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  additionDate: '2019-11-14T19:27:27Z'
  biotoolsCURIE: biotools:PolySTest
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  collectionID: []
  confidence_flag: tool
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  credit: []
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  elixirNode:
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        uri: http://edamontology.org/format_3751
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
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        term: Q-value
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      - term: CSV
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        term: P-value
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      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Heat map
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      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Histogram
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      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:
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  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
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    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
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  - term: Statistics and probability
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- accessibility: Open access
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  biotoolsCURIE: biotools:vsclust
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    fundrefid: null
    gridid: null
    name: Veit Schwämmle
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
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    url: null
  description: Feature-based variance-sensitive clustering of omics data. Optimizes
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  - note: null
    type:
    - General
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    input:
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    note: null
    operation:
    - term: Expression profile pathway mapping
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    - term: Expression profile clustering
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    - 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
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      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:
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  lastUpdate: '2025-11-08T12:32:14.933981Z'
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  link:
  - note: null
    type:
    - Repository
    url: https://bitbucket.org/veitveit/vsclust/src/master/
  maturity: null
  name: VSClust
  operatingSystem:
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  owner: veits@bmb.sdu.dk
  publication:
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    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
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  - 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: '2025-11-05T14:50:14.996722Z'
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  confidence_flag: null
  cost: Free of charge
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  description: The Spectra package defines an efficient infrastructure for storing
    and handling mass spectrometry spectra and functionality to subset, process, visualize
    and compare spectra data. It provides different implementations (backends) to
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    and processing and backends for very large data sets ensuring a small memory footprint.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://rformassspectrometry.github.io/Spectra/
  - note: null
    type:
    - Training material
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  language:
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  lastUpdate: '2025-11-07T11:38:15.960655Z'
  license: Artistic-2.0
  link:
  - note: null
    type:
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    url: https://github.com/Rformassspectrometry/Spectra
  - note: Main documentation
    type:
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    url: https://rformassspectrometry.github.io/Spectra/
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  name: Spectra
  operatingSystem:
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  - Linux
  - Mac
  otherID: []
  owner: jorainer
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  validated: 0
  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
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  function:
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      # 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:
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        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence
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      format:
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        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Differential protein expression profiling
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    output:
    - data:
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        uri: http://edamontology.org/data_2603
      format:
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      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
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      format:
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    note: null
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
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      format:
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        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
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        term: Expression data
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      format:
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    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
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        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:
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  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:
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  - 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
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    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 0.0.6
  relation: []
  toolType:
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  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2023-07-13T08:14:40.190855Z'
  biotoolsCURIE: biotools:nlmced_filter
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  confidence_flag: null
  cost: Free of charge
  credit:
  - email: ferielromdhane@yahoo.fr
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    gridid: null
    name: Feriel Romdhane
    note: null
    orcidid: https://orcid.org/0000-0002-5854-9341
    rorid: null
    typeEntity: null
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    url: null
  description: The NLmCED (Non Local mean Coherence Enhancing Diffusion) filter is
    a denoising tool aimed to reduce Rician Noise in 3D MR images. It is a combination
    between two filters such as the Non-Local mean filter and the Anisotropic Diffusion
    tensor method with an estimator of Rician noise. The NLmCED filter can benefit
    from the noise reduction capabilities of the NLM filter while maintaining the
    edge-preserving characteristics of anisotropic diffusion.
  documentation: []
  download: []
  editPermission:
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  function:
  - cmd: null
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
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      uri: http://edamontology.org/operation_3695
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: JPG
        uri: http://edamontology.org/format_3579
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: MAT
        uri: http://edamontology.org/format_3626
  homepage: https://github.com/Feriel87/Denoising-CEST-MRI/tree/main/NLmCED_Filter
  homepage_status: 0
  language:
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  - MATLAB
  lastUpdate: '2025-11-05T12:10:02.656053Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: Github Link
    type:
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    url: https://github.com/FerielRamdhane/Denoising-CEST-MRI/tree/main/NLmCED_Filter
  maturity: null
  name: NLmCED Filter
  operatingSystem:
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  otherID: []
  owner: Feriel
  publication:
  - doi: 10.1504/IJCVR.2018.090012
    metadata:
      abstract: ''
      authors: []
      citationCount: 3
      date: '2018-01-01T00:00:00Z'
      journal: International Journal of Computational Vision and Robotics
      title: A new method for three-dimensional magnetic resonance images denoising
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1002/mrm.28676
    metadata:
      abstract: ''
      authors: []
      citationCount: 20
      date: '2021-06-01T00:00:00Z'
      journal: Magnetic Resonance in Medicine
      title: Evaluation of a similarity anisotropic diffusion denoising approach for
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    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Script
  topic:
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2025-11-05T11:45:08.078589Z'
  biotoolsCURIE: biotools:sub-saharan_africa_brain_glioma_segmenter
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  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Daniel Capellán-Martín
    note: null
    orcidid: https://orcid.org/0000-0002-9743-0845
    rorid: null
    typeEntity: null
    typeRole:
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    - Contributor
    - Support
    url: null
  - email: pabhijeet@childrensnational.org
    fundrefid: null
    gridid: null
    name: Abhijeet Parida
    note: null
    orcidid: https://orcid.org/0000-0002-4978-0576
    rorid: null
    typeEntity: null
    typeRole:
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    - Contributor
    - Support
    - Maintainer
    url: null
  - email: zjiang@childrensnational.org
    fundrefid: null
    gridid: null
    name: Zhifan Jiang
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
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    - Developer
    - Support
    url: null
  - email: mj.ledesma@upm.es
    fundrefid: null
    gridid: null
    name: María Jesus Ledesma-Carbayo
    note: null
    orcidid: https://orcid.org/0000-0001-6846-3923
    rorid: null
    typeEntity: null
    typeRole:
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    - Contributor
    url: null
  - email: mlingura@childrensnational.org
    fundrefid: null
    gridid: null
    name: Marius George Linguraru
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
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    url: null
  description: The Sub-Saharan Africa Brain Glioma Segmenter is a software tool developed
    by researchers from Universidad Politécnica de Madrid and Children’s National
    Hospital for the segmentation and analysis of intercranial meningiomas in magnetic
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    of gliomas in brain MRI scans to support clinical decision-making in both diagnosis
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  documentation:
  - note: null
    type:
    - API documentation
    - Citation instructions
    - Terms of use
    - Code of conduct
    - Release notes
    - User manual
    - General
    - Quick start guide
    url: https://docs.hope4kids.io/HOPE-Segmenter-Kids/
  download: []
  editPermission:
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  elixirNode: []
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  elixir_badge: 0
  function:
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    input: []
    note: null
    operation:
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    output: []
  homepage: https://segmenter.hope4kids.io/
  homepage_status: 0
  language:
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  lastUpdate: '2025-11-05T11:45:08.081083Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: Main app webpage
    type:
    - Other
    url: https://segmenter.hope4kids.io/
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids
  maturity: Mature
  name: Sub-Saharan Africa Brain Glioma Segmenter
  operatingSystem:
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  - Mac
  - Linux
  otherID: []
  owner: dani-capellan
  publication:
  - doi: 10.1007/978-3-031-76163-8_20
    metadata:
      abstract: ''
      authors: []
      citationCount: 2
      date: '2024-01-01T00:00:00Z'
      journal: Lecture Notes in Computer Science (including subseries Lecture Notes
        in Artificial Intelligence and Lecture Notes in Bioinformatics)
      title: Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1109/ISBI56570.2024.10635469
    metadata:
      abstract: ''
      authors: []
      citationCount: 1
      date: '2024-01-01T00:00:00Z'
      journal: Proceedings - International Symposium on Biomedical Imaging
      title: 'Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble
        with Adaptive Post-Processing'
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04094
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04111
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Workflow
  - Web application
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2025-11-05T10:35:32.782850Z'
  biotoolsCURIE: biotools:intercranial_meningioma_segmenter
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  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit:
  - email: daniel.capellan@upm.es
    fundrefid: null
    gridid: null
    name: Daniel Capellán-Martín
    note: null
    orcidid: https://orcid.org/0000-0002-9743-0845
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  description: 'The MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform
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    note: Use MINERVA API to access systems biology formats for modelling
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    output: []
  homepage: https://minerva.uni.lu
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  language: []
  lastUpdate: '2025-10-29T08:54:40.647322Z'
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  link:
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    type:
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  - note: Issue tracker for core functionalities (data and format handling, service
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  publication:
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    metadata:
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    type:
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      date: '2019-11-01T00:00:00Z'
      journal: Bioinformatics
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    note: null
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    type:
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      date: '2019-07-10T00:00:00Z'
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    note: null
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      journal: Environmental Pollution
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  - term: Translational medicine
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  - term: Systems biology
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  description: TEtranscripts is a software package for including transposable elements
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    note: null
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  topic:
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  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
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- accessibility: Open access
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  download: []
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  link: []
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  name: NetworkX
  operatingSystem:
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  owner: Julia.Villarroel
  publication:
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    metadata: null
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  biotoolsCURIE: biotools:ms_annika
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  description: MS Annika is a crosslink search engine based on MS Amanda, aimed at
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  documentation:
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  - note: null
    type:
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  publication:
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  - doi: 10.1073/pnas.1523899113
    metadata:
      abstract: Listeria monocytogenes is responsible for gastroenteritis in healthy
        individuals and for a severe invasive disease in immunocompromised patients.
        Among the three identified L. monocytogenes evolutionary lineages, lineage
        I strains are overrepresented in epidemic listeriosis outbreaks, but the mechanisms
        underlying the higher virulence potential of strains of this lineage remain
        elusive. Here, we demonstrate that Listeriolysin S (LLS), a virulence factor
        only present in a subset of lineage I strains, is a bacteriocin highly expressed
        in the intestine of orally infected mice that alters the host intestinal microbiota
        and promotes intestinal colonization by L. monocytogenes, as well as deeper
        organ infection. To our knowledge, these results therefore identify LLS as
        the first bacteriocin described in L. monocytogenes and associate modulation
        of host microbiota by L. monocytogenes epidemic strains to increased virulence.
      authors:
      - name: Quereda J.J.
      - name: Dussurget O.
      - name: Nahori M.-A.
      - name: Ghozlane A.
      - name: Volant S.
      - name: Dillies M.-A.
      - name: Regnault B.
      - name: Kennedy S.
      - name: Mondot S.
      - name: Villoing B.
      - name: Cossart P.
      - name: Pizarro-Cerda J.
      citationCount: 87
      date: '2016-05-17T00:00:00Z'
      journal: Proceedings of the National Academy of Sciences of the United States
        of America
      title: Bacteriocin from epidemic Listeria strains alters the host intestinal
        microbiota to favor infection
    note: null
    pmcid: PMC4878514
    pmid: '27140611'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2025-10-23T09:01:44.958137Z'
  biotoolsCURIE: biotools:vivo_platform
  biotoolsID: vivo_platform
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: canudobarreras@unizar.es
    fundrefid: null
    gridid: null
    name: Guillermo Canudo-Barreras
    note: Researcher at Spanish National Research Council (CSIC). Developer.
    orcidid: https://orcid.org/0000-0002-1949-9185
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    - Maintainer
    - Support
    url: null
  - email: eromanos.iacs@aragon.es
    fundrefid: null
    gridid: null
    name: Eduardo Romanos
    note: Researcher at Biomedical Research Center of Aragon (CIBA).
    orcidid: https://orcid.org/0000-0002-9918-3374
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: raquelph@unizar.es
    fundrefid: null
    gridid: null
    name: Raquel P. Herrera
    note: Senior scientist at Spanish National Research Council (CSIC).
    orcidid: https://orcid.org/0000-0002-5244-9569
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: gimeno@unizar.es
    fundrefid: null
    gridid: null
    name: M. Concepción Gimeno
    note: Full professor at Spanish National Research Council (CSIC).
    orcidid: https://orcid.org/0000-0003-0553-0695
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: 'ViVo Platform is a free, open-access web application for the analysis
    of in vivo tumor growth data in mouse models.

    Designed to standardize in vivo efficacy analysis, improve research reproducibility,
    and reduce animal usage, it provides tools to upload tumor volume or bioluminescence
    imaging (BLI) datasets, configure analysis parameters, detect outliers, and automatically
    compute tumor growth rates (TGR), group comparisons, and reports.


    By standardizing data processing and incorporating advanced temporal modeling,
    ViVo Platform enhances statistical power and contributes to the 3Rs principle
    by reducing the number of animals needed in preclinical efficacy studies.'
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/gcanudo-barreras/ViVo-Platform/blob/main/README.md
  - note: null
    type:
    - User manual
    url: https://github.com/gcanudo-barreras/ViVo-Platform/blob/main/ViVo_USER_MANUAL.md
  - note: Full methodology
    type:
    - Other
    url: https://www.biorxiv.org/content/10.1101/2025.10.14.682266v1
  - note: null
    type:
    - Release notes
    url: https://github.com/gcanudo-barreras/ViVo-Platform/releases/tag/v1.0-beta
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data analysis
      uri: http://edamontology.org/operation_2945
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output: []
  - cmd: null
    input:
    - data:
        term: Physiology parameter
        uri: http://edamontology.org/data_3722
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Morphology parameter
        uri: http://edamontology.org/data_3723
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: CSV
        uri: http://edamontology.org/format_3752
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://gcanudo-barreras.github.io/ViVo-Platform/
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2025-10-23T09:09:29.560348Z'
  license: MIT
  link:
  - note: null
    type:
    - Service
    url: https://gcanudo-barreras.github.io/ViVo-Platform/
  - note: bioRxiv preprint
    type:
    - Other
    url: https://www.biorxiv.org/content/10.1101/2025.10.14.682266v1
  - note: null
    type:
    - Repository
    url: https://github.com/gcanudo-barreras/ViVo-Platform
  maturity: Emerging
  name: ViVo Platform
  operatingSystem: []
  otherID: []
  owner: gcanudo-barreras
  publication:
  - doi: 10.1101/2025.10.14.682266
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Method
    version: Research Beta 1.0
  relation: []
  toolType:
  - Web application
  topic:
  - term: Preclinical and clinical studies
    uri: http://edamontology.org/topic_3379
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Laboratory animal science
    uri: http://edamontology.org/topic_3386
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - Research Beta 1.0
- accessibility: Open access
  additionDate: '2025-09-22T13:08:24.320192Z'
  biotoolsCURIE: biotools:nf-core_proteinfamilies
  biotoolsID: nf-core_proteinfamilies
  collectionID:
  - nf-core
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: nf-core/proteinfamilies is a bioinformatics pipeline that generates
    protein families from amino acid sequences and/or updates existing families with
    new sequences. It takes a protein fasta file as input, clusters the sequences
    and then generates protein family Hiden Markov Models (HMMs) along with their
    multiple sequence alignments (MSAs). Optionally, paths to existing family HMMs
    and MSAs can be given (must have matching base filenames one-to-one) in order
    to update with new sequences in case of matching hits.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/nf-core/proteinfamilies
  homepage_status: 0
  language:
  - Groovy
  lastUpdate: '2025-10-22T08:47:05.530398Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/nf-core/proteinfamilies
  maturity: Mature
  name: nf-core-proteinfamilies
  operatingSystem: []
  otherID:
  - type: rrid
    value: RRID:SCR_027374
    version: 1.3.0
  owner: vangelis
  publication:
  - doi: 10.1101/2025.08.12.670010
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  validated: 0
  version:
  - 2.0.0
- accessibility: Open access
  additionDate: '2025-10-20T03:29:21.364200Z'
  biotoolsCURIE: biotools:afexcore
  biotoolsID: afexcore
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: afexgenesis@gmail.com
    fundrefid: null
    gridid: null
    name: Nirmal Weerapperuma
    note: i'm the guy :)
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: https://www.instagram.com/nipun_weerapperuma
  description: AfexCore brings 12 essential bioinformatics tools into one intuitive
    GUI - built for researchers who need quick, reliable sequence analysis without
    the complexity (or price tag) of enterprise software.
  documentation: []
  download:
  - note: null
    type: Software package
    url: https://github.com/AfexGenesis/AfexCore/releases/tag/v2.1.4
    version: AfexCore 2.1.4 Beta Release
  editPermission:
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    type: private
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  elixir_badge: 0
  function: []
  homepage: https://afexgenesis.netlify.app
  homepage_status: 0
  language: []
  lastUpdate: '2025-10-20T03:29:21.366577Z'
  license: AGPL-3.0
  link:
  - note: Official Github Repository of the Software
    type:
    - Repository
    url: https://github.com/AfexGenesis/AfexCore
  - note: Official Website of the Software/Organization
    type:
    - Service
    url: https://afexgenesis.netlify.app
  maturity: null
  name: AfexCore
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: AnimateAI
  publication: []
  relation: []
  toolType:
  - Bioinformatics portal
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  validated: 0
  version:
  - Beta 2.1.4
- accessibility: Open access
  additionDate: '2025-10-14T12:23:40.079667Z'
  biotoolsCURIE: biotools:dynamont
  biotoolsID: dynamont
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A Dynamic Programming Approach to Segment ONT Signals. Dynamont is
    a segmentation/resquiggling tool for ONT signals.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/rnajena/dynamont
  homepage_status: 0
  language:
  - Python
  - C++
  lastUpdate: '2025-10-14T12:27:29.187590Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: Dynamont
  operatingSystem:
  - Linux
  otherID: []
  owner: Jannes
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - 0.7.2
- accessibility: Open access
  additionDate: '2025-09-23T15:11:59.204153Z'
  biotoolsCURIE: biotools:cells2visium
  biotoolsID: cells2visium
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: segmenting H&E images from Visium to assign each visium spot to the
    number of cell, occupancy and other morphological features of cells
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/cellgeni/cells2visium
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-10-14T09:04:03.542177Z'
  license: MIT
  link: []
  maturity: null
  name: cells2visium
  operatingSystem: []
  otherID: []
  owner: camlloyd
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-09-23T15:10:25.737722Z'
  biotoolsCURIE: biotools:bin2cell
  biotoolsID: bin2cell
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Join subcellular Visium HD bins into cells.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/Teichlab/bin2cell
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-10-14T09:02:29.580064Z'
  license: MIT
  link: []
  maturity: null
  name: bin2cell
  operatingSystem: []
  otherID: []
  owner: camlloyd
  publication:
  - doi: 10.1093/bioinformatics/btae546
    metadata:
      abstract: ''
      authors: []
      citationCount: 21
      date: '2024-09-01T00:00:00Z'
      journal: Bioinformatics
      title: Bin2cell reconstructs cells from high resolution Visium HD data
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - 0.3.3
- accessibility: null
  additionDate: '2025-10-07T12:12:24.732038Z'
  biotoolsCURIE: biotools:exposomeshiny_-_a_toolbox_for_exposome_data_analysis
  biotoolsID: exposomeshiny_-_a_toolbox_for_exposome_data_analysis
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: ExposomeShiny is a standalone web application implemented in R. It
    is available as source files and can be installed in any server or computer avoiding
    problems with data confidentiality. It is executed in RStudio which opens a browser
    window with the web application and provides a bridge between researchers and
    most of the state-of-the-art exposome analysis methodologies, without the need for advanced
    programming skills.
  documentation:
  - note: null
    type:
    - User manual
    url: https://isglobal-brge.github.io/exposome_bookdown/
  download: []
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    authors: []
    type: private
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  elixir_badge: 0
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  homepage: https://github.com/isglobal-brge/exposomeShiny/tree/master
  homepage_status: 0
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  license: null
  link: []
  maturity: null
  name: exposomeShiny
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  - Linux
  - Mac
  - Windows
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  owner: rodney
  publication:
  - doi: 10.1093/ije/dyab220
    metadata:
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      authors: []
      citationCount: 3
      date: '2022-02-01T00:00:00Z'
      journal: International Journal of Epidemiology
      title: 'Software Application Profile: ExposomeShiny - A toolbox for exposome
        data analysis'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
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  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-03-07T20:51:08.529472Z'
  biotoolsCURIE: biotools:oncoanalyser
  biotoolsID: oncoanalyser
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: Oncoanalyser is an nf-core Nextflow implementation of the tools developed
    by Hartwig Medical Foundation. The workflow is designed to comprehensively detect
    all variant types (SNV. MNV, InDel, SV, CNV, Fusions, Viral insertions, Telomere
    length, Genetic Immune Escape, mutational processes) as well as key tumor characteristics
    (purity, ploidy, TMB, MSI) from data derived from different short read platforms.
    The tooling is optimised for paired whole genome samples (90x tumor, 30x normal)
    but can be run on exome or panel (targeted) data. There is support for GRCh37
    and GRCh38 human reference genome builds.
  documentation: []
  download: []
  editPermission:
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    - jdeligt
    - VKasalica
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  homepage: https://github.com/nf-core/oncoanalyser/tree/dev
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2025-10-09T07:39:49.943872Z'
  license: GPL-3.0
  link:
  - note: GitHub page for issue tracking of Nextflow workflow implementation
    type:
    - Issue tracker
    - Repository
    url: https://github.com/nf-core/oncoanalyser/tree/dev
  - note: GitHub repository of underlying tools with issue tracking
    type:
    - Repository
    - Issue tracker
    url: https://github.com/hartwigmedical/hmftools
  maturity: Mature
  name: oncoanalyser
  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: jdeligt
  publication: []
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version:
  - '5.34'
- accessibility: Open access
  additionDate: '2025-08-25T14:36:13.568250Z'
  biotoolsCURIE: biotools:datmat
  biotoolsID: datmat
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: alexander.harms@health-ri.nl
    fundrefid: null
    gridid: null
    name: Alexander Harms
    note: null
    orcidid: https://orcid.org/0009-0001-5727-6732
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: h.achterberg@erasmusmc.nl
    fundrefid: null
    gridid: null
    name: Hakim Achterberg
    note: null
    orcidid: https://orcid.org/0000-0003-3772-4582
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Erasmus MC
    note: null
    orcidid: null
    rorid: 018906e22
    typeEntity: Institute
    typeRole: []
    url: null
  description: ‘datmat’ is a Python package aimed to easily gather data from a variety
    of sources and materialize it into a standardized format. It can download projects
    of imaging data from XNAT into the EUCAIM folder structure, and is designed to
    be extendible to support other inputs and outputs.
  documentation:
  - note: null
    type:
    - General
    url: https://datmat.readthedocs.io/latest/
  download:
  - note: null
    type: Software package
    url: https://pypi.org/project/datmat/
    version: null
  - note: null
    type: Source code
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    version: null
  editPermission:
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_2422
    output: []
  - cmd: null
    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_3802
    output: []
  homepage: https://gitlab.com/radiology/infrastructure/data-materialisation/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-10-07T13:06:50.742010Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://pypi.org/project/datmat/
  maturity: Emerging
  name: datmat
  operatingSystem:
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  - Mac
  otherID: []
  owner: agjharms
  publication: []
  relation:
  - biotoolsID: xnatpy
    type: uses
  toolType:
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  topic: []
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2025-08-25T14:46:01.217831Z'
  biotoolsCURIE: biotools:img2catalog
  biotoolsID: img2catalog
  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit:
  - email: alexander.harms@health-ri.nl
    fundrefid: null
    gridid: null
    name: Alexander Harms
    note: null
    orcidid: https://orcid.org/0009-0001-5727-6732
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Health-RI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole: []
    url: https://www.health-ri.nl/
  description: This tool, 'img2catalog', is built to extract metadata from imaging
    data repositories, map it to a model class, and export it to a catalog. The tool
    is set up to be modular, but it currently supports extracting metadata from an
    XNAT server, converting it to the Health-RI Core v2 metadata model (https://github.com/Health-RI/health-ri-metadata/tree/v2.0.0),
    based on DCAT-AP v3 and Health-DCAT AP, as defined in Pydantic classes using SeMPyRO
    (https://github.com/Health-RI/SeMPyRO), and either writing it to an RDF file,
    or pushing it to a FAIR Data Point (FDP).
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/Health-RI/img2catalog/blob/main/README.md
  download:
  - note: null
    type: Source code
    url: https://github.com/Health-RI/img2catalog
    version: null
  - note: null
    type: Software package
    url: https://pypi.org/project/img2catalog/
    version: null
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output: []
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  description: 'Tree-driven and alignment-free protein assignment to subfamilies outperforms
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  description: A web application for Streamlined Processing and Analysis of Large-Scale
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