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  additionDate: '2025-12-23T13:32:58.320710Z'
  biotoolsCURIE: biotools:opencausal
  biotoolsID: opencausal
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Hüseyin Küçükali
    note: null
    orcidid: https://orcid.org/0000-0003-1669-3107
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  description: An open platform for sharing, discussing and reusing causal graphs.
  documentation: []
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  homepage: https://opencausal.org/
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  lastUpdate: '2025-12-23T14:56:55.440549Z'
  license: null
  link: []
  maturity: Emerging
  name: Open Causal
  operatingSystem: []
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  owner: hkucukali
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version: []
- accessibility: Restricted access
  additionDate: '2025-05-16T09:56:39.880752Z'
  biotoolsCURIE: biotools:data_integration_quality_check_tool_diqct
  biotoolsID: data_integration_quality_check_tool_diqct
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  confidence_flag: null
  cost: Commercial
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    gridid: null
    name: Ioanna Chouvarda
    note: null
    orcidid: https://orcid.org/0000-0001-8915-6658
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    url: null
  description: A tool that checks the clinical metadata quality (validity, completeness),
    the integrity between images and clinical metadata provided as well as their accuracy,  the
    de-identification protocol applied, and existence of annotation together with
    the consistency between the images and the annotation files and informs the user
    on corrective actions prior to data upload.
  documentation:
  - note: null
    type:
    - Other
    url: https://docs.google.com/document/d/1b_5-pf94_QeOZVT2wVdG1YpWkAiTskwa/edit?usp=sharing&ouid=106267739460923945711&rtpof=true&sd=true
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  homepage: https://www.mdpi.com/2939712
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  language:
  - Python
  - R
  lastUpdate: '2025-12-23T13:36:06.026155Z'
  license: Proprietary
  link:
  - note: Link to the Harbor image
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    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicqt/
  - note: Link to the temporary license of the tool
    type:
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    url: https://drive.google.com/drive/folders/15HotbC4RnBXe83lzWEnOQZksB0pZa1JY
  maturity: Mature
  name: Data Integration Quality Check Tool (DIQCT)
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  - Windows
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    metadata:
      abstract: ''
      authors: []
      citationCount: 7
      date: '2024-09-01T00:00:00Z'
      journal: Information (Switzerland)
      title: Toward Ensuring Data Quality in Multi-Site Cancer Imaging Repositories
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1109/EMBC48229.2022.9871018
    metadata:
      abstract: ''
      authors: []
      citationCount: 5
      date: '2022-01-01T00:00:00Z'
      journal: Proceedings of the Annual International Conference of the IEEE Engineering
        in Medicine and Biology Society, EMBS
      title: 'Data Quality Check in Cancer Imaging Research: Deploying and Evaluating
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    note: null
    pmcid: null
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    type: []
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  relation: []
  toolType:
  - Desktop application
  - Suite
  topic:
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-28T23:55:08.439649Z'
  biotoolsCURIE: biotools:dicom_image_similarity-duplicate_checker
  biotoolsID: dicom_image_similarity-duplicate_checker
  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Detects duplicate or visually similar DICOM series using a tiered
    approach that combines metadata analysis, hash-based comparison, and pixel-level
    similarity metrics.

    Ideal for:

    1. High-level series comparison and classification, and

    2. Detecting duplicates even after post-processing (e.g., denoising, filtering).


    For scenarios requiring strict, image-level deduplication based on pixel content,
    fully agnostic to metadata changes, consider using [https://bio.tools/image_duplicate_check_tool]'
  documentation:
  - note: null
    type:
    - General
    url: https://docs.google.com/document/d/10GsrgRCeyrZrdus04iI-967llth0o9yE/edit?usp=drive_link&ouid=108776251279939449410&rtpof=true&sd=true
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  homepage: https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologies
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  language:
  - Python
  lastUpdate: '2025-12-23T13:24:16.938179Z'
  license: Apache-2.0
  link:
  - note: Link to the Harbor image
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/deduplication_tool
  maturity: Mature
  name: Image Duplicates Checker
  operatingSystem:
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  otherID: []
  owner: difoto
  publication: []
  relation:
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    type: includedIn
  toolType:
  - Command-line tool
  topic:
  - term: Data quality management
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  validated: 0
  version:
  - '2.0'
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T10:38:08.771699Z'
  biotoolsCURIE: biotools:ct-based_neuroblastoma_tumour_detection_and_segmentation
  biotoolsID: ct-based_neuroblastoma_tumour_detection_and_segmentation
  collectionID:
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  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
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    gridid: null
    name: GIBI230 - HULAFE
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    typeEntity: Institute
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  - email: pedromiguel_martinez@iislafe.es
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    name: Pedro-Miguel Martinez-Girones
    note: null
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    - Support
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  - email: adrian_galiana@iislafe.es
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    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
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  - email: carina_soler@iislafe.es
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  - email: luis_marti@iislafe.es
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  description: The tool performs by deep learning an automatic segmentation of the
    possible neuroblastoma tumours on Contrast Enhanced CT images (CE-CTs). Model
    architecture is Unet-based with residual operations, atrous dilation convolution
    and specific batch generator. It applies preprocessing steps as RAS conversion,
    resizing, z-score normalization, patching; and postprocessing operations. It takes
    DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.
  documentation:
  - note: null
    type:
    - Terms of use
    url: https://drive.google.com/file/d/1mvGl_fexQIqBR7njGl73V81VdZ7ycPBs/view?usp=drive_link
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  function:
  - cmd: "docker run --rm --gpus all \\\n\t-v /path/to/input:/input \\\n\t-v /path/to/output:/output\
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    input:
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    - data:
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      format:
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      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
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      uri: http://edamontology.org/operation_3553
    output:
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        term: Image
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      format:
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      - term: DICOM format
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ct-based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab
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  language:
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  lastUpdate: '2025-12-23T03:53:03.484226Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
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  name: CT-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-022_T-01-02-005)
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  owner: casopon
  publication:
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    metadata:
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      citationCount: 10
      date: '2021-04-02T00:00:00Z'
      journal: Applied Sciences (Switzerland)
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    type:
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  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
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  validated: 0
  version:
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- accessibility: null
  additionDate: '2025-12-23T00:16:25.679615Z'
  biotoolsCURIE: biotools:spatial_proteomics
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  collectionID: []
  confidence_flag: null
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  credit:
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    name: Ling-Hong Hung
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  - email: kayee@uw.edu
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  description: End-to-end spatial proteomics analysis workflow with QuPath integration.
    Our workflow consists of cell segmentation, batch correction, unsupervised clustering,
    validation of clusters on the image, and cell type clustering results visualization.
  documentation: []
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    type: Source code
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  language:
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  - R
  lastUpdate: '2025-12-23T00:29:13.711774Z'
  license: MIT
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  maturity: null
  name: Spatial Proteomics
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  publication:
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  version: []
- accessibility: null
  additionDate: '2016-06-24T11:36:59Z'
  biotoolsCURIE: biotools:oma
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  description: Project that aims to identify orthologs among publicly available, complete
    genomes. With many hundreds of genomes analyzed to date, it is one of the largest
    projects of its kind.
  documentation:
  - note: null
    type:
    - General
    url: https://omabrowser.org/oma/about/
  download: []
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  function:
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    input:
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    note: orthology prediction and paralogy OMA group
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  homepage: http://omabrowser.org/oma/home/
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  lastUpdate: '2025-12-22T16:58:22.083280Z'
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  owner: adrian.altenhoff
  publication:
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    metadata:
      abstract: ''
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      citationCount: 160
      date: '2015-01-28T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The OMA orthology database in 2015: Function predictions, better plant
        support, synteny view and other improvements'
    note: null
    pmcid: PMC4383958
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    type:
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  - doi: 10.1093/nar/gkad1020
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      citationCount: 46
      date: '2024-01-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'OMA or tholog y in 2024: impro v ed prokary ot e co v erãg e,ãncestralãnd
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    pmcid: PMC10767875
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    type:
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  - doi: 10.1093/nar/gkaa1007
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      citationCount: 144
      date: '2021-01-08T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'OMA orthology in 2021: Website overhaul, conserved isoforms, ancestral
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  - doi: 10.1093/nar/gkx1019
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      citationCount: 169
      date: '2018-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The OMA orthology database in 2018: Retrieving evolutionary relationships
        among all domains of life through richer web and programmatic interfaces'
    note: null
    pmcid: PMC5753216
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    type:
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  relation: []
  toolType:
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  - Web application
  - Database portal
  topic:
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  validated: 1
  version: []
- accessibility: null
  additionDate: '2025-05-29T09:54:35.422273Z'
  biotoolsCURIE: biotools:dicomseg_converter
  biotoolsID: dicomseg_converter
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  confidence_flag: null
  cost: null
  credit:
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    fundrefid: null
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    name: Mario Verdicchio
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  - email: marco.aiello@synlab.it
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    note: null
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  description: 'This repository provides tools for segmentation files conversion in
    DicomSEG, with a primary focus on: DICOM RTSTRUCT to DICOM SEG: A Python script
    (rtstruct/rtstruct2dcmseg.py) converts DICOM Radiotherapy Structure Set (RTSTRUCT)
    files, along with their referenced DICOM image series, into DICOM Segmentation
    (SEG) objects. It can also optionally convert the individual Regions of Interest
    (ROIs) defined in the RTSTRUCT into separate NIfTI (.nii.gz) files. Nifti Conversions
    via dcmqi and Custom Scripts: The Docker image built from this repository also
    includes command-line tools from dcmqi (DICOM Quantitative Imaging Toolkit) and
    custom Python scripts for various conversions, such as: ITK image formats (NIfTI,
    NRRD) to/from DICOM SEG. DICOM series to NIfTI. DICOM SEG to NIfTI (custom alternative).'
  documentation:
  - note: null
    type:
    - Command-line options
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  function:
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      \ /data/dicom_series \\\n  --outputDICOM /output/demo2_nifti_to_dicomseg/output.dcm"
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    note: null
    operation:
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      format:
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  - cmd: "docker run --rm \\\n  -v $(pwd)/DATA:/data \\\n  -v $(pwd)/demo_output:/output\
      \ \\\n  harbor.eucaim.cancerimage.eu/ingestion-tools/dicomseg_converter:1.4.0\
      \ \\\n  itkimage \\\n  --inputDICOM /data/dicomseg_input.dcm \\\n  --outputDirectory\
      \ /output/nifti_output \\\n  -t nifti"
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  - cmd: "docker run --rm \\\n  -v $(pwd)/DATA:/data \\\n  -v $(pwd)/demo_output:/output\
      \ \\\n  harbor.eucaim.cancerimage.eu/ingestion-tools/dicomseg_converter:1.4.0\
      \ \\\n  rtstruct2seg \\\n  /data/dicom_ct_series \\\n  /data/rtstruct_file.dcm\
      \ \\\n  /output/seg_from_rtstruct.dcm"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    output:
    - data:
        term: Image
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      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://github.com/marver17/DICOMSEG_Converter
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-22T15:55:00.949114Z'
  license: Apache-2.0
  link:
  - note: null
    type:
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  maturity: null
  name: Annotation Seg Converter
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: marioverd
  publication:
  - doi: 10.1186/s13244-021-01081-8
    metadata:
      abstract: ''
      authors: []
      citationCount: 34
      date: '2021-12-01T00:00:00Z'
      journal: Insights into Imaging
      title: How does DICOM support big data management? Investigating its use in
        medical imaging community
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  validated: 0
  version:
  - 1.4.0
- accessibility: Restricted access
  additionDate: '2025-05-22T12:06:46.866961Z'
  biotoolsCURIE: biotools:breast_dense_tissue_segmentation
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    gridid: null
    name: Ana María Arias Beltrán
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    typeEntity: Person
    typeRole:
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  description: The tool takes a digital mammogram and performs an automatic segmentation
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  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://drive.eucaim.cancerimage.eu/s/agktHMkYfy5pHes
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    type:
    - Training material
    url: https://youtu.be/_X68b2wjrj0?si=zCH_NRR_V9e8NUwh
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        term: Image
        uri: http://edamontology.org/data_2968
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    note: 'input_dcm_path: input path to the 2D DICOM image (FFDM); output_directory:
      output directory to store the results'
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    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
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      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/image_batch_iti-breast
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  language:
  - Python
  lastUpdate: '2025-12-22T14:34:39.139482Z'
  license: Proprietary
  link:
  - note: Scientific paper
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    - Other
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  - note: Harbor repository with the tool's Docker images
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/image_batch_iti-breast
  maturity: Mature
  name: Breast Dense Tissue Segmentation
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: dsilveira
  publication:
  - doi: 10.3390/diagnostics12081822
    metadata:
      abstract: ''
      authors: []
      citationCount: 7
      date: '2022-08-01T00:00:00Z'
      journal: Diagnostics
      title: 'Breast Dense Tissue Segmentation with Noisy Labels: A Hybrid Threshold-Based
        and Mask-Based Approach'
    note: null
    pmcid: PMC9406546
    pmid: '36010173'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version:
  - v1.0.6
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T09:19:51.404419Z'
  biotoolsCURIE: biotools:mr-based_dipg_tumour_detection_and_segmentation
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    typeEntity: Person
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    name: Pedro-Miguel Martinez-Girones
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    typeRole:
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    - Documentor
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    note: null
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    name: Carina Soler-Pons
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  description: The tool performs an automatic segmentation of the possible DIPG tumours
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    and Flair/T2-weighted magnetic resonance images. The tool includes a complete
    workflow from DICOM images to DICOM seg tumoral masks.
  documentation:
  - note: null
    type:
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    url: https://link.springer.com/article/10.1007/s10278-025-01557-9
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        term: Image
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    - data:
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    note: null
    operation:
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    note: null
    operation:
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        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/artifacts-tab
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  language:
  - Python
  lastUpdate: '2025-12-22T13:54:01.962965Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
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    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_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 DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: casopon
  publication:
  - doi: 10.1007/s10278-025-01557-9
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-01-01T00:00:00Z'
      journal: Journal of Imaging Informatics in Medicine
      title: Deep Learning Auto-segmentation of Diffuse Midline Glioma on Multimodal
        Magnetic Resonance 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 (with restrictions)
  additionDate: '2025-05-29T12:09:16.704255Z'
  biotoolsCURIE: biotools:mr-based_glioblastoma_tumour_detection_and_segmentation
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  collectionID:
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  cost: Free of charge (with restrictions)
  credit:
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    orcidid: null
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    url: null
  - email: maria_beser@iislafe.es
    fundrefid: null
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    name: Maria Beser-Robles
    note: null
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  description: 'The tool performs an automatic segmentation of the possible glioblastoma
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    edema (Peritumoral vasogenic edema), enhancing (Contrast-enhancing tumor region),
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    (Total tumor fusioning of necrosis+edema+enhancing). It applies preprocessing
    steps as skull stripping, intra-patient registration, z-score normalization, patching,
    among others. It takes DICOM images as input and generates tumoral masks in DICOM
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  - note: null
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  - note: null
    type:
    - Terms of use
    url: https://drive.google.com/file/d/1eqM5V0oILLlcuv5NF0ib4Gb6p2kA5EzU/view?usp=drive_link
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  function:
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        term: Image
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    note: null
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  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input \\\n  -v /path/to/output:/output\
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/artifacts-tab
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  language:
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  lastUpdate: '2025-12-22T13:47:41.562901Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
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  maturity: Mature
  name: MR-based glioblastoma tumour detection and segmentation (EUCAIM-SW-021_T-01-02-004)
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  otherID: []
  owner: casopon
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      abstract: ''
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      citationCount: 8
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      journal: International Journal of Computer Assisted Radiology and Surgery
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    note: null
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  - term: Machine learning
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  additionDate: '2025-12-22T13:40:13.527477Z'
  biotoolsCURIE: biotools:fastoma
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  owner: lsaint-aubert
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  - note: Source code. Also, use GitHub issue tracker to send bug reports and extension
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    type:
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  toolType:
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  topic:
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  description: MicroMiner assists in identifying single-residue substitutions in protein
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  description: JAMDA enables the preparation of individual protein structures and
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  description: PoseEdit automatically generates 2D diagrams of protein-ligand complexes,
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  description: DoGSite3 was developed for predicting robust and reliable small molecule
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  description: LifeSoaks was designed to find solvent channels in macromolecular structures
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  description: This kit uses Sandwich-CLIA as the method. The micro CLIA plate provided
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    immunoassay analyzer. The RLU value is positively associated with the concentration
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    the RLU value of the samples to the standard curve.
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  description: 'Hari ini keberuntungan kamu lagi bagus…

    Coba klik link ini, siapa tau “spin pertama langsung hoki” 🎰✨


    🎁 Yang join hari ini dapat bonus random!

    🔗 https://blackinhaler.com/Na9aG4c0R'
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    typeEntity: Project
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    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: SAMtools and BCFtools are widely used programs for processing and analysing
    high-throughput sequencing data. They include tools for file format conversion
    and manipulation, sorting, querying, statistics, variant calling, and effect analysis
    amongst other methods.
  documentation:
  - note: HowTos for samtools
    type:
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    url: http://www.htslib.org/doc/#howtos
  - note: null
    type:
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    url: http://www.htslib.org/doc/#manual-pages
  - note: null
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  function:
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      - term: SAM
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      - term: BAM
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    note: null
    operation:
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      uri: http://edamontology.org/operation_3695
    - term: Visualisation
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    - term: Data formatting
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    - term: Indexing
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    - term: Data parsing
      uri: http://edamontology.org/operation_1812
    - term: Data sorting
      uri: http://edamontology.org/operation_3802
    - term: Data editing
      uri: http://edamontology.org/operation_3096
    output:
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        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: BAM
        uri: http://edamontology.org/format_2572
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
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  lastUpdate: '2025-12-16T15:42:24.521617Z'
  license: MIT
  link:
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    type:
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    url: https://github.com/samtools/samtools
  - note: null
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    url: http://www.htslib.org/support/#lists
  - note: null
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    url: https://github.com/samtools/samtools/issues
  maturity: Mature
  name: SAMtools
  operatingSystem:
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  otherID: []
  owner: awhitwham
  publication:
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    metadata:
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      citationCount: 44891
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      journal: Bioinformatics
      title: The Sequence Alignment/Map format and SAMtools
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
    pmid: '19505943'
    type:
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    metadata:
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      citationCount: 8157
      date: '2021-02-01T00:00:00Z'
      journal: GigaScience
      title: Twelve years of SAMtools and BCFtools
    note: Twelve years of SAMtools and BCFtools.
    pmcid: PMC7931819
    pmid: '33590861'
    type:
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    version: null
  - doi: 10.1093/bioinformatics/btr509
    metadata:
      abstract: ''
      authors: []
      citationCount: 4643
      date: '2011-11-01T00:00:00Z'
      journal: Bioinformatics
      title: A statistical framework for SNP calling, mutation discovery, association
        mapping and population genetical parameter estimation from sequencing data
    note: null
    pmcid: PMC3198575
    pmid: '21903627'
    type: []
    version: null
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    type: uses
  toolType:
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  - Suite
  topic:
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    uri: http://edamontology.org/topic_0102
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 1
  version:
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  - '1.1'
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  - '1.3'
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  - '1.12'
  - '1.13'
  - '1.14'
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  - '1.16'
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  - '1.22'
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- accessibility: Open access
  additionDate: '2017-08-20T16:07:58Z'
  biotoolsCURIE: biotools:htslib
  biotoolsID: htslib
  collectionID:
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  description: The main purpose of HTSlib is to provide access to genomic information
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    reference data in FASTA format and tab-delimited files with genomic coordinates.
    It is utilized and incorporated into both SAMtools and BCFtools.
  documentation:
  - note: null
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      - term: FASTA
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    - data:
        term: Sequence variations
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      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
    note: null
    operation:
    - term: Data handling
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    output:
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        term: Sequence trace
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      format:
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      - term: CRAM
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      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
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        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
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  lastUpdate: '2025-12-16T15:41:44.904477Z'
  license: MIT
  link:
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  - note: null
    type:
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    url: http://www.htslib.org/support/#lists
  - note: null
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  maturity: Mature
  name: HTSlib
  operatingSystem:
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  validated: 1
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  description: BCFtools is a set of utilities that manipulate variant calls in the
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  documentation:
  - note: null
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  - note: A workflow for BCFtools.
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    note: Multiple data munging operations.
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    note: The Sequence Alignment/Map format and SAMtools.
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      citationCount: 8157
      date: '2021-02-01T00:00:00Z'
      journal: GigaScience
      title: Twelve years of SAMtools and BCFtools
    note: Twelve years of SAMtools and BCFtools.
    pmcid: PMC7931819
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  - term: GWAS study
    uri: http://edamontology.org/topic_3517
  - term: Genotyping experiment
    uri: http://edamontology.org/topic_3516
  validated: 1
  version:
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  - '1.2'
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  - 1.3.1
  - '1.4'
  - 1.4.1
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  biotoolsCURIE: biotools:nnunet
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    orcidid: null
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  description: "nnU-Net is a self-configuring method for deep learning-based biomedical\
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    \ Imaging and the Division of Medical Image Computing at the German Cancer Research\
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    \ Kidney and kidney tumor segmentation, Brain Tumor segmentation and Hippocampus\
    \ (MR data) segmentation"
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  - note: Docker containers and other relevant instructions
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    - User manual
    url: https://github.com/MIC-DKFZ/nnunet-eucaim-docker/
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    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet pretrained on Task007_Pancreas targeting are pancras and pancreas
      tumor
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
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    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet model pretrained on Task029_LiTS targeting are liver and liver
      tumor
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
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  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-hippocampus-segmentation
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet pretrained on Task004_Hippocampus MRI data targeting posterior
      and anterior parts of the hippocampus
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-colon-cancer
    input:
    - data:
        term: Raw image
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      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet pretrained on Task010_Colon targeting are colon cancer primaries.
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-brain-tumour-pet
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet pretrained on Task169_BrainTumorPET targeting are brain tumor
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-abdominal-organ-segmentation
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUNet model pretrained on Task017_AbdominalOrganSegmentation targeting
      thirteen different abdominal organs
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-kidney-tumour
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUNet model pretrained on Task135_KiTS2021 targeting are kidney, tumor
      and cyst.
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://github.com/MIC-DKFZ/nnUNet/tree/nnunetv1
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-16T12:04:54.619598Z'
  license: Apache-2.0
  link: []
  maturity: Mature
  name: nnUNet
  operatingSystem:
  - Linux
  otherID: []
  owner: ASHISR
  publication:
  - doi: 10.1038/s41592-020-01008-z
    metadata:
      abstract: ''
      authors: []
      citationCount: 6593
      date: '2021-02-01T00:00:00Z'
      journal: Nature Methods
      title: 'nnU-Net: a self-configuring method for deep learning-based biomedical
        image segmentation'
    note: null
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic: []
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2025-12-16T11:00:25.334832Z'
  biotoolsCURIE: biotools:globalamfungi
  biotoolsID: globalamfungi
  collectionID:
  - ELIXIR-CZ
  - Czech Republic
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: vetrovsky@biomed.cas.cz
    fundrefid: null
    gridid: null
    name: Tomas Vetrovsky
    note: null
    orcidid: https://orcid.org/0000-0002-0831-486X
    rorid: 02p1jz666
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-CZ
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole: []
    url: null
  description: The GlobalAMFungi Database is an open-access, global repository of
    arbuscular mycorrhizal (AM) fungal occurrence data compiled from high-throughput
    sequencing studies. It aggregates millions of DNA sequence observations of AM
    fungi from thousands of geographically referenced environmental samples, together
    with rich metadata on sampling location and environmental context, to map the
    global distribution and diversity of these key plant symbionts. The resource is
    designed to be community-driven and FAIR (Findable, Accessible, Interoperable,
    Reusable), supporting research into AM fungal ecology, biogeography, and how environmental
    factors shape their diversity.
  documentation:
  - note: null
    type:
    - User manual
    - Citation instructions
    - Quick start guide
    - Contributions policy
    - General
    url: https://globalamfungi.com/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity:
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  elixirNode:
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  elixirPlatform:
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  elixir_badge: 0
  function:
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    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Data deposition
      uri: http://edamontology.org/operation_3431
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: FASTA-HTML
        uri: http://edamontology.org/format_2310
  homepage: https://globalamfungi.com/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-12-16T11:00:25.337448Z'
  license: CC-BY-4.0
  link:
  - note: null
    type:
    - Helpdesk
    - Repository
    - Service
    url: https://globalamfungi.com/
  maturity: Mature
  name: globalamfungi
  operatingSystem: []
  otherID: []
  owner: TomasVetrovsky
  publication:
  - doi: 10.1111/nph.19283
    metadata:
      abstract: null
      authors: []
      citationCount: 0
      date: null
      journal: null
      title: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Database portal
  - Web application
  topic:
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  validated: 0
  version: []
- 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:
    authors: []
    type: private
  elixirCommunity:
  - Metabolomics
  - Proteomics
  - Rare Diseases
  elixirNode:
  - France
  elixirPlatform:
  - Tools
  - 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: null
  additionDate: '2025-12-16T07:02:36.779362Z'
  biotoolsCURIE: biotools:kg-microbe
  biotoolsID: kg-microbe
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: KG-Microbe is a standardized, interoperable framework for constructing
    modular microbial knowledge graphs that harmonize information about bacteria and
    archaea, e.g., organismal traits, environments and growth preferences, media,
    assays, and genome annotations. Starting from a core KG, the framework generates
    a hierarchy of related KGs ranging from millions to over 0.5 billion edges (KG-Microbe-Core,
    -Biomedical, -Function, -Biomedical-Function) structured according to the Biolink
    Model. KG-Microbe supports customizable taxa subsets and host organisms. The framework
    uses standard TSV formats but also outputs n-triples.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/Knowledge-Graph-Hub/kg-microbe
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-16T07:02:36.781707Z'
  license: null
  link: []
  maturity: null
  name: kg-microbe
  operatingSystem: []
  otherID: []
  owner: marcin
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - '20250307'
- 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:
    authors:
    - pedromiguel_martinez_HULAFE
    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:
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    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:
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    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'
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  toolType:
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  - Web service
  topic:
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    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: Restricted access
  additionDate: '2025-05-22T14:58:20.772120Z'
  biotoolsCURIE: biotools:extended_a_priori_probability_tool
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  collectionID:
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  credit:
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    fundrefid: null
    gridid: null
    name: Ana María Arias Beltrán
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
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    name: Instituto Tecnológico de Informática (ITI)
    note: null
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    typeEntity: Institute
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  description: The tool provides a semi-supervised metric (EAPP) for binary classification
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    bias present in the dataset, as well as other features that could provide a relatively
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  documentation:
  - note: null
    type:
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  - note: Tool License Agreement in DOCX format
    type:
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  - note: Tool License Summary in TXT format
    type:
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    url: https://drive.eucaim.cancerimage.eu/s/Z8mYAoPk2JjZLFL
  download: []
  editPermission:
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    input:
    - data:
        term: Structure
        uri: http://edamontology.org/data_0883
      format:
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        uri: http://edamontology.org/format_3752
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
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        uri: http://edamontology.org/format_3548
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
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        uri: http://edamontology.org/format_3603
    note: 'input_data_class0_path:  Input path for class 0 data; input_data_class1_path:
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      in a folder or compressed into a ZIP file, or a 3D DICOM series file; output_path:
      directory and filename (JSON format) where the results will be saved'
    operation:
    - term: Data analysis
      uri: http://edamontology.org/operation_2945
    output:
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        term: Structure
        uri: http://edamontology.org/data_0883
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/image_batch_iti-eapp
  homepage_status: 0
  language:
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  lastUpdate: '2025-12-15T12:21:49.565380Z'
  license: Proprietary
  link:
  - note: Scientific paper
    type:
    - Other
    url: https://ieeexplore.ieee.org/document/9950248
  - note: Harbor repository with the tool's Docker images
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/image_batch_iti-eapp
  maturity: Mature
  name: EAPP - Extended a Priori Probability tool
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: dsilveira
  publication:
  - doi: 10.1109/ACCESS.2022.3221936
    metadata:
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      authors: []
      citationCount: 0
      date: '2022-01-01T00:00:00Z'
      journal: IEEE Access
      title: 'Extended a Priori Probability (EAPP): A Data-Driven Approach for Machine
        Learning Binary Classification Tasks'
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3474
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  validated: 0
  version:
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  additionDate: '2025-12-15T11:29:08.759624Z'
  biotoolsCURIE: biotools:mitsorter
  biotoolsID: mitsorter
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Sharon Natasha Cox
    note: Researcher at University of Bari
    orcidid: https://orcid.org/0000-0002-8488-440X
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: angelovarvara94@gmail.com
    fundrefid: null
    gridid: null
    name: Angelo Sante Varvara
    note: PhD Student at SEMM Institute
    orcidid: https://orcid.org/0009-0005-3559-8430
    rorid: null
    typeEntity: Person
    typeRole:
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    url: https://www.linkedin.com/in/angelo-sante-varvara-b514661a6/
  description: Stand-alone tool for methylation-based discrimination of mitochondrial
    DNA ONT reads
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    type:
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    url: https://github.com/asvarvara/MitSorter/blob/main/README.md
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  language:
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  lastUpdate: '2025-12-15T11:29:47.221679Z'
  license: GPL-3.0
  link:
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    type:
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    url: https://github.com/asvarvara/MitSorter
  maturity: Emerging
  name: MitSorter
  operatingSystem:
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  publication:
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    metadata:
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      authors: []
      citationCount: 0
      date: '2025-01-01T00:00:00Z'
      journal: Bioinformatics Advances
      title: 'MitSorter: a standalone tool for accurate discrimination of mtDNA and
        NuMT ONT reads based on differential methylation'
    note: null
    pmcid: PMC12275464
    pmid: '40688360'
    type:
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    version: null
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  toolType:
  - Command-line tool
  - Workflow
  topic:
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    uri: http://edamontology.org/topic_0102
  validated: 0
  version: []
- accessibility: null
  additionDate: '2020-03-17T13:50:50Z'
  biotoolsCURIE: biotools:seqfu
  biotoolsID: seqfu
  collectionID: []
  confidence_flag: null
  cost: null
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  description: A collection of utilities to manipulate FASTA and FASTQ files, supporting
    Gzipped input.
  documentation:
  - note: null
    type:
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    url: https://telatin.github.io/seqfu2/
  download:
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    type: Software package
    url: https://github.com/telatin/seqfu2
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  - note: null
    type: Downloads page
    url: https://github.com/telatin/seqfu2/releases
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    type: Software package
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  function:
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    input:
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        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    note: null
    operation:
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    output:
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        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format: []
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  homepage_status: 0
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  link:
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    url: https://telatin.github.io/seqfu2
  - note: null
    type:
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    url: https://github.com/telatin/seqfu2/
  maturity: null
  name: seqfu
  operatingSystem: []
  otherID: []
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  publication:
  - doi: 10.3390/bioengineering8050059
    metadata:
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      authors: []
      citationCount: 36
      date: '2021-01-01T00:00:00Z'
      journal: Bioengineering
      title: 'Seqfu: A suite of utilities for the robust and reproducible manipulation
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    note: null
    pmcid: PMC8148589
    pmid: '34066939'
    type:
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    version: '1.0'
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0077
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
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  version:
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  - 1.13.0
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  - 1.16.0
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  - 1.20.0
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- accessibility: Open access
  additionDate: '2022-04-19T09:32:41.303637Z'
  biotoolsCURIE: biotools:metagwgs
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  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Claire Hoede
    note: null
    orcidid: https://orcid.org/0000-0001-5054-7731
    rorid: null
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    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: GenoToul bioinformatics facility
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole:
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  description: metagWGS is a workflow dedicated to the analysis of metagenomic data.
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    genes. Since release 2.3, binning step with the possibility of cross-alignment
    is included. It has been developed in collaboration with several CATI BIOS4biol
    agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France
    Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm
    funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.
  documentation:
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    type:
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    url: https://genotoul-bioinfo.pages-forge.inrae.fr/metagwgs/master/index.html
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    type: Test data
    url: https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets
    version: null
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  function:
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    input:
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        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
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        uri: http://edamontology.org/format_1930
    note: null
    operation:
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    output:
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      format:
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  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
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        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Gene functional annotation
      uri: http://edamontology.org/operation_3672
    output:
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        term: Count matrix
        uri: http://edamontology.org/data_3917
      format:
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        uri: http://edamontology.org/format_1915
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
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        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    output:
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        uri: http://edamontology.org/data_3494
      format:
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        uri: http://edamontology.org/format_1929
  homepage: https://forgemia.inra.fr/genotoul-bioinfo/metagwgs
  homepage_status: 0
  language:
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  lastUpdate: '2025-12-11T14:51:44.804907Z'
  license: GPL-3.0
  link:
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    type:
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    url: https://forge.inrae.fr/genotoul-bioinfo/metagwgs
  maturity: Mature
  name: metagWGS
  operatingSystem:
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  otherID: []
  owner: choede
  publication: []
  relation: []
  toolType:
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  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version:
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  - 2.5.0
- accessibility: Open access
  additionDate: '2025-12-11T14:36:21.061830Z'
  biotoolsCURIE: biotools:easy16s
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  confidence_flag: null
  cost: Free of charge
  credit:
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    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:
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  elixir_badge: 0
  function:
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    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_3744
    output: []
  homepage: https://easy16s.migale.inrae.fr/
  homepage_status: 0
  language:
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  lastUpdate: '2025-12-11T14:36:21.065324Z'
  license: AGPL-3.0
  link:
  - note: null
    type:
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    url: https://forge.inrae.fr/migale/easy16s
  - note: null
    type:
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    url: https://doi.org/10.57745/ZN1HXQ
  maturity: Mature
  name: easy16S
  operatingSystem:
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  - Windows
  - Linux
  otherID: []
  owner: cmidoux
  publication:
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    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  relation: []
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  topic:
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    uri: http://edamontology.org/topic_3174
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2019-02-13T17:01:40Z'
  biotoolsCURIE: biotools:Jalview
  biotoolsID: Jalview
  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Jim Procter
    note: null
    orcidid: https://orcid.org/0000-0002-7865-7382
    rorid: null
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  - email: null
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    rorid: null
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    url: https://www.lifesci.dundee.ac.uk/people/geoff-barton
  description: Jalview is a free cross-platform program for multiple sequence alignment
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    analyse them with phylogenetic trees and principal components analysis (PCA) plots
    and explore molecular structures and annotation.
  documentation:
  - note: null
    type:
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    url: https://www.jalview.org/about/citation
  - note: Hands-on exercises, Training courses and Training videos
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  - note: null
    type:
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  - note: null
    type:
    - User manual
    url: https://www.jalview.org/help/documentation/
  download:
  - note: null
    type: Downloads page
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    version: null
  - note: null
    type: Source code
    url: https://www.jalview.org/download/source/
    version: null
  - note: Binaries for all platforms
    type: Binaries
    url: https://www.jalview.org/download/?os=all
    version: null
  - note: null
    type: Icon
    url: https://www.jalview.org/favicon.svg
    version: null
  - note: Executable JAR file
    type: Binaries
    url: https://www.jalview.org/download/other/jar/
    version: null
  editPermission:
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  function:
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    input:
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        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
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        uri: http://edamontology.org/format_1948
      - term: FASTA
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      - term: FASTA-aln
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      - term: Pileup
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      - term: GFF2-seq
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      - term: BLC
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      - term: RNAML
        uri: http://edamontology.org/format_3311
      - term: Format
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      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: mmCIF
        uri: http://edamontology.org/format_1477
      - term: PHYLIP format
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      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
      - term: GCG MSF
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    - data:
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        uri: http://edamontology.org/data_0886
      format:
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        uri: http://edamontology.org/format_1476
    note: 'Other Input formats:

      AMSA (.amsa);

      JnetFile (.concise, .jnet);

      PFAM (.pfam);

      Substitution matrix (.matrix);

      Jalview Project File (.jvp);

      Jalview Feature File (.features, .jvfeatures);

      Jalview Annotations File (.annotations, .jvannotations);

      Predicted Aligned Error (PAE) Matrix File (.json)

      ...

      Other Output formats:

      PFAM (.pfam);

      BioJS (.biojs) (interactive HTML/Javascript);

      Jalview Project File (.jvp);'
    operation:
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    - term: Phylogenetic tree analysis
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      uri: http://edamontology.org/operation_0564
    output:
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      - term: FASTA
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      - term: Pileup
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      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: Format
        uri: http://edamontology.org/format_1915
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
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    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
      - term: GenBank format
        uri: http://edamontology.org/format_1936
    note: null
    operation:
    - term: Metabolic network modelling
      uri: http://edamontology.org/operation_3660
    output:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: Biological pathway or network format
        uri: http://edamontology.org/format_2013
  homepage: https://github.com/AuReMe/mpwt
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-10T12:34:59.619365Z'
  license: LGPL-3.0
  link: []
  maturity: Mature
  name: mpwt
  operatingSystem: []
  otherID: []
  owner: agnesbarnabe
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 0
  version:
  - v0.8.8
- accessibility: null
  additionDate: '2025-11-24T15:38:31.636921Z'
  biotoolsCURIE: biotools:prolipipe
  biotoolsID: prolipipe
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Large-scale assessment of metabolic profiles on bacteria focusing on
    specific pathways.
  documentation: []
  download:
  - note: conda install -c fermentsdufutur prolipipe
    type: Software package
    url: https://anaconda.org/fermentsdufutur
    version: v0.1.1
  editPermission:
    authors:
    - Noe_Robert
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: prolipipe -d DIRECTORY --tax TAXFILE --pwy PWY_FOLD
    input:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: Biological pathway or network format
        uri: http://edamontology.org/format_2013
      - term: TSV
        uri: http://edamontology.org/format_3475
    note: "Extract pathways of interest from AuFAMe workflow output which reconstructs\
      \ metabolic pathway based on bacterial genomes. \nReturn an interactive report\
      \ and TSV files with completion for each pathway."
    operation:
    - term: Pathway analysis
      uri: http://edamontology.org/operation_3928
    output:
    - data:
        term: Pathway or network report
        uri: http://edamontology.org/data_2984
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://github.com/AuReMe/prolipipe
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-10T11:49:38.729308Z'
  license: GPL-3.0
  link: []
  maturity: Emerging
  name: Prolipipe
  operatingSystem: []
  otherID: []
  owner: agnesbarnabe
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 0
  version: []
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