    pmid: '11159318'
    type: []
    version: null
  - doi: 10.1101/gr.789803
    metadata:
      abstract: In this paper we describe a new global alignment method called AVID.
        The method is designed to be fast, memory efficient, and practical for sequence
        alignments of large genomic regions up to megabases long. We present numerous
        applications of the method, ranging from the comparison of assemblies to alignment
        of large syntenic genomic regions and whole genome human/mouse alignments.
        We have also performed a quantitative comparison of AVID with other popular
        alignment tools. To this end, we have established a format for the representation
        of alignments and methods for their comparison. These formats and methods
        should be useful for future studies. The tools we have developed for the alignment
        comparisons, as well as the AVID program, are publicly available. See Web
        Site References section for AVID Web address and Web addresses for other programs
        discussed in this paper.
      authors:
      - name: Bray N.
      - name: Dubchak I.
      - name: Pachter L.
      citationCount: 350
      date: '2003-01-01T00:00:00Z'
      journal: Genome research
      title: 'AVID: A global alignment program.'
    note: null
    pmcid: PMC430967
    pmid: '12529311'
    type: []
    version: null
  - doi: 10.1101/gr.926603
    metadata:
      abstract: To compare entire genomes from different species, biologists increasingly
        need alignment methods that are efficient enough to handle long sequences,
        and accurate enough to correctly align the conserved biological features between
        distant species. We present LAGAN, a system for rapid global alignment of
        two homologous genomic sequences, and Multi-LAGAN, a system for multiple global
        alignment of genomic sequences. We tested our systems on a data set consisting
        of greater than 12 Mb of high-quality sequence from 12 vertebrate species.
        All the sequence was derived from the genomic region orthologous to an ∼1.5-Mb
        region on human chromosome 7q31.3. We found that both LAGAN and Multi-LAGAN
        compare favorably with other leading alignment methods in correctly aligning
        protein-coding exons, especially between distant homologs such as human and
        chicken, or human and fugu. Multi-LAGAN produced the most accurate alignments,
        while requiring just 75 minutes on a personal computer to obtain the multiple
        alignment of all 12 sequences. Multi-LAGAN is a practical method for generating
        multiple alignments of long genomic sequences at any evolutionary distance.
        Our systems are publicly available at http://lagan.stanford.edu.
      authors:
      - name: Brudno M.
      - name: Do C.B.
      - name: Cooper G.M.
      - name: Kim M.F.
      - name: Davydov E.
      - name: Green E.D.
      - name: Sidow A.
      - name: Batzoglou S.
      citationCount: 803
      date: '2003-04-01T00:00:00Z'
      journal: Genome Research
      title: 'LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment
        of genomic DNA'
    note: null
    pmcid: PMC430158
    pmid: '12654723'
    type: []
    version: null
  - doi: 10.1093/nar/gkh458
    metadata:
      abstract: Comparison of DNA sequences from different species is a fundamental
        method for identifying functional elements in genomes. Here, we describe the
        VISTA family of tools created to assist biologists in carrying out this task.
        Our first VISTA server at http://www-gsd.Ibl.gov/vista/ was launched in the
        summer of 2000 and was designed to align long genomic sequences and visualize
        these alignments with associated functional annotations. Currently the VISTA
        site includes multiple comparative genomics tools and provides users with
        rich capabilities to browse pre-computed whole-genome alignments of large
        vertebrate genomes and other groups of organisms with VISTA Browser, to submit
        their own sequences of interest to several VISTA servers for various types
        of comparative analysis and to obtain detailed comparative analysis results
        for a set of cardiovascular genes. We illustrate capabilities of the VISTA
        site by the analysis of a 180 kb interval on human chromosome 5 that encodes
        for the kinesin family member 3A (KIF3A) protein. © Oxford University Press
        2004; all rights reserved.
      authors:
      - name: Frazer K.A.
      - name: Pachter L.
      - name: Poliakov A.
      - name: Rubin E.M.
      - name: Dubchak I.
      citationCount: 1303
      date: '2004-07-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'VISTA: Computational tools for comparative genomics'
    note: null
    pmcid: PMC441596
    pmid: '15215394'
    type: []
    version: null
  - doi: 10.1093/nar/gkl822
    metadata:
      abstract: Despite the known existence of distant-acting cis-regulatory elements
        in the human genome, only a small fraction of these elements has been identified
        and experimentally characterized in vivo. This paucity of enhancer collections
        with defined activities has thus hindered computational approaches for the
        genome-wide prediction of enhancers and their functions. To fill this void,
        we utilize comparative genome analysis to identify candidate enhancer elements
        in the human genome coupled with the experimental determination of their in
        vivo enhancer activity in transgenic mice [L. A. Pennacchio et al. (2006)
        Nature, in press]. These data are available through the VISTA Enhancer Browser
        (http://enhancer.lbl.gov). This growing database currently contains over 250
        experimentally tested DNA fragments, of which more than 100 have been validated
        as tissue-specific enhancers. For each positive enhancer, we provide digital
        images of whole-mount embryo staining at embryonic day 11.5 and an anatomical
        description of the reporter gene expression pattern. Users can retrieve elements
        near single genes of interest, search for enhancers that target reporter gene
        expression to a particular tissue, or download entire collections of enhancers
        with a defined tissue specificity or conservation depth. These experimentally
        validated training sets are expected to provide a basis for a wide range of
        downstream computational and functional studies of enhancer function. © 2007
        Oxford University Press.
      authors:
      - name: Visel A.
      - name: Minovitsky S.
      - name: Dubchak I.
      - name: Pennacchio L.A.
      citationCount: 589
      date: '2007-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: VISTA Enhancer Browser - A database of tissue-specific human enhancers
    note: null
    pmcid: PMC1716724
    pmid: '17130149'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Database portal
  topic:
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 1
  version: []
- 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:
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    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: '2026-02-12T16:06:53.794717Z'
  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
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  description: This tool calculates segmentation metrics (Dice score, intersection
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      config_path:/config harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0
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        term: Text data
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    - data:
        term: Text data
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      format:
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        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Clustering
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    output:
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        term: Text data
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      format:
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      - term: xlsx
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      - term: xlsx
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    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: TIDE TXT
        uri: http://edamontology.org/format_3835
  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0
      --file_path /input/data.xlsx --identifier patient_id --start_col original_shape_Elongation
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      /output/results --min_clusters 2 --max_clusters 100 --results full --approach
      soft --small_groups merge
    input:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    note: null
    operation:
    - term: Clustering
      uri: http://edamontology.org/operation_3432
    output:
    - data:
        term: Text data
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      format:
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    - data:
        term: Text data
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      format:
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      - term: xlsx
        uri: http://edamontology.org/format_3620
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: TIDE TXT
        uri: http://edamontology.org/format_3835
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/artifacts-tab
  homepage_status: 0
  language:
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  lastUpdate: '2026-02-03T12:10:11.102129Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/artifacts-tab
  - note: null
    type:
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  maturity: Emerging
  name: Cluster based harmonization (EUCAIM-SW-044_T-01-03-006)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: casopon
  publication: []
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  toolType:
  - Library
  topic:
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  validated: 0
  version:
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- accessibility: Open access (with restrictions)
  additionDate: '2025-06-06T10:00:26.469620Z'
  biotoolsCURIE: biotools:2d_digital_mammography_harmonization
  biotoolsID: 2d_digital_mammography_harmonization
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
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    name: GIBI230 - HULAFE
    note: null
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    typeRole: []
    url: null
  - email: manuel_marfil@iislafe.es
    fundrefid: null
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    name: Manuel Marfil-Trujillo
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    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
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    typeRole:
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  description: This preprocessing tool is design for 2D digital mammograms in DICOM  format.
    It standardizes and harmonizes images through a configurable pipeline that includes
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    optional denoising, contrast enhancement, and mask processing (if available).
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/CC3yJTjPz9N7Ggg
  - note: null
    type:
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    url: https://drive.eucaim.cancerimage.eu/s/rdHWqMkNf7frQRY
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=IrZhMp2lB7g&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=13
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        term: Image
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    note: null
    operation:
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    output:
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      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/processing-tools/2d_digital_mammography_harmonization:1.1.0
      --input_directory dataset_id --output_directory gaussian_output --num_workers
      4 --series_number 2301101 --series_description_suffix _harmonized --zscore_enabled
      true --zscore_p_low 1.0 --zscore_p_high 99.0 --denoise_method gaussian --gaussian_ksize
      3 --gaussian_sigma 0.8 --clahe_enabled true --clahe_clip_limit 0.01
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Command Arguments
    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/2d_digital_mammography_harmonization/artifacts-tab
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  lastUpdate: '2026-02-03T12:05:59.818541Z'
  license: CC-BY-NC-ND-4.0
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    type:
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  maturity: Emerging
  name: 2D Digital Mammography Harmonization (EUCAIM-SW-046_T-01-03-008)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication: []
  relation: []
  toolType:
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  topic:
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
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- accessibility: Open access (with restrictions)
  additionDate: '2025-11-25T09:58:37.569343Z'
  biotoolsCURIE: biotools:ml_model_for_mr_series_categorisation
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    rorid: null
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    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
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    name: Leonor Cerda-Alberich
    note: null
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    rorid: null
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    url: null
  description: A tool based on artificial intelligence that is able to perform a categorisation
    of MRI series by using standardized DICOM tags. The categorisation includes the
    type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W,
    DCE, ...), the presence of fat suppression and the detection of non-relevant /
    junk series (e.g. localizers, calibrations, screenshots...).
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/rpm56rD5FfXAHyb
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/8r3CzyQXrd7ERFp
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=gudDCiuJIf8&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=11
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  editPermission:
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  function:
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      \ \\\n  -v \"<output_path>:/output\" \\\n  harbor.eucaim.cancerimage.eu/processing-tools/ml_model_for_mr_series_categorisation:<version>\
      \ \\\n  --config-string \"{'output_name': 'classification_results.json'}\""
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
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        uri: http://edamontology.org/format_3548
    note: null
    operation:
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      format:
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        uri: http://edamontology.org/format_3464
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab
  homepage_status: 0
  language:
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  lastUpdate: '2026-02-03T12:02:23.334589Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab
  - note: null
    type:
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    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: ML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication:
  - doi: 10.1186/s40537-025-01086-w
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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  relation: []
  toolType:
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  topic:
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  - term: Data acquisition
    uri: http://edamontology.org/topic_3077
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
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- accessibility: Open access (with restrictions)
  additionDate: '2025-11-21T13:49:36.578343Z'
  biotoolsCURIE: biotools:time_coherence_tool
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  cost: Free of charge (with restrictions)
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    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
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    name: Adrian Galiana-Bordera
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  description: "Tool that aims to validate visually the chronological order and logical\
    \ consistency of dates associated with a patient's medical history. It generates\
    \ a timeline visualization for each patient from an Excel file and highlights\
    \ rule violations.\n \nStatus : Containerized"
  documentation:
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    type:
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    url: https://drive.eucaim.cancerimage.eu/s/M23wDa4RWXenzxX
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/9QbdWjnLBeMYSWR
  - note: null
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    url: https://www.youtube.com/watch?v=j4J_UPQqYR4&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=10
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  function:
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    input:
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    note: null
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/time_coherence_tool/artifacts-tab
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  lastUpdate: '2026-02-03T12:00:24.202390Z'
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  maturity: Emerging
  name: Time Coherence Tool (EUCAIM-SW-001_T-01-01-001)
  operatingSystem:
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  - Mac
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  otherID: []
  owner: casopon
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  toolType:
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  topic:
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  - term: Computer science
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  validated: 0
  version:
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  additionDate: '2025-05-29T10:38:08.771699Z'
  biotoolsCURIE: biotools:ct-based_neuroblastoma_tumour_detection_and_segmentation
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  description: The tool performs by deep learning an automatic segmentation of the
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    architecture is Unet-based with residual operations, atrous dilation convolution
    and specific batch generator. It applies preprocessing steps as RAS conversion,
    resizing, z-score normalization, patching; and postprocessing operations. It takes
    DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.
  documentation:
  - note: null
    type:
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    url: https://drive.eucaim.cancerimage.eu/s/GxJrJPrYBnzecqT
  - note: null
    type:
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    url: https://www.youtube.com/watch?v=JQ0dtAE_6uc&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=37
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  function:
  - cmd: "docker run --rm --gpus all \\\n\t-v /path/to/input:/input \\\n\t-v /path/to/output:/output\
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      \ \\\n\t--series_csv /output/config/series_to_segment.csv \\\n\t--output_dir\
      \ /output"
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      - term: nii
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    note: null
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    metadata: null
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  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
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  additionDate: '2025-05-29T12:09:16.704255Z'
  biotoolsCURIE: biotools:mr-based_glioblastoma_tumour_detection_and_segmentation
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  description: 'The tool performs an automatic segmentation of the possible glioblastoma
    tumours on MRI images and its subregions: necrosis (Intratumoral necrotic core),
    edema (Peritumoral vasogenic edema), enhancing (Contrast-enhancing tumor region),
    total (Total tumor including edema and necrosis by a single model) and total-fused
    (Total tumor fusioning of necrosis+edema+enhancing). It applies preprocessing
    steps as skull stripping, intra-patient registration, z-score normalization, patching,
    among others. It takes DICOM images as input and generates tumoral masks in DICOM
    SEG or NIFTI formats.'
  documentation:
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  description: The tool performs an automatic segmentation of the possible DIPG tumours
    on MR images. DIPG (Diffuse Intrinsic Pontine Glioma), or more recently, DMG (Diffuse
    Midline Glioma) is a H3 K27M–mutant pediatric brainstem cancer detected in T1W
    and Flair/T2-weighted magnetic resonance images. The tool includes a complete
    workflow from DICOM images to DICOM seg tumoral masks.
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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
    Registry 62, others 12).

    -Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105),
    Canon (3).'
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      \ \\\n  --gpus all \\\n  harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0\
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    type: private
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  function: []
  homepage: https://github.com/F0nz0/NanoSpeech_basecaller
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-30T01:11:47.413342Z'
  license: CC-BY-NC-4.0
  link: []
  maturity: Emerging
  name: NanoSpeech_basecaller
  operatingSystem:
  - Linux
  otherID: []
  owner: adriano
  publication:
  - doi: 10.1093/bib/bbaf709
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: 0.0.1
  relation: []
  toolType:
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  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2021-05-08T17:25:21Z'
  biotoolsCURIE: biotools:bakta
  biotoolsID: bakta
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: oliver.schwengers@cb.jlug.de
    fundrefid: null
    gridid: null
    name: Oliver Schwengers
    note: null
    orcidid: https://orcid.org/0000-0003-4216-2721
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://github.com/oschwengers
  - email: null
    fundrefid: null
    gridid: null
    name: Justus Liebig University Giessen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uni-giessen.de
  description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/oschwengers/bakta/blob/main/README.md
  - note: null
    type:
    - Contributions policy
    url: https://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.md
  - note: null
    type:
    - Code of conduct
    url: https://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.md
  - note: null
    type:
    - User manual
    url: https://bakta.readthedocs.io/
  download:
  - note: Mandatory annotation database
    type: Other
    url: https://zenodo.org/records/14916843
    version: v6.0
  editPermission:
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  elixir_badge: 0
  function:
  - cmd: bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fasta
    input:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence features metadata
        uri: http://edamontology.org/data_2914
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF3
        uri: http://edamontology.org/format_1975
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Hidden Markov model
        uri: http://edamontology.org/data_1364
      format:
      - term: HMMER3
        uri: http://edamontology.org/format_3329
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output:
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: GenBank format
        uri: http://edamontology.org/format_1936
      - term: GFF3
        uri: http://edamontology.org/format_1975
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Nucleic acid sequence record
        uri: http://edamontology.org/data_2887
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://github.com/oschwengers/bakta
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-01-29T12:11:19.042627Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/oschwengers/bakta
  - note: null
    type:
    - Issue tracker
    url: https://github.com/oschwengers/bakta/issues
  - note: null
    type:
    - Other
    url: https://bioconda.github.io/recipes/bakta/README.html
  - note: null
    type:
    - Service
    url: https://bakta.computational.bio
  maturity: Mature
  name: Bakta
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: oschwengers
  publication:
  - doi: 10.1099/mgen.0.000685
    metadata: null
    note: null
    pmcid: PMC8743544
    pmid: '34739369'
    type:
    - Primary
    version: '1.1'
  - doi: 10.1093/nar/gkaf335
    metadata: null
    note: null
    pmcid: PMC12230652
    pmid: '40271661'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: diamond
    type: uses
  - biotoolsID: hmmer3
    type: uses
  - biotoolsID: infernal
    type: uses
  - biotoolsID: trnascan-se
    type: uses
  - biotoolsID: blast
    type: uses
  - biotoolsID: aragorn
    type: uses
  - biotoolsID: pilercr
    type: uses
  - biotoolsID: deepsig
    type: uses
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - v1.12.0
next: ?page=2
previous: null
