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  description: A tool that checks the clinical metadata quality (validity, completeness),
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  description: D-GENIES – for Dot plot large Genomes in an Interactive, Efficient
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  description: The GlobalAMFungi Database is an open-access, global repository of
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  description: The tool performs an automatic segmentation of the possible DIPG tumours
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      journal: Journal of Imaging Informatics in Medicine
      title: Deep Learning Auto-segmentation of Diffuse Midline Glioma on Multimodal
        Magnetic Resonance Images
    note: null
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  relation: []
  toolType:
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  topic:
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  - term: Data architecture, analysis and design
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  description: 'The tool performs an automatic segmentation of the possible glioblastoma
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        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-16T08:22:56.322315Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: MR-based glioblastoma tumour detection and segmentation (EUCAIM-SW-021_T-01-02-004)
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: casopon
  publication:
  - doi: 10.1007/s11548-024-03205-z
    metadata:
      abstract: ''
      authors: []
      citationCount: 8
      date: '2024-09-01T00:00:00Z'
      journal: International Journal of Computer Assisted Radiology and Surgery
      title: Deep learning automatic semantic segmentation of glioblastoma multiforme
        regions on multimodal magnetic resonance images
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
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  topic:
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - 2.1.1
- accessibility: Open access
  additionDate: '2025-12-16T08:20:17.123908Z'
  biotoolsCURIE: biotools:profiler
  biotoolsID: profiler
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: michel.salzet@univ-lille.fr
    fundrefid: null
    gridid: null
    name: Michel Salzet
    note: Professor Michel Salzet known for his work in immunology, oncology and proteomic
    orcidid: https://orcid.org/0000-0003-4318-0817
    rorid: null
    typeEntity: Person
    typeRole: []
    url: https://www.laboratoire-prism.fr/member/michel-salzet/
  description: 'Profiler is a peer-reviewed, open-source web platform and desktop
    version for end-to-end multi-omics data analysis, integrating statistical methods,
    machine learning, and artificial intelligence into a unified workflow.


    The platform supports proteomics, metabolomics, lipidomics, transcriptomics, genomics,
    and other omics datasets from raw or tabular inputs. Profiler provides automated
    preprocessing, data exploration, biomarker discovery, AI-driven modeling, survival
    analysis, and biological interpretation using enrichment analysis.


    Designed for both bioinformaticians and experimental scientists, Profiler enables
    reproducible, explainable, and high-performance omics analysis through an intuitive
    web interface.


    Profiler is developed by the PRISM U1192 laboratory and protected by INSERM Transfer.'
  documentation:
  - note: null
    type:
    - Citation instructions
    url: https://prism-profiler.univ-lille.fr/citation/
  download:
  - note: null
    type: Source code
    url: https://doi.org/10.5281/zenodo.17478158
    version: null
  - note: null
    type: Test data
    url: https://github.com/yanisZirem/Profiler_v1_requests_datatests
    version: '1.0'
  - note: null
    type: Software package
    url: https://prism-profiler.univ-lille.fr/app/
    version: null
  editPermission:
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    type: private
  elixirCommunity:
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  - Proteomics
  - Rare Diseases
  elixirNode:
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  elixirPlatform:
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  - Training
  - Interoperability
  elixir_badge: 0
  function: []
  homepage: https://prism-profiler.univ-lille.fr/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-16T08:20:49.442259Z'
  license: Other
  link:
  - note: softeware link
    type:
    - Other
    url: https://prism-profiler.univ-lille.fr/
  - note: dataset examples
    type:
    - Repository
    url: https://github.com/yanisZirem/Profiler_v1_requests_datatests
  - note: Desktop version
    type:
    - Repository
    url: https://github.com/yanisZirem/prism-profiler
  maturity: Mature
  name: Profiler
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID:
  - type: doi
    value: doi:10.1093/bioinformatics/btaf644
    version: '1.0'
  owner: YZirem
  publication:
  - doi: 10.1093/bioinformatics/btaf644
    metadata: null
    note: null
    pmcid: null
    pmid: '41324558'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Desktop application
  - Web application
  - Workflow
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  validated: 0
  version:
  - '1.0'
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T09:08:44.174795Z'
  biotoolsCURIE: biotools:mr-based_neuroblastoma_tumour_detection_and_segmentation
  biotoolsID: mr-based_neuroblastoma_tumour_detection_and_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: dianaveigac@gmail.com
    fundrefid: null
    gridid: null
    name: Diana Veiga Canuto
    note: null
    orcidid: https://orcid.org/0000-0002-6048-2940
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Support
    - Documentor
    - Developer
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    - 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: '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).'
  documentation:
  - note: null
    type:
    - General
    url: https://www.mdpi.com/2072-6694/14/15/3648
  - note: null
    type:
    - Terms of use
    url: https://drive.google.com/file/d/1xzmrPQx9LfZr6WS5OR80RkipukoO_3Gw/view?usp=drive_link
  download: []
  editPermission:
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    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run --rm \\\n  -v \"<input_path>:/input\" \\\n  -v \"<output_path>:/output\"\
      \ \\\n  --gpus all \\\n  harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0\
      \ \\\n  --mode dicom-seg \\\n  --series-selector /output/config/series_to_segment.csv\
      \ \\\n  --seg-series-number 2302001 \\\n  --seg-algorithm-name \"nnUNet_Neuroblastoma_Primage_training\"\
      \ \\\n  --seg-coordinating-center \"EUCAIM Consortium\" \\\n  --keep-nifti false"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-16T01:53:35.476918Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: MR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: casopon
  publication:
  - doi: 10.3390/cancers14153648
    metadata:
      abstract: ''
      authors: []
      citationCount: 33
      date: '2022-08-01T00:00:00Z'
      journal: Cancers
      title: Comparative Multicentric Evaluation of Inter-Observer Variability in
        Manual and Automatic Segmentation of Neuroblastic Tumors in Magnetic Resonance
        Images
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.3390/cancers15051622
    metadata:
      abstract: ''
      authors: []
      citationCount: 16
      date: '2023-03-01T00:00:00Z'
      journal: Cancers
      title: Independent Validation of a Deep Learning nnU-Net Tool for Neuroblastoma
        Detection and Segmentation in MR Images
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  validated: 0
  version:
  - 2.0.0
- accessibility: Open access
  additionDate: '2025-12-15T14:17:14.627791Z'
  biotoolsCURIE: biotools:asafind
  biotoolsID: asafind
  collectionID:
  - ELIXIR-CZ
  - Czech Republic
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: mvohnoutova@jcu.cz
    fundrefid: null
    gridid: null
    name: Marta Vohnoutová
    note: null
    orcidid: https://orcid.org/0000-0002-8915-8626
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    - Maintainer
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699
  - email: agruber@prf.jcu.cz
    fundrefid: null
    gridid: null
    name: Ansgar Gruber
    note: null
    orcidid: https://orcid.org/0000-0002-5876-4391
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401
  description: "ASAFind is a software that predicts the intracellular location of\
    \ proteins in cells with four membrane-bound complex plastids of red algal origin.\
    \ \nThese plastids evolved via eukaryote-eukaryote endosymbiosis and for example\
    \ can be found in diatoms and cryptophytes. ASAFind uses protein sequence data\
    \ and external predictions of signal peptides (by the tools SignalP and TargetP),\
    \ and predicts plastid proteins, and proteins that are targeted to the periplastidic\
    \ compartment from these data; optionally, a graphical output can generated."
  documentation:
  - note: null
    type:
    - Installation instructions
    url: https://asafind.jcu.cz/download-page/
  download:
  - note: Download page on web-service, links to repository
    type: Downloads page
    url: https://asafind.jcu.cz/download-page/
    version: '2.0'
  editPermission:
    authors:
    - agruber
    type: group
  elixirCommunity:
  - Plant Sciences
  - Marine Metagenomics
  - Microbial Biotechnology
  elixirNode:
  - Czech Republic
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format: []
    note: null
    operation:
    - term: Subcellular localisation prediction
      uri: http://edamontology.org/operation_2489
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format: []
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format: []
  homepage: https://asafind.jcu.cz/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-15T17:36:43.189214Z'
  license: CC-BY-SA-4.0
  link:
  - note: Web Service
    type:
    - Service
    url: https://asafind.jcu.cz
  - note: Information and source code, for local installation or development
    type:
    - Repository
    url: https://github.com/ASAFind/ASAFind-2
  maturity: Mature
  name: ASAFind
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: martavohnoutova
  publication:
  - doi: 10.1111/tpj.70138
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-06-01T00:00:00Z'
      journal: Plant Journal
      title: 'ASAFind 2.0: multi-class protein targeting prediction for diatoms and
        algae with complex plastids'
    note: Publication of the current version of ASAFind (2.0)
    pmcid: PMC12136025
    pmid: '40464854'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1111/tpj.12734
    metadata:
      abstract: ''
      authors: []
      citationCount: 138
      date: '2015-02-01T00:00:00Z'
      journal: Plant Journal
      title: Plastid proteome prediction for diatoms and other algae with secondary
        plastids of the red lineage
    note: Publication of the first version of ASAFind
    pmcid: PMC4329603
    pmid: '25438865'
    type:
    - Other
    version: '1.0'
  - doi: 10.48550/arXiv.2303.02509
    metadata: null
    note: Benchmarking of the performance of the first version of ASAFind
    pmcid: null
    pmid: null
    type:
    - Benchmarking study
    version: '1.0'
  relation:
  - biotoolsID: signalp
    type: uses
  - biotoolsID: targetp
    type: uses
  toolType:
  - Script
  - Command-line tool
  - Web service
  topic:
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - '2.0'
- accessibility: null
  additionDate: '2020-03-17T13:50:50Z'
  biotoolsCURIE: biotools:seqfu
  biotoolsID: seqfu
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: A collection of utilities to manipulate FASTA and FASTQ files, supporting
    Gzipped input.
  documentation:
  - note: null
    type:
    - User manual
    url: https://telatin.github.io/seqfu2/
  download:
  - note: null
    type: Software package
    url: https://github.com/telatin/seqfu2
    version: null
  - note: null
    type: Downloads page
    url: https://github.com/telatin/seqfu2/releases
    version: null
  - note: null
    type: Software package
    url: https://bioconda.github.io/recipes/seqfu/README.html
    version: 1.0.0-1.22.3
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: seqfu [subcommand] FASTX > FASTX
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    note: null
    operation:
    - term: Nucleic acid sequence analysis
      uri: http://edamontology.org/operation_2478
    output:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format: []
  homepage: https://telatin.github.io/seqfu2/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-12T21:43:34.328705Z'
  license: null
  link:
  - note: Documentation
    type:
    - Other
    url: https://telatin.github.io/seqfu2
  - note: null
    type:
    - Repository
    url: https://github.com/telatin/seqfu2/
  maturity: null
  name: seqfu
  operatingSystem: []
  otherID: []
  owner: telatin
  publication:
  - doi: 10.3390/bioengineering8050059
    metadata:
      abstract: ''
      authors: []
      citationCount: 36
      date: '2021-01-01T00:00:00Z'
      journal: Bioengineering
      title: 'Seqfu: A suite of utilities for the robust and reproducible manipulation
        of sequence files'
    note: null
    pmcid: PMC8148589
    pmid: '34066939'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - 1.10.0
  - 1.11.0
  - 1.12.0
  - 1.13.0
  - 1.14.0
  - 1.15.0
  - 1.16.0
  - 1.17.0
  - 1.19.0
  - 1.20.0
  - 1.21.0
  - 1.22.0
  - 1.22.3
- accessibility: Open access
  additionDate: '2025-12-11T14:36:21.061830Z'
  biotoolsCURIE: biotools:easy16s
  biotoolsID: easy16s
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: cedric.midoux@inrae.fr
    fundrefid: null
    gridid: null
    name: Cédric Midoux
    note: null
    orcidid: https://orcid.org/0000-0002-7964-0929
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Easy16S is designed to facilitate the exploration, visualization, and
    analysis of microbiome data.
  documentation:
  - note: null
    type:
    - General
    - User manual
    url: https://easy16s.migale.inrae.fr/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Multiple sample visualisation
      uri: http://edamontology.org/operation_3744
    output: []
  homepage: https://easy16s.migale.inrae.fr/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-12-11T14:36:21.065324Z'
  license: AGPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://forge.inrae.fr/migale/easy16s
  - note: null
    type:
    - Repository
    url: https://doi.org/10.57745/ZN1HXQ
  maturity: Mature
  name: easy16S
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: cmidoux
  publication:
  - doi: 10.21105/joss.06704
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType: []
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version:
  - v25.07
- accessibility: null
  additionDate: '2025-05-22T17:46:59.585364Z'
  biotoolsCURIE: biotools:mainzelliste
  biotoolsID: mainzelliste
  collectionID:
  - eucaim
  - EUCAIM
  - Samply
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Mainzelliste is a web-based first-level pseudonymization service. It
    allows for the creation of personal identifiers (PID) from identifying attributes
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  description: Mapping-based Genome Size Estimation (MGSE) predicts the size of a
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  - term: Comparative genomics
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  description: Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology
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  topic:
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  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
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  documentation:
  - note: null
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      \ \\\n  -v \"<output_path>:/output\" \\\n  harbor.eucaim.cancerimage.eu/processing-tools/ml_model_for_mr_series_categorisation:<version>\
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        uri: http://edamontology.org/format_3548
    note: null
    operation:
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    - data:
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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
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  language:
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  lastUpdate: '2025-12-03T15:35:26.140884Z'
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  link:
  - note: null
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    - Software catalogue
    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:
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  - Linux
  - Mac
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication:
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    metadata:
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      authors: []
      citationCount: 0
      date: '2025-12-01T00:00:00Z'
      journal: Journal of Big Data
      title: Automatic magnetic resonance imaging series labelling for large repositories
    note: null
    pmcid: null
    pmid: null
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  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
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  biotoolsCURIE: biotools:auto-prostate-sequence-classifier
  biotoolsID: auto-prostate-sequence-classifier
  collectionID:
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  cost: Free of charge (with restrictions)
  credit:
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    fundrefid: null
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    name: José Guilherme de Almeida
    note: null
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  description: XGBoost-based automatic classification of sequence types for prostate
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    alone. Works as a CLI, allows direct application to DICOM datasets or CSV/tsv/Excel/parquet
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    was applied to all data on ProCAncer-I to derive initial results for sequence
    types. Refines predictions using rule-based heuristics for T2W, DWI and ADC.
  documentation:
  - note: Repository containing the code, README and additional information on how
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    type:
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    url: https://github.com/CCIG-Champalimaud/metadata-classification
  download: []
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    input:
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        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
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        uri: http://edamontology.org/format_3548
    note: 'The input can be provided as a DICOM dataset (which will require --dicom-recursion,
      details below or in the documentation) or as a single DICOM study. This command
      will print a CSV with 5 columns:  i) patient_id, ii) study_uid, iii) series_uid,
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      The provided <dicom-recursion> refers to the number of folders until a DICOM
      series is found. So if the provided input is a patient folder with nested studies
      with nested series, the level of DICOM recursion should be 2. If the provided
      input is a directory with patient folders, the level of DICOM recursion should
      be 3.'
    operation:
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      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Keyword
        uri: http://edamontology.org/data_0968
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/champ-autoproseq
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-03T09:27:04.489071Z'
  license: MIT
  link:
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    type:
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  maturity: Emerging
  name: AutoProSeq - automatic classification of sequence types for prostate mpMRI
  operatingSystem:
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  otherID: []
  owner: josegcpa
  publication:
  - doi: 10.1186/s13244-025-01938-2
    metadata:
      abstract: ''
      authors: []
      citationCount: 1
      date: '2025-12-01T00:00:00Z'
      journal: Insights into Imaging
      title: Automatic sequence identification in multicentric prostate multiparametric
        MRI datasets for clinical machine-learning
    note: null
    pmcid: PMC12187622
    pmid: '40146375'
    type:
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  toolType:
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  topic:
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  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2025-12-02T12:03:53.282983Z'
  biotoolsCURIE: biotools:aggreprot
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  description: AggreProt is a web server to predict and engineer protein aggregation.
    The tool provides a per-residue numerical aggregation propensity value and an
    overall protein aggregation propensity profile. Along with the protein solvent
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  additionDate: '2021-01-18T10:10:48Z'
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  description: APE (the Automated Pipeline Explorer) as a command-line tool and API
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  documentation:
  - note: null
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    note: null
    operation:
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      - term: CWL
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  license: Apache-2.0
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    note: null
    pmcid: PMC8041394
    pmid: '33720735'
    type:
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  toolType:
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  topic:
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  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 1
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- accessibility: Open access
  additionDate: '2017-08-03T18:45:53Z'
  biotoolsCURIE: biotools:hbat
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  description: "HBAT (Hydrogen Bond Analysis Tool) is a package to automate the analysis\
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    \ continue to be available via SourceForge. \n\nHBAT 2.0 was introduced in 2025\
    \ and a completed rewrite of original implementation with cross-platform support.\
    \ HBAT 2.0 is open sourced under MIT License."
  documentation:
  - note: null
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    - API documentation
    - Citation instructions
    - Command-line options
    - Installation instructions
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  download:
  - note: Cross-platform PyPI Python Package
    type: Software package
    url: https://pypi.org/project/hbat/
    version: 2.x
  - note: Mac and Linux Binaries including  AppImage, .deb, standalone executables.
    type: Binaries
    url: https://github.com/abhishektiwari/hbat/releases
    version: 2.x
  - note: Windows Binaries download from SourceForge
    type: Binaries
    url: https://sourceforge.net/projects/hbat/
    version: 1.0, 1.1
  editPermission:
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  function:
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    input:
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      format:
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        uri: http://edamontology.org/format_1476
    note: null
    operation:
    - term: Protein structure analysis
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    output:
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      format: []
  homepage: https://hbat.abhishek-tiwari.com
  homepage_status: 0
  language:
  - Perl
  - Python
  lastUpdate: '2025-11-29T17:30:01.186940Z'
  license: MIT
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  - note: null
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  maturity: Mature
  name: HBAT
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  owner: abhishektiwari
  publication:
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    metadata: null
    note: Peer-reviewed paper for HBAT 1.0
    pmcid: null
    pmid: '18467777'
    type:
    - Primary
    version: null
  - doi: 10.5281/zenodo.17645321
    metadata: null
    note: Preprint for HBAT 2.x software
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  validated: 1
  version:
  - 2.x
  - 1.1, 1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-11-07T18:15:49.962044Z'
  biotoolsCURIE: biotools:prostate_zone_segmentation_tool
  biotoolsID: prostate_zone_segmentation_tool
  collectionID:
  - EUCAIM
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  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: https://josegcpa.net
  - email: null
    fundrefid: null
    gridid: null
    name: Nickolas Papanikolaou
    note: null
    orcidid: https://orcid.org/0000-0003-3298-2072
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Nuno Rodrigues
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: 'This tool automatically segments the the prostate into two zones:
    the central and transition zones (TZ+CZ) and the peripheral zone (PZ). It takes
    as input a T2-weighted image and produces a segmentation in the same input format.


    Three datasets were used to train this model: ProstateX (n=152), Prostate158 (n=119)
    and ProstateNet (the ProCAncer-I dataset; n=532). We used the T2-weighted images
    available in each dataset and trained a standard three-class nnU-Net model with
    three classes: background, peripheral zone and the combination of the transition
    and central zones as annotated by radiologists. Using 149 cases from the three
    previously noted datasets, this model achieved DSC=0.81 (95% CI=[0.59, 0.92])
    for PZ and 0.87 (95% CI=[0.60, 0.96]) for CZ+TZ. In a clinical validation using
    ProCAncer-I data, this model achieved, for PZ and TZ+CZ, DSC=0.65 and DSC=0.77,
    respectively, comparable to the observed between-radiologist DSC for a subset
    of cases (DSC=0.61 and DSC=0.73, respectively).'
  documentation:
  - note: This is the repository containing all of the code together with a comprehensive
      README for deployment and examplar files.
    type:
    - API documentation
    url: https://github.com/josegcpa/nnunet_serve
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: docker run --shm-size=1gb -v $(pwd)/example:/data/input:ro -v $(pwd)/test_output:/data/output:rw
      --gpus="all" test-eucaim:latest nnunet-predict --study_path /data/input --series_folders
      <series-folder> --output_dir /data/output
    input:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: 'Image annotation for individual DICOM and Nifti images: Please note that
      it is easier to mount the input and output paths path and keep `--study_path`
      always as `/data/input` and `--output_dir` always as `/data/output`. This way
      only `--series_folders` requires any change. `--series_folders` can refer both
      to a Nifti file (if the input is Nifti) or the a DICOM series folder.


      If the input is DICOM, `--is_dicom` should be used.'
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --shm-size=1gb -v $(pwd)/example_dataset:/data/input:ro -v $(pwd)/test_output:/data/output:rw
      --gpus="all" test-eucaim:latest nnunet-predict-batch {{--data_json /data/input/<dataset_json>.json|--data_dir
      /data/input --output_dir /data/output}}
    input:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: "Batch image annotation for DICOM and Nifti images using dataset JSON and\
      \ data directory supports two methods: using a dataset JSON and using a data\
      \ directory. \n\nThe dataset JSON-based method relies on having a dataset JSON\
      \ which has a list of dictionaries that follow this structure: `{\"study_path\"\
      : str, \"series_folders\": [[str]], \"output_dir\": str}`. These are analogous\
      \ to the previous modes. Be mindful that paths should be specified accordingly\
      \ for the Docker file-system. The dataset JSON should be specified using `--data_json`.\n\
      \nThe data directory-based method relies on having a directory structured as\
      \ patient/study/series, where each series follows an nnU-Net-like convention\
      \ (i.e. `<series_id>_0000`, `<series_id>_0001`, etc.). In this case, it should\
      \ be `<series-id>_0000`. The data directory should be specified using `--data_dir`\
      \ and requires the specification of an `--output_dir`.\n\nIf the input is DICOM,\
      \ `--is_dicom` should be specified."
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/champ-prostate-zone-segmentation
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-28T12:18:55.232382Z'
  license: CC-BY-NC-4.0
  link:
  - note: This is the nnunet_serve repository, containing the generic nnU-Net building
      and serving functionalities used by the Computational Clinical Imaging Group
      at Champalimaud Foundation. This should also be used as documentation.
    type:
    - Repository
    url: https://github.com/josegcpa/nnunet_serve
  - note: The EUCAIM model card for this model, containing details on model training,
      data and libraries.
    type:
    - Other
    url: https://docs.google.com/spreadsheets/d/1bcdhs9Xg2MxAH0WDGz08SjEVMFr3e-TP/edit?usp=sharing&ouid=111102743696297094705&rtpof=true&sd=true
  maturity: Emerging
  name: Prostate zone segmentation tool
  operatingSystem:
  - Linux
  otherID: []
  owner: josegcpa
  publication:
  - doi: 10.1016/j.compbiomed.2024.108216
    metadata:
      abstract: ''
      authors: []
      citationCount: 9
      date: '2024-03-01T00:00:00Z'
      journal: Computers in Biology and Medicine
      title: Analysis of domain shift in whole prostate gland, zonal and lesions segmentation
        and detection, using multicentric retrospective data
    note: null
    pmcid: null
    pmid: '38442555'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: nnunet
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  validated: 0
  version: []
- accessibility: null
  additionDate: '2020-02-26T09:24:43Z'
  biotoolsCURIE: biotools:South_Green_Genome_Hubs
  biotoolsID: South_Green_Genome_Hubs
  collectionID:
  - Genome Hub
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: droc@cirad.fr
    fundrefid: null
    gridid: null
    name: Gaetan Droc
    note: null
    orcidid: https://orcid.org/0000-0003-1849-1269
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Provider
    - Support
    url: null
  - email: alexis.dereeper@ird.fr
    fundrefid: null
    gridid: null
    name: Alexis Dereeper
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: m.rouard@cgiar.org
    fundrefid: null
    gridid: null
    name: Mathieu Rouard
    note: null
    orcidid: https://orcid.org/0000-0003-1849-1269
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Maintainer
    - Support
    url: null
  - email: v.guignon@cgiar.org
    fundrefid: null
    gridid: null
    name: Valentin Guignon
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: christine.tranchant@ird.fr
    fundrefid: null
    gridid: null
    name: Chrisitine Tranchant
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: stephanie.sidibe-bocs@cirad.fr
    fundrefid: null
    gridid: null
    name: Stéphanie Bocs
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: The South Green Genome Hub is a suite of crop-specific community portals
    to manage genomic datasets with focus on tropical and Mediterranean plants. Currently
    developed on Banana, Cacao, Coffee, Grass, Rice, Vanilla, Citrus and Sugarcane,
    genome hubs provide access to multiple datasets (e.g. assemblies, gene product
    information, metabolic pathways, gene families, transcriptomics and genetic markers).
  documentation:
  - note: null
    type:
    - Terms of use
    url: https://banana-genome-hub.southgreen.fr/content/term-service
  download: []
  editPermission:
    authors:
    - gdroc
    - Droc
    type: group
  elixirCommunity: []
  elixirNode:
  - France
  elixirPlatform:
  - Data
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Keyword
        uri: http://edamontology.org/data_0968
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Genome visualisation
      uri: http://edamontology.org/operation_3208
    - term: Sequence database search
      uri: http://edamontology.org/operation_0338
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
  homepage: https://banana-genome-hub.southgreen.fr/
  homepage_status: 0
  language:
  - JavaScript
  - PHP
  lastUpdate: '2025-11-27T09:14:28.500250Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/SouthGreenPlatform/genomehubs
  maturity: Mature
  name: South Green Genome Hubs
  operatingSystem: []
  otherID: []
  owner: mrouard
  publication:
  - doi: 10.1093/database/bat035
    metadata:
      abstract: ''
      authors: []
      citationCount: 150
      date: '2013-12-01T00:00:00Z'
      journal: Database
      title: The banana genome hub
    note: null
    pmcid: PMC3662865
    pmid: '23707967'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gku1108
    metadata:
      abstract: ''
      authors: []
      citationCount: 52
      date: '2015-01-28T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The coffee genome hub: A resource for coffee genomes'
    note: null
    pmcid: PMC4383925
    pmid: '25392413'
    type:
    - Primary
    version: null
  - doi: 10.1093/hr/uhac221
    metadata:
      abstract: ''
      authors: []
      citationCount: 29
      date: '2022-01-01T00:00:00Z'
      journal: Horticulture Research
      title: 'The banana genome hub: a community database for genomics in the Musaceae'
    note: null
    pmcid: PMC9720444
    pmid: '36479579'
    type:
    - Primary
    version: null
  - doi: 10.1016/j.xplc.2022.100330
    metadata:
      abstract: ''
      authors: []
      citationCount: 26
      date: '2022-09-12T00:00:00Z'
      journal: Plant Communications
      title: A chromosome-level, haplotype-phased Vanilla planifolia genome highlights
        the challenge of partial endoreplication for accurate whole-genome assembly
    note: null
    pmcid: PMC9482989
    pmid: '35617961'
    type:
    - Usage
    version: null
  relation:
  - biotoolsID: tripal
    type: uses
  - biotoolsID: banana_genome_hub
    type: includes
  - biotoolsID: coffee_genome_hub
    type: includes
  - biotoolsID: cocoa_genome_hub
    type: includes
  - biotoolsID: rice_genome_hub
    type: includes
  - biotoolsID: sugarcane_genome_hub
    type: includes
  - biotoolsID: southgreen
    type: includedIn
  toolType:
  - Database portal
  topic:
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-11-20T09:46:36.870345Z'
  biotoolsCURIE: biotools:gpcrvs
  biotoolsID: gpcrvs
  collectionID:
  - gpcr
  confidence_flag: null
  cost: null
  credit:
  - email: dlatek@chem.uw.edu.pl
    fundrefid: null
    gridid: null
    name: Dorota Latek
    note: null
    orcidid: https://orcid.org/0000-0002-0429-0637
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  description: Machine learning based webtool for predicting the activity of compounds
    and their interactions with G protein-coupled receptors (GPCRs).
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://gpcrvs.chem.uw.edu.pl/result/example
  - note: null
    type:
    - Terms of use
    url: https://gpcrvs.chem.uw.edu.pl/terms
  - note: null
    type:
    - User manual
    url: https://dlatek.chem.uw.edu.pl/pdf/GPCRVS_tutorial.pdf
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://gpcrvs.chem.uw.edu.pl/
  homepage_status: 0
  language: []
  lastUpdate: '2025-11-26T09:19:02.835678Z'
  license: null
  link: []
  maturity: null
  name: GPCRVS
  operatingSystem: []
  otherID: []
  owner: laasfeld
  publication:
  - doi: 10.3390/ijms26052160
    metadata:
      abstract: ''
      authors: []
      citationCount: 3
      date: '2025-03-01T00:00:00Z'
      journal: International Journal of Molecular Sciences
      title: GPCRVS - AI-driven Decision Support System for GPCR Virtual Screening
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Computational chemistry
    uri: http://edamontology.org/topic_3332
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  validated: 0
  version: []
- accessibility: null
  additionDate: '2021-10-04T08:14:41.487821Z'
  biotoolsCURIE: biotools:jasp
  biotoolsID: jasp
  collectionID: []
  confidence_flag: tool
  cost: null
  credit: []
  description: JASP is an open-source statistics program that is free, friendly, and
    flexible. Armed with an easy-to-use GUI, JASP allows both classical and Bayesian
    analyses.
  documentation:
  - note: null
    type:
    - Installation instructions
    url: https://jasp-stats.org/installation-guide/
  - note: null
    type:
    - FAQ
    url: https://jasp-stats.org/faq/
  download:
  - note: null
    type: Downloads page
    url: https://jasp-stats.org/download/
    version: null
  editPermission:
    authors:
    - n.m.palmblad@lumc.nl
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    output: []
  homepage: https://jasp-stats.org/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-11-25T11:09:12.512597Z'
  license: AGPL-3.0
  link: []
  maturity: null
  name: JASP
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.31234/OSF.IO/67DCB
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Surgery
    uri: http://edamontology.org/topic_3421
  - term: Electron microscopy
    uri: http://edamontology.org/topic_0611
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-11-23T16:04:41.658509Z'
  biotoolsCURIE: biotools:almondcv2
  biotoolsID: almondcv2
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Jorge Mas Gómez
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  description: Open RGB Imaging Workflow for Morphological and Morphometric Analysis
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/jorgemasgomez/almondcv2
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/jorgemasgomez/almondcv2
  homepage_status: 0
  language:
  - Python
  - R
  lastUpdate: '2025-11-23T16:12:22.606390Z'
  license: GPL-3.0
  link:
  - note: Repository
    type:
    - Repository
    url: https://github.com/jorgemasgomez/almondcv2
  maturity: Emerging
  name: almondcv2
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: jmgomez
  publication:
  - doi: 10.1101/2025.05.05.652179
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  validated: 0
  version: []
- accessibility: null
  additionDate: '2024-12-23T12:44:47.964606Z'
  biotoolsCURIE: biotools:gibi230_radiomic_features_extraction
  biotoolsID: gibi230_radiomic_features_extraction
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit: []
  description: "Implemented by GIBI230, this tool is a Docker-based software designed\
    \ for extracting radiomic features from 3D medical images in NIfTI format using\
    \ the PyRadiomics library (if DICOM images, the DICOM to NIFTI converter must\
    \ be run before using this tool). It streamlines the radiomics calculation process\
    \ by generating a structured CSV file containing all extracted variables from\
    \ medical images.\nThe dockerized software enables users to configure parameters\
    \ like filters, bin width, resampling spacing, and normalization settings can\
    \ be specified. The output radiomic variables provide quantitative information\
    \ for further analysis in medical imaging research and machine learning applications.\
    \ \nSpecially important the parameter selection of the band width. For robust\
    \ and reproducible results, a bin width of 5 is commonly recommended, but it should\
    \ be adjusted based on image resolution, modality, and noise levels."
  documentation: []
  download: []
  editPermission:
    authors: []
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.acim.lafe.san.gva.es/acim/?page_id=675&lang=es
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-20T17:07:08.487226Z'
  license: null
  link: []
  maturity: null
  name: Radiomic features extraction (EUCAIM-SW-055_T-02-01-003)
  operatingSystem: []
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication:
  - doi: 10.1148/ryai.230208
    metadata:
      abstract: ''
      authors: []
      citationCount: 1
      date: '2024-07-01T00:00:00Z'
      journal: 'Radiology: Artificial Intelligence'
      title: Reproducibility Analysis of Radiomic Features on T2-weighted MR Images
        after Processing and Segmentation Alterations in Neuroblastoma Tumors
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - 1.0.0
- accessibility: Open access
  additionDate: '2025-10-15T12:28:27.006057Z'
  biotoolsCURIE: biotools:tabular_data_curator
  biotoolsID: tabular_data_curator
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit: []
  description: A fully automated service which can be applied on any kind of tabular
    data (e.g. clinical) to automatically identify duplicated fields (lexically similar
    and/or highly correlated features), outliers, data inconsistencies. It can also
    deal with missing values through the application of data imputers.
  documentation:
  - note: null
    type:
    - Training material
    url: https://docs.google.com/document/d/1UfTeZeXi5TzUWsQox3HNRolkpCROcfn8/edit?usp=drive_link&ouid=105979482259582415027&rtpof=true&sd=true
  - note: null
    type:
    - API documentation
    url: https://github.com/vpz4/TDC
  download:
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  description: Automated high-throughput platform for state-of-the-art genome-based
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    metadata:
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        compared to conventional small molecule drugs. However, the experimental identification
        of ACPs still remains a time-consuming and expensive endeavor. Therefore,
        it is desirable to develop and improve upon existing computational models
        for predicting and characterizing ACPs. In this study, we present a bioinformatics
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        distinguishing characteristics that ACPs possess: (i) hydrophobic residue
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        penetration; (ii) the amphipathic nature of the α-helical structure plays
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        online.'
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      - name: Nantasenamat C.
      - name: Prachayasittikul V.
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    type:
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  description: Web application designed for the identification of regulated metabolite
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  description: StrainInfo provides resolution of microbial strain identifiers by storing
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  description: ComplexBrowser is a R based software for supervised analysis of changes
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  link:
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    note: null
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  topic:
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  description: Blazing fast toolkit to work with .hic and .cool files
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  - note: null
    type:
    - Issue tracker
    url: https://github.com/paulsengroup/hictk/issues
  - note: null
    type:
    - Helpdesk
    url: https://github.com/paulsengroup/hictk/discussions
  maturity: Mature
  name: hictk
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: robomics
  publication:
  - doi: 10.1093/bioinformatics/btae408
    metadata:
      abstract: ''
      authors: []
      citationCount: 1
      date: '2024-07-01T00:00:00Z'
      journal: Bioinformatics
      title: 'hictk: blazing fast toolkit to work with. hic and. cool files'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: hictkpy
    type: usedBy
  - biotoolsID: hictkr
    type: usedBy
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
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  - 2.0.0
  - 2.0.1
  - 2.0.2
  - 2.1.0
  - 2.1.1
  - 2.1.2
  - 2.1.3
  - 2.1.4
  - 2.1.5
  - 2.2.0
- accessibility: null
  additionDate: '2025-03-20T09:46:51.356874Z'
  biotoolsCURIE: biotools:spacedust
  biotoolsID: spacedust
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Spacedust is a modular toolkit for identification of conserved gene
    clusters among multiple genomes based on homology and conservation of gene neighborhood.
    Spacedust adapts the fast and sensitive structure comparisons of Foldseek and
    homology search capabilities of MMseqs2. It introduces a novel approach of aggregating
    sets of homologous hits between pairs of genomes and identifies cluster of hits
    with conserved gene neighborhood between each using agglomerative hierarchical
    clustering algorithm.
  documentation: []
  download: []
  editPermission:
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    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/soedinglab/spacedust/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-11-10T08:37:07.602568Z'
  license: GPL-3.0
  link: []
  maturity: Emerging
  name: Spacedust
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: milot-mirdita
  publication:
  - doi: 10.1101/2024.10.02.616292v1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1038/s41592-025-02816-x
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-10-01T00:00:00Z'
      journal: Nature Methods
      title: De novo discovery of conserved gene clusters in microbial genomes with
        Spacedust
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2019-11-14T19:27:27Z'
  biotoolsCURIE: biotools:PolySTest
  biotoolsID: PolySTest
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: Robust statistical testing of quantitative proteomics data. The tool
    comprises and combines different tests and includes a new method for combined
    statistics of quantitative and missing values.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode:
  - Denmark
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Statistical modelling
      uri: http://edamontology.org/operation_3664
    - term: Differential protein expression profiling
      uri: http://edamontology.org/operation_3741
    output:
    - data:
        term: Q-value
        uri: http://edamontology.org/data_3932
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: P-value
        uri: http://edamontology.org/data_1669
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Heat map
        uri: http://edamontology.org/data_1636
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Histogram
        uri: http://edamontology.org/data_3905
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Gene expression profile
        uri: http://edamontology.org/data_0928
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: http://computproteomics.bmb.sdu.dk/app_direct/PolySTest
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-11-08T12:32:48.900143Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/computproteomics/PolySTest
  maturity: Mature
  name: PolySTest
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: veits@bmb.sdu.dk
  publication:
  - doi: 10.1074/mcp.RA119.001777
    metadata:
      abstract: ''
      authors: []
      citationCount: 26
      date: '2020-08-01T00:00:00Z'
      journal: Molecular and Cellular Proteomics
      title: 'PolySTest: Robust statistical testing of proteomics data with missing
        values improves detection of biologically relevant features'
    note: null
    pmcid: PMC8015005
    pmid: '32424025'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2018-06-02T07:03:53Z'
  biotoolsCURIE: biotools:vsclust
  biotoolsID: vsclust
  collectionID:
  - Proteomics
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: veits@bmb.sdu.dk
    fundrefid: null
    gridid: null
    name: Veit Schwämmle
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Feature-based variance-sensitive clustering of omics data. Optimizes
    cluster assignment by taking into account individual feature variance .
  documentation:
  - note: null
    type:
    - General
    url: https://bitbucket.org/veitveit/vsclust
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Expression profile pathway mapping
      uri: http://edamontology.org/operation_0533
    - term: Expression profile clustering
      uri: http://edamontology.org/operation_0313
    - term: Statistical modelling
      uri: http://edamontology.org/operation_3664
    - term: Principal component analysis
      uri: http://edamontology.org/operation_3960
    output:
    - data:
        term: Clustered expression profiles
        uri: http://edamontology.org/data_3768
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Q-value
        uri: http://edamontology.org/data_3932
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: http://computproteomics.bmb.sdu.dk/app_direct/VSClust/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-11-08T12:32:14.933981Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://bitbucket.org/veitveit/vsclust/src/master/
  maturity: null
  name: VSClust
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: veits@bmb.sdu.dk
  publication:
  - doi: 10.1093/bioinformatics/bty224
    metadata:
      abstract: ''
      authors: []
      citationCount: 27
      date: '2018-09-01T00:00:00Z'
      journal: Bioinformatics
      title: 'VSClust: Feature-based variance-sensitive clustering of omics data'
    note: null
    pmcid: null
    pmid: '29635359'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web service
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Omics
    uri: http://edamontology.org/topic_3391
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2025-02-28T15:04:33.594183Z'
  biotoolsCURIE: biotools:prolfquapp
  biotoolsID: prolfquapp
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A command-line tool for differential expression analysis in quantitative
    proteomics
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/prolfqua/prolfquapp/blob/master/README.md
  download:
  - note: null
    type: Downloads page
    url: https://github.com/prolfqua/prolfquapp/releases/tag/0.1.6
    version: 0.1.6
  editPermission:
    authors:
    - thatmariia
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: './prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis
      -s DIANN

      # and again you run the version within the docker container with

      # ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y
      config.yaml -w NameOfAnalysis -s DIANN'
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Differential protein expression profiling
      uri: http://edamontology.org/operation_3741
    output:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
    note: null
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    output:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: https://github.com/prolfqua/prolfquapp
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-11-06T14:37:12.116175Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/prolfqua/prolfquapp
  - note: null
    type:
    - Issue tracker
    url: https://github.com/prolfqua/prolfquapp/issues
  maturity: Emerging
  name: prolfquapp
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1021/acs.jproteome.4c00911
    metadata:
      abstract: ''
      authors: []
      citationCount: 1
      date: '2025-02-07T00:00:00Z'
      journal: Journal of Proteome Research
      title: prolfquapp ─ A User-Friendly Command-Line Tool Simplifying Differential
        Expression Analysis in Quantitative Proteomics
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 0.0.6
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version:
  - 0.1.6
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