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    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/samtools/issues
  maturity: Mature
  name: SAMtools
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/bioinformatics/btp352
    metadata:
      abstract: ''
      authors: []
      citationCount: 44891
      date: '2009-08-01T00:00:00Z'
      journal: Bioinformatics
      title: The Sequence Alignment/Map format and SAMtools
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
    pmid: '19505943'
    type:
    - Primary
    version: null
  - doi: 10.1093/gigascience/giab008
    metadata:
      abstract: ''
      authors: []
      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:
    - Primary
    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
  relation:
  - biotoolsID: htslib
    type: uses
  toolType:
  - Command-line tool
  - Suite
  topic:
  - term: Mapping
    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:
  - '1.0'
  - '1.1'
  - '1.2'
  - '1.3'
  - 1.3.1
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - 1.16.1
  - '1.17'
  - '1.18'
  - '1.19'
  - 1.19.1
  - 1.19.2
  - '1.20'
  - '1.21'
  - '1.22'
  - '1.23'
- accessibility: Open access
  additionDate: '2015-08-24T08:35:55Z'
  biotoolsCURIE: biotools:bcftools
  biotoolsID: bcftools
  collectionID:
  - BCFtools
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: BCFtools is a set of utilities that manipulate variant calls in the
    Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently
    with both VCFs and BCFs, both uncompressed and BGZF-compressed.
  documentation:
  - note: null
    type:
    - General
    url: http://www.htslib.org/doc/bcftools.html
  - note: A workflow for BCFtools.
    type:
    - Other
    url: http://www.htslib.org/workflow/#mapping_to_variant
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: Multiple data munging operations.
    operation:
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2025-12-16T15:40:43.213782Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/bcftools
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/bcftools/issues
  maturity: Mature
  name: BCFtools
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/bioinformatics/btp352
    metadata:
      abstract: ''
      authors: []
      citationCount: 44891
      date: '2009-08-01T00:00:00Z'
      journal: Bioinformatics
      title: The Sequence Alignment/Map format and SAMtools
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
    pmid: '19505943'
    type:
    - Primary
    version: null
  - doi: 10.1093/gigascience/giab008
    metadata:
      abstract: ''
      authors: []
      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:
    - Primary
    version: null
  relation:
  - biotoolsID: htslib
    type: uses
  toolType:
  - Command-line tool
  - Suite
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: GWAS study
    uri: http://edamontology.org/topic_3517
  - term: Genotyping experiment
    uri: http://edamontology.org/topic_3516
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - '1.3'
  - 1.3.1
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - 1.10.1
  - 1.10.2
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - '1.17'
  - '1.18'
  - '1.19'
  - '1.20'
  - '1.21'
  - '1.22'
  - '1.23'
- accessibility: null
  additionDate: '2025-07-21T09:36:40.711284Z'
  biotoolsCURIE: biotools:nnunet
  biotoolsID: nnunet
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit:
  - email: r.floca@Dkfz-Heidelberg.de
    fundrefid: null
    gridid: null
    name: DKFZ Heidelberg
    note: Group Lead and Board Member, Medical Image Computing department, DKFZ Heidelberg
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Contributor
    - Maintainer
    url: https://www.dkfz.de/
  description: "nnU-Net is a self-configuring method for deep learning-based biomedical\
    \ image segmentation, developed by the Applied Computer Vision Lab (ACVL) of Helmholtz\
    \ Imaging and the Division of Medical Image Computing at the German Cancer Research\
    \ Center (DKFZ). It is designed to automatically adapt to a given dataset, analyzing\
    \ the provided training cases to configure a matching U-Net-based segmentation\
    \ pipeline without requiring expertise from the user.\nThe tool provides pretrained\
    \ models for \nPancreas and Pancreas tumor segmentation, Colon cancer primaries\
    \ segmentation, Abdominal organ segmentation, Liver and liver tumor segmentation,\
    \ Kidney and kidney tumor segmentation, Brain Tumor segmentation and Hippocampus\
    \ (MR data) segmentation"
  documentation:
  - note: GitHub Readme
    type:
    - General
    url: https://github.com/MIC-DKFZ/nnUNet/tree/nnunetv1
  - note: Docker containers and other relevant instructions
    type:
    - User manual
    url: https://github.com/MIC-DKFZ/nnunet-eucaim-docker/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: docker run --rm -v /host/dataset/study_001/:/home/eucaim/nnUNet_input -v
      /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-pancreas-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 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
      --gpus all nnunet-liver-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 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
        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-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
        uri: http://edamontology.org/data_3424
      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: '2025-12-15T14:17:14.627791Z'
  biotoolsCURIE: biotools:asafind
  biotoolsID: asafind
  collectionID:
  - ELIXIR-CZ
  - Czech Republic
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: mvohnoutova@jcu.cz
    fundrefid: null
    gridid: null
    name: Marta Vohnoutová
    note: null
    orcidid: https://orcid.org/0000-0002-8915-8626
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    - Maintainer
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699
  - email: agruber@prf.jcu.cz
    fundrefid: null
    gridid: null
    name: Ansgar Gruber
    note: null
    orcidid: https://orcid.org/0000-0002-5876-4391
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401
  description: "ASAFind is a software that predicts the intracellular location of\
    \ proteins in cells with four membrane-bound complex plastids of red algal origin.\
    \ \nThese plastids evolved via eukaryote-eukaryote endosymbiosis and for example\
    \ can be found in diatoms and cryptophytes. ASAFind uses protein sequence data\
    \ and external predictions of signal peptides (by the tools SignalP and TargetP),\
    \ and predicts plastid proteins, and proteins that are targeted to the periplastidic\
    \ compartment from these data; optionally, a graphical output can generated."
  documentation:
  - note: null
    type:
    - Installation instructions
    url: https://asafind.jcu.cz/download-page/
  download:
  - note: Download page on web-service, links to repository
    type: Downloads page
    url: https://asafind.jcu.cz/download-page/
    version: '2.0'
  editPermission:
    authors:
    - agruber
    type: group
  elixirCommunity:
  - Plant Sciences
  - Marine Metagenomics
  - Microbial Biotechnology
  elixirNode:
  - Czech Republic
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format: []
    note: null
    operation:
    - term: Subcellular localisation prediction
      uri: http://edamontology.org/operation_2489
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format: []
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format: []
  homepage: https://asafind.jcu.cz/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-15T17:36:43.189214Z'
  license: CC-BY-SA-4.0
  link:
  - note: Web Service
    type:
    - Service
    url: https://asafind.jcu.cz
  - note: Information and source code, for local installation or development
    type:
    - Repository
    url: https://github.com/ASAFind/ASAFind-2
  maturity: Mature
  name: ASAFind
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: martavohnoutova
  publication:
  - doi: 10.1111/tpj.70138
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-06-01T00:00:00Z'
      journal: Plant Journal
      title: 'ASAFind 2.0: multi-class protein targeting prediction for diatoms and
        algae with complex plastids'
    note: Publication of the current version of ASAFind (2.0)
    pmcid: PMC12136025
    pmid: '40464854'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1111/tpj.12734
    metadata:
      abstract: ''
      authors: []
      citationCount: 138
      date: '2015-02-01T00:00:00Z'
      journal: Plant Journal
      title: Plastid proteome prediction for diatoms and other algae with secondary
        plastids of the red lineage
    note: Publication of the first version of ASAFind
    pmcid: PMC4329603
    pmid: '25438865'
    type:
    - Other
    version: '1.0'
  - doi: 10.48550/arXiv.2303.02509
    metadata: null
    note: Benchmarking of the performance of the first version of ASAFind
    pmcid: null
    pmid: null
    type:
    - Benchmarking study
    version: '1.0'
  relation:
  - biotoolsID: signalp
    type: uses
  - biotoolsID: targetp
    type: uses
  toolType:
  - Script
  - Command-line tool
  - Web service
  topic:
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - '2.0'
- accessibility: Open access
  additionDate: '2025-12-15T17:27:55.661547Z'
  biotoolsCURIE: biotools:thaf
  biotoolsID: thaf
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: contact@verdanta.tech
    fundrefid: null
    gridid: null
    name: Audrius Meskauskas
    note: Verdanta is an early startup in Switzerland, providing curated RNASeq pipeline.
      Thaf is part of our software stack that is released open source.
    orcidid: https://orcid.org/0009-0006-1714-3691
    rorid: null
    typeEntity: Person
    typeRole: []
    url: https://verdanta.info
  description: thaf is a command-line tool to extract transcript sequences from a
    genome FASTA file based on GFF3 annotation files. It can also generate transcript-to-gene
    mapping files compatible with tools such as Salmon.
  documentation:
  - note: README provides enough information to use the tool
    type:
    - General
    url: https://crates.io/crates/thaf
  download:
  - note: Use Cargo commands to install the application. Cargo will build it from
      the source.
    type: Other
    url: https://crates.io/crates/thaf
    version: 0.0.4
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "thaf \\\n  -f <INPUT_GFF3> \\\n  -d <DNA_FASTA> \\\n  -t <OUTPUT_FASTA>\
      \ \\\n  [-g <GENEMAP_FILE>]\n  [-e <FEATURES>]"
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format: []
    note: Produce transcriptome file from genomic DNA and gff3
    operation:
    - term: Sequence coordinate conversion
      uri: http://edamontology.org/operation_3267
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format: []
  homepage: https://crates.io/crates/thaf
  homepage_status: 0
  language:
  - Rust
  lastUpdate: '2025-12-15T17:31:34.066168Z'
  license: BSD-3-Clause
  link:
  - note: Crates.io page providing installation instructions and README.
    type:
    - Software catalogue
    url: https://crates.io/crates/thaf
  - note: Source code. Also, use GitHub issue tracker to send bug reports and extension
      proposals.
    type:
    - Repository
    url: https://github.com/bourumir-wyngs/thaf
  maturity: Emerging
  name: thaf
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Bourumir
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version:
  - 0.0.4
- accessibility: Restricted access
  additionDate: '2025-05-22T14:58:20.772120Z'
  biotoolsCURIE: biotools:extended_a_priori_probability_tool
  biotoolsID: extended_a_priori_probability_tool
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit:
  - email: aarias@iti.es
    fundrefid: null
    gridid: null
    name: Ana María Arias Beltrán
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Instituto Tecnológico de Informática (ITI)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: The tool provides a semi-supervised metric (EAPP) for binary classification
    tasks that considers not only the a priori probability but also some possible
    bias present in the dataset, as well as other features that could provide a relatively
    trivial separability of the target classes. Therefore, it allows for evaluating
    the ease or complexity of the task or bias of the data beyond the well-established
    baseline for any binary classification.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://drive.eucaim.cancerimage.eu/s/Ld2AgbGZmm4qcke
  - note: Tool License Agreement in DOCX format
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/CAwxZaC4xDzkCA5
  - note: Tool License Summary in TXT format
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/Z8mYAoPk2JjZLFL
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: jobman submit -i image_batch_EAPP -r small gpu -- -i0 input_data_class0_path
      -i1 input_data_class1_path -o output_directory/results.json
    input:
    - data:
        term: Structure
        uri: http://edamontology.org/data_0883
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - 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: PNG
        uri: http://edamontology.org/format_3603
    note: 'input_data_class0_path:  Input path for class 0 data; input_data_class1_path:
      Input path for class 1 data. In both cases it must be a CSV file, images stored
      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:
    - data:
        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:
  - Python
  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:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: dsilveira
  publication:
  - doi: 10.1109/ACCESS.2022.3221936
    metadata:
      abstract: ''
      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:
  - Command-line tool
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  validated: 0
  version:
  - v1.0.1
- accessibility: Restricted access
  additionDate: '2025-05-22T12:06:46.866961Z'
  biotoolsCURIE: biotools:breast_dense_tissue_segmentation
  biotoolsID: breast_dense_tissue_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit:
  - email: aarias@iti.es
    fundrefid: null
    gridid: null
    name: Ana María Arias Beltrán
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Instituto Tecnológico de Informática (ITI)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: The tool takes a digital mammogram and performs an automatic segmentation
    of the breast area and the dense tissue. After the mammogram segmentation, the
    tool returns a DICOM-SEG image with both the dense tissue and the breast tissue
    mask combined.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://drive.eucaim.cancerimage.eu/s/agktHMkYfy5pHes
  - note: Tool License Agreement in DOCX format
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/gPcqYKakCDSXGjN
  - note: Tool License Summary in TXT format
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/7ZPfQqsJ6YRjgpe
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: 'jobman submit -i mammography-density-segmenter -r small-gpu -- -p

      input_dcm_path -o output_directory'
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: 'input_dcm_path: input path to the 2D DICOM image (FFDM); output_directory:
      output directory to store the results'
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/image_batch_iti-breast
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-15T12:09:26.486490Z'
  license: Proprietary
  link:
  - note: Scientific paper
    type:
    - Other
    url: https://pubmed.ncbi.nlm.nih.gov/36010173/
  - 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
  - Linux
  - Windows
  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
  additionDate: '2025-12-15T11:29:08.759624Z'
  biotoolsCURIE: biotools:mitsorter
  biotoolsID: mitsorter
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: sharonnatasha.cox@uniba.it
    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:
    - Primary contact
    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:
    - Developer
    url: https://www.linkedin.com/in/angelo-sante-varvara-b514661a6/
  description: Stand-alone tool for methylation-based discrimination of mitochondrial
    DNA ONT reads
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://github.com/asvarvara/MitSorter/blob/main/README.md
  download: []
  editPermission:
    authors:
    - sharonnatasha.cox
    type: group
  elixirCommunity:
  - Federated Human Data
  elixirNode:
  - Italy
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://github.com/asvarvara/MitSorter
  homepage_status: 0
  language:
  - Python
  - Shell
  lastUpdate: '2025-12-15T11:29:47.221679Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/asvarvara/MitSorter
  maturity: Emerging
  name: MitSorter
  operatingSystem:
  - Linux
  otherID: []
  owner: asvarvara
  publication:
  - doi: 10.1093/bioadv/vbaf135
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-01-01T00:00:00Z'
      journal: Bioinformatics Advances
      title: 'MitSorter: a standalone tool for accurate discrimination of mtDNA and
        NuMT ONT reads based on differential methylation'
    note: null
    pmcid: PMC12275464
    pmid: '40688360'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Workflow
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  validated: 0
  version: []
- accessibility: null
  additionDate: '2020-03-17T13:50:50Z'
  biotoolsCURIE: biotools:seqfu
  biotoolsID: seqfu
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: A collection of utilities to manipulate FASTA and FASTQ files, supporting
    Gzipped input.
  documentation:
  - note: null
    type:
    - User manual
    url: https://telatin.github.io/seqfu2/
  download:
  - note: null
    type: Software package
    url: https://github.com/telatin/seqfu2
    version: null
  - note: null
    type: Downloads page
    url: https://github.com/telatin/seqfu2/releases
    version: null
  - note: null
    type: Software package
    url: https://bioconda.github.io/recipes/seqfu/README.html
    version: 1.0.0-1.22.3
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: seqfu [subcommand] FASTX > FASTX
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    note: null
    operation:
    - term: Nucleic acid sequence analysis
      uri: http://edamontology.org/operation_2478
    output:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format: []
  homepage: https://telatin.github.io/seqfu2/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-12T21:43:34.328705Z'
  license: null
  link:
  - note: Documentation
    type:
    - Other
    url: https://telatin.github.io/seqfu2
  - note: null
    type:
    - Repository
    url: https://github.com/telatin/seqfu2/
  maturity: null
  name: seqfu
  operatingSystem: []
  otherID: []
  owner: telatin
  publication:
  - doi: 10.3390/bioengineering8050059
    metadata:
      abstract: ''
      authors: []
      citationCount: 36
      date: '2021-01-01T00:00:00Z'
      journal: Bioengineering
      title: 'Seqfu: A suite of utilities for the robust and reproducible manipulation
        of sequence files'
    note: null
    pmcid: PMC8148589
    pmid: '34066939'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - 1.10.0
  - 1.11.0
  - 1.12.0
  - 1.13.0
  - 1.14.0
  - 1.15.0
  - 1.16.0
  - 1.17.0
  - 1.19.0
  - 1.20.0
  - 1.21.0
  - 1.22.0
  - 1.22.3
- accessibility: null
  additionDate: '2025-04-18T15:04:18.411979Z'
  biotoolsCURIE: biotools:dicom_tags_extractor
  biotoolsID: dicom_tags_extractor
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: BC|Platforms
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://www.bcplatforms.com/
  description: Scans the DICOM files of a defined directory at the series level, and
    produces as output either 1/one single csv file containing all preselected DICOM
    tags for each detected series; 2/ one single csv file only containing the patientID
    and the corresponding StudyUIDs.
  documentation:
  - note: null
    type:
    - General
    url: https://docs.google.com/document/d/1QCRHohdMe7lX1xTYaw8WxOW_9v2D9EAl/edit
  download:
  - note: '1- Install ORAS tool (https://oras.land/docs/installation).

      2- Login in the registry using the command oras login harbor.eucaim.cancerimage.eu,
      and provide a username and a token

      3- Download the file by using the command oras pull harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_tag_extraction:1.0'
    type: Software package
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories
    version: '1.1'
  editPermission:
    authors:
    - ThomasTrouillard
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  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:
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output: []
  - 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:
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output: []
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_tag_selection/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-12T08:46:59.476389Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Other
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_tag_selection/info-tab
  maturity: Legacy
  name: DICOM tags extractor
  operatingSystem:
  - Linux
  - Windows
  otherID: []
  owner: lsaint-aubert
  publication: []
  relation:
  - biotoolsID: eetl_toolset
    type: usedBy
  - biotoolsID: eucaim_wizard_tool
    type: usedBy
  toolType:
  - Command-line tool
  topic:
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version:
  - '1.1'
- accessibility: Open access
  additionDate: '2019-02-13T17:01:40Z'
  biotoolsCURIE: biotools:Jalview
  biotoolsID: Jalview
  collectionID:
  - ELIXIR-UK
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Jim Procter
    note: null
    orcidid: https://orcid.org/0000-0002-7865-7382
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.lifesci.dundee.ac.uk/people/jim-procter
  - email: null
    fundrefid: null
    gridid: null
    name: Geoff Barton
    note: null
    orcidid: https://orcid.org/0000-0002-9014-5355
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://www.lifesci.dundee.ac.uk/people/geoff-barton
  description: Jalview is a free cross-platform program for multiple sequence alignment
    editing, visualisation and analysis. Use it to align, view and edit sequence alignments,
    analyse them with phylogenetic trees and principal components analysis (PCA) plots
    and explore molecular structures and annotation.
  documentation:
  - note: null
    type:
    - Citation instructions
    url: https://www.jalview.org/about/citation
  - note: Hands-on exercises, Training courses and Training videos
    type:
    - Training material
    url: https://www.jalview.org/training/
  - note: null
    type:
    - FAQ
    url: https://www.jalview.org/help/faq
  - note: null
    type:
    - User manual
    url: https://www.jalview.org/help/documentation/
  download:
  - note: null
    type: Downloads page
    url: https://www.jalview.org/download
    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:
    authors:
    - ben_s
    - jimprocter
    type: group
  elixirCommunity: []
  elixirNode:
  - UK
  elixirPlatform:
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: GFF2-seq
        uri: http://edamontology.org/format_1938
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: RNAML
        uri: http://edamontology.org/format_3311
      - term: Format
        uri: http://edamontology.org/format_1915
      - 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
        uri: http://edamontology.org/format_1997
      - 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
        uri: http://edamontology.org/format_1947
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: PDB
        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:
    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - 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
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      - term: PNG
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  homepage_status: 0
  language: []
  lastUpdate: '2025-12-11T14:16:30.074724Z'
  license: GPL-3.0
  link:
  - note: null
    type:
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    url: https://discourse.jalview.org/
  - note: null
    type:
    - Issue tracker
    url: https://issues.jalview.org/
  - note: Latest development version
    type:
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    url: https://www.jalview.org/development/jalview_develop/
  - note: null
    type:
    - Repository
    url: https://gitlab.jalview.org/jalview/jalview.git
  - note: Twitter feed
    type:
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  - note: YouTube training videos
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  - note: null
    type:
    - Social media
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  maturity: Mature
  name: Jalview
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: ben_s
  publication:
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    metadata:
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      authors: []
      citationCount: 7717
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      journal: Bioinformatics
      title: Jalview Version 2-A multiple sequence alignment editor and analysis workbench
    note: null
    pmcid: PMC2672624
    pmid: '19151095'
    type: []
    version: null
  relation:
  - biotoolsID: jabaws
    type: uses
  - biotoolsID: chimera
    type: uses
  - biotoolsID: chimerax
    type: uses
  - biotoolsID: pymol
    type: uses
  - biotoolsID: bioconda
    type: includedIn
  - biotoolsID: 3d-beacons
    type: uses
  - biotoolsID: uniprot
    type: uses
  - biotoolsID: pfam
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  - biotoolsID: ensembl
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    type: uses
  - biotoolsID: rfam
    type: uses
  - biotoolsID: 3d-beacons
    type: uses
  toolType:
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  - Command-line tool
  topic:
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    uri: http://edamontology.org/topic_0080
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 1
  version:
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- accessibility: Open access
  additionDate: '2025-12-08T13:54:29.684754Z'
  biotoolsCURIE: biotools:oct-to-tiff
  biotoolsID: oct-to-tiff
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A command line tool for converting optical coherence tomography angiography
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  documentation: []
  download: []
  editPermission:
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  homepage_status: 0
  language:
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  lastUpdate: '2025-12-10T22:41:05.503948Z'
  license: BSD-3-Clause
  link: []
  maturity: null
  name: oct-to-tiff
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: camlloyd
  publication: []
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3452
  - term: Ophthalmology
    uri: http://edamontology.org/topic_3417
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2025-12-10T13:18:28.703003Z'
  biotoolsCURIE: biotools:emapper2gbk
  biotoolsID: emapper2gbk
  collectionID:
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  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Arnaud
    note: null
    orcidid: https://orcid.org/0000-0003-1170-0785
    rorid: null
    typeEntity: Person
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  description: creation of genbank files from Eggnog-mapper annotation outputs
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  - note: null
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    - User manual
    url: https://github.com/AuReMe/emapper2gbk
  download:
  - note: null
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  function:
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        term: Sequence assembly
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    note: Genomic -single mode
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  language:
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  - note: Access to Python library
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  operatingSystem:
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  otherID: []
  owner: Noe_Robert
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  toolType:
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  topic:
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  validated: 0
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- accessibility: null
  additionDate: '2024-12-21T15:24:55.662209Z'
  biotoolsCURIE: biotools:stripepy
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  description: StripePy recognizes architectural stripes in 3C and Hi-C contact maps
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    type:
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  - note: null
    type: Container file
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  - note: null
    type: Test data
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    version: null
  - note: null
    type: Binaries
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  - note: null
    type: Binaries
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    type:
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  - note: null
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      journal: Bioinformatics
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    note: null
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  description: Pathway Tools multiprocessing wrapper (for PathoLogic).
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  download:
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      - term: GenBank format
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    note: null
    operation:
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      format:
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  name: mpwt
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  toolType:
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  validated: 0
  version:
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- accessibility: null
  additionDate: '2025-11-24T15:38:31.636921Z'
  biotoolsCURIE: biotools:prolipipe
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  description: Large-scale assessment of metabolic profiles on bacteria focusing on
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  documentation: []
  download:
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      format:
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    note: "Extract pathways of interest from AuFAMe workflow output which reconstructs\
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    operation:
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    output:
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      format:
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  homepage: https://github.com/AuReMe/prolipipe
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  language:
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  lastUpdate: '2025-12-10T11:49:38.729308Z'
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  link: []
  maturity: Emerging
  name: Prolipipe
  operatingSystem: []
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  owner: agnesbarnabe
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  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0602
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-11-14T17:30:28.515260Z'
  biotoolsCURIE: biotools:raptor-rnaseq
  biotoolsID: raptor-rnaseq
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: RAPTOR intelligently recommends and benchmarks RNA-seq pipelines by
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    sample size). Multi-criteria scoring provides personalized pipeline recommendations
    from eight production-ready workflows (STAR-RSEM-DESeq2, Salmon-edgeR, Kallisto-Sleuth,
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    accuracy, efficiency, and reproducibility metrics across all pipelines on user
    data with customizable priority modes.
  documentation:
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    type:
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    - Code of conduct
    - Command-line options
    - FAQ
    - General
    - Installation instructions
    - Quick start guide
    - Release notes
    - Terms of use
    - Training material
    - User manual
    url: https://github.com/AyehBlk/RAPTOR
  download:
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  elixirNode:
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      format:
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      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: CSV
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    note: 'Comprehensive statistical characterization of RNA-seq datasets: library
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      biological coefficient of variation (BCV), mean-variance relationships, sequencing
      depth assessment, and experimental design balance.'
    operation:
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    - term: Sequencing quality control
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    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
  - cmd: raptor run --pipeline 3 --data your_fastq/ --output results/
    input:
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        term: Statistical estimate score
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      format:
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      - term: CSV
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    - data:
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      format:
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      - term: CSV
        uri: http://edamontology.org/format_3752
    note: 'Intelligent recommendation system analyzing data characteristics (library
      size variation, zero-inflation, BCV, sample size, sequencing depth, design complexity)
      and matching them to pipeline strengths using multi-criteria scoring (0-200).
      Recommends from 8 pipelines: STAR-RSEM-DESeq2 (high accuracy), HISAT2-StringTie-Ballgown
      (novel transcripts), Salmon-edgeR (balanced), Kallisto-Sleuth (ultra-fast),
      STAR-HTSeq-limma (complex designs), STAR-featureCounts-NOISeq (non-parametric),
      Bowtie2-RSEM-EBSeq (Bayesian), HISAT2-Cufflinks-Cuffdiff (legacy). Priority
      modes: accuracy, speed, memory, or balanced.'
    operation:
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    - term: Optimisation and refinement
      uri: http://edamontology.org/operation_2425
    - term: Comparison
      uri: http://edamontology.org/operation_2424
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ-like format (text)
        uri: http://edamontology.org/format_2182
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
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        uri: http://edamontology.org/format_2305
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: 'Comprehensive benchmarking framework comparing 8 RNA-seq pipelines. Evaluates:
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      (2) Efficiency metrics: runtime, memory, CPU utilization, disk space; (3) Reproducibility
      metrics: between-run concordance, fold-change correlation, p-value correlation.
      Benchmark datasets: simulated data (Polyester), SEQC/MAQC validation, and user
      data. Runtime: 2-4 hours (small datasets) to 8-24 hours (large datasets). Outputs:
      HTML dashboard, CSV/TSV tables, publication-ready figures.'
    operation:
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      uri: http://edamontology.org/operation_0337
    - term: Validation
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    - term: Comparison
      uri: http://edamontology.org/operation_2424
    output:
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        term: Report
        uri: http://edamontology.org/data_2048
      format:
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        uri: http://edamontology.org/format_2331
    - data:
        term: Score
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      format:
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    - data:
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      format:
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      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Gene expression profile
        uri: http://edamontology.org/data_0928
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
    - data:
        term: Matrix
        uri: http://edamontology.org/data_2082
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/AyehBlk/RAPTOR
  homepage_status: 0
  language:
  - Shell
  - Python
  - R
  lastUpdate: '2025-12-10T08:58:59.523684Z'
  license: MIT
  link:
  - note: null
    type:
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    url: https://github.com/AyehBlk/RAPTOR
  maturity: Emerging
  name: RAPTOR
  operatingSystem:
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  otherID:
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    value: doi:10.5281/zenodo.17607161
    version: v2.1.0
  owner: AyehBlk
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  validated: 0
  version:
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- 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
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    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 [insert link to Champalimaud/s
    implementation]'
  documentation:
  - note: null
    type:
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    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:
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  lastUpdate: '2025-12-09T23:38:40.427406Z'
  license: Apache-2.0
  link: []
  maturity: Mature
  name: Image Duplicates Checker
  operatingSystem:
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  - Mac
  - Windows
  otherID: []
  owner: difoto
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    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    - term: Variant effect prediction
      uri: http://edamontology.org/operation_0331
    output: []
  homepage: http://loschmidt.chemi.muni.cz/soluprotmutdb
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-03T12:49:50.125351Z'
  license: null
  link: []
  maturity: null
  name: SoluProtMutsupDB
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: velda
  publication:
  - doi: 10.1016/J.CSBJ.2022.11.009
    metadata:
      abstract: © 2022 The Author(s)Protein solubility is an attractive engineering
        target primarily due to its relation to yields in protein production and manufacturing.
        Moreover, better knowledge of the mutational effects on protein solubility
        could connect several serious human diseases with protein aggregation. However,
        we have limited understanding of the protein structural determinants of solubility,
        and the available data have mostly been scattered in the literature. Here,
        we present SoluProtMutDB – the first database containing data on protein solubility
        changes upon mutations. Our database accommodates 33 000 measurements of 17
        000 protein variants in 103 different proteins. The database can serve as
        an essential source of information for the researchers designing improved
        protein variants or those developing machine learning tools to predict the
        effects of mutations on solubility. The database comprises all the previously
        published solubility datasets and thousands of new data points from recent
        publications, including deep mutational scanning experiments. Moreover, it
        features many available experimental conditions known to affect protein solubility.
        The datasets have been manually curated with substantial corrections, improving
        suitability for machine learning applications. The database is available at
        loschmidt.chemi.muni.cz/soluprotmutdb.
      authors:
      - name: Velecky J.
      - name: Hamsikova M.
      - name: Stourac J.
      - name: Musil M.
      - name: Damborsky J.
      - name: Bednar D.
      - name: Mazurenko S.
      citationCount: 0
      date: '2022-01-01T00:00:00Z'
      journal: Computational and Structural Biotechnology Journal
      title: 'SoluProtMutDB: A manually curated database of protein solubility changes
        upon mutations'
    note: null
    pmcid: PMC9678803
    pmid: '36420168'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Data submission, annotation and curation
    uri: http://edamontology.org/topic_0219
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2025-12-02T17:37:57.215347Z'
  biotoolsCURIE: biotools:auto-prostate-sequence-classifier
  biotoolsID: auto-prostate-sequence-classifier
  collectionID:
  - EUCAIM
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: jose.almeida@research.fchampalimaud.org
    fundrefid: null
    gridid: null
    name: José Guilherme de Almeida
    note: null
    orcidid: https://orcid.org/0000-0002-1887-0157
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://josegcpa.net
  - email: null
    fundrefid: null
    gridid: null
    name: Nikolaos Papanikolaou
    note: null
    orcidid: https://orcid.org/0000-0003-3298-2072
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: XGBoost-based automatic classification of sequence types for prostate
    mpMRI into T2W, DWI, ADC, DCE and others (any other sequence type) using metadata
    alone. Works as a CLI, allows direct application to DICOM datasets or CSV/tsv/Excel/parquet
    datasets, features integration for Orthanc and DICOM-web as RESTful APIs. This
    was applied to all data on ProCAncer-I to derive initial results for sequence
    types. Refines predictions using rule-based heuristics for T2W, DWI and ADC.
  documentation:
  - note: Repository containing the code, README and additional information on how
      to run the tool. If used as an API (when integrated with Orthanc or DICOM-web),
      the documentation is available upon launching the API at <api-url>/docs.
    type:
    - Other
    url: https://github.com/CCIG-Champalimaud/metadata-classification
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: docker run -v <dir-with-dicom>:/data  harbor.eucaim.cancerimage.eu/processing-tools/champ-autoproseq
      --dicom_recursion <dicom-recursion> --input_paths /data
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: 'The input can be provided as a DICOM dataset (which will require --dicom-recursion,
      details below or in the documentation) or as a single DICOM study. This command
      will print a CSV with 5 columns:  i) patient_id, ii) study_uid, iii) series_uid,
      iv) classification from the XGBoost model, v) classification after heuristics-based
      corrections.

      The sequence classification is performed between T2W, DWI, ADC, DCE or others.
      The provided <dicom-recursion> refers to the number of folders until a DICOM
      series is found. So if the provided input is a patient folder with nested studies
      with nested series, the level of DICOM recursion should be 2. If the provided
      input is a directory with patient folders, the level of DICOM recursion should
      be 3.'
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Keyword
        uri: http://edamontology.org/data_0968
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/champ-autoproseq
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-03T09:27:04.489071Z'
  license: MIT
  link:
  - note: Repository containing code, README and additional usage information for
      this tool.
    type:
    - Repository
    url: https://github.com/CCIG-Champalimaud/metadata-classification
  maturity: Emerging
  name: AutoProSeq - automatic classification of sequence types for prostate mpMRI
  operatingSystem:
  - Linux
  otherID: []
  owner: josegcpa
  publication:
  - doi: 10.1186/s13244-025-01938-2
    metadata:
      abstract: ''
      authors: []
      citationCount: 1
      date: '2025-12-01T00:00:00Z'
      journal: Insights into Imaging
      title: Automatic sequence identification in multicentric prostate multiparametric
        MRI datasets for clinical machine-learning
    note: null
    pmcid: PMC12187622
    pmid: '40146375'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web API
  - Command-line tool
  topic:
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  validated: 0
  version:
  - v0.1
- accessibility: Open access
  additionDate: '2025-11-26T13:27:32.776575Z'
  biotoolsCURIE: biotools:iqa_dce_tool
  biotoolsID: iqa_dce_tool
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: The purpose of the tool is to provide a complete framework for automatic
    detection of image quality for Breast DCE MR images. The assessment is performed
    on the first post-contrast dynamic phase in order to assess the most clinically
    relevant sequence among a number of identical acquisitions. Two categories are
    available for image classification, i.e. high and low quality, depending on the
    level of noise, degree of blurring and presence of artifacts.
  documentation:
  - note: null
    type:
    - General
    url: https://docs.google.com/document/d/1hG_M21gvO4D8zkHmwtbavT8Dp6bliRU4/edit
  download:
  - note: null
    type: Container file
    url: https://hub.docker.com/r/billykforth/iqa_dce_tool
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://hub.docker.com/repository/docker/billykforth/iqa_dce_tool/general
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-03T06:46:13.717361Z'
  license: EUPL-1.1
  link: []
  maturity: Mature
  name: IQA DCE tool
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: billyk
  publication:
  - doi: 10.3390/jimaging11110417
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  validated: 0
  version:
  - '1.0'
- accessibility: Restricted access
  additionDate: '2025-12-01T09:36:32.395959Z'
  biotoolsCURIE: biotools:dicom_defacing_anonymation
  biotoolsID: dicom_defacing_anonymation
  collectionID:
  - EUCAIM
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit: []
  description: This tool can be used to remove facial features ("defacing") from DICOM
    images. It may be used 1) only for facial removing, or 2) for a complete import
    and anonymization using DICOM transfer. Defaced images needs to be manually quality
    checked, and this is done through a web interface  to a local server supplied
    with the Docker containers.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.dicom2usb.com
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-01T16:25:11.338723Z'
  license: Proprietary
  link: []
  maturity: Emerging
  name: DICOM defacing anonymisation
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: janaxelsson
  publication: []
  relation: []
  toolType:
  - Command-line tool
  - Desktop application
  - Workflow
  topic:
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  - term: Data protection
    uri: http://edamontology.org/topic_4044
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2021-01-18T10:10:48Z'
  biotoolsCURIE: biotools:ape
  biotoolsID: ape
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: vedran.kasalica@health-ri.nl
    fundrefid: null
    gridid: null
    name: Vedran Kasalica
    note: null
    orcidid: https://orcid.org/0000-0002-0097-1056
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: anna-lena.lamprecht@uni-potsdam.de
    fundrefid: null
    gridid: null
    name: Anna-Lena Lamprecht
    note: null
    orcidid: https://orcid.org/0000-0003-1953-5606
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: APE (the Automated Pipeline Explorer) as a command-line tool and API
    for automated composition of scientific workflows. APE is easily configured to
    a new application domain by providing it with a domain ontology and semantically
    annotated tools. It can then be used to synthesize purpose-specific workflows
    based on a specification of the available workflow inputs, desired outputs and
    possibly additional constraints.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://ape-framework.readthedocs.io/
  download:
  - note: Download APE java library or the CLI
    type: Software package
    url: https://mvnrepository.com/artifact/io.github.sanctuuary/APE/2.1.7
    version: 2.1.7
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Workflow metadata
        uri: http://edamontology.org/data_0949
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Generation
      uri: http://edamontology.org/operation_3429
    output:
    - data:
        term: Workflow metadata
        uri: http://edamontology.org/data_0949
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: CWL
        uri: http://edamontology.org/format_3857
      - term: PNG
        uri: http://edamontology.org/format_3603
  homepage: https://github.com/sanctuuary/APE/
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2025-12-01T13:47:56.062392Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/sanctuuary/ape
  maturity: Mature
  name: APE
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: VKasalica
  publication:
  - doi: null
    metadata: null
    note: null
    pmcid: PMC7304703
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1021/acs.jproteome.0c00983
    metadata:
      abstract: ''
      authors: []
      citationCount: 7
      date: '2021-04-02T00:00:00Z'
      journal: Journal of Proteome Research
      title: 'APE in the Wild: Automated Exploration of Proteomics Workflows in the
        bio.tools Registry'
    note: null
    pmcid: PMC8041394
    pmid: '33720735'
    type:
    - Benchmarking study
    version: null
  relation: []
  toolType:
  - Library
  - Web API
  - Command-line tool
  topic:
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 1
  version:
  - 2.1.7
- accessibility: Open access
  additionDate: '2017-08-03T18:45:53Z'
  biotoolsCURIE: biotools:hbat
  biotoolsID: hbat
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Abhishek Tiwari
    note: null
    orcidid: https://orcid.org/0000-0003-2222-2395
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://www.abhishek-tiwari.com
  description: "HBAT (Hydrogen Bond Analysis Tool) is a package to automate the analysis\
    \ of potential hydrogen bonds and similar type of weak interactions in macromolecular\
    \ structures, available in Protein Data Bank (PDB) file format. HBAT uses a geometric\
    \ approach to identify molecular interactions by analysing distance and angular\
    \ criteria.\n\nHBAT 1.1 was released in 2007 as closed source Windows binary and\
    \ continue to be available via SourceForge. \n\nHBAT 2.0 was introduced in 2025\
    \ and a completed rewrite of original implementation with cross-platform support.\
    \ HBAT 2.0 is open sourced under MIT License."
  documentation:
  - note: null
    type:
    - General
    - API documentation
    - Citation instructions
    - Command-line options
    - Installation instructions
    - Quick start guide
    url: https://hbat.abhishek-tiwari.com
  download:
  - note: Cross-platform PyPI Python Package
    type: Software package
    url: https://pypi.org/project/hbat/
    version: 2.x
  - note: Mac and Linux Binaries including  AppImage, .deb, standalone executables.
    type: Binaries
    url: https://github.com/abhishektiwari/hbat/releases
    version: 2.x
  - note: Windows Binaries download from SourceForge
    type: Binaries
    url: https://sourceforge.net/projects/hbat/
    version: 1.0, 1.1
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: hbat input.pdb
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: null
    operation:
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    output:
    - data:
        term: Protein hydrogen bonds
        uri: http://edamontology.org/data_1549
      format: []
  homepage: https://hbat.abhishek-tiwari.com
  homepage_status: 0
  language:
  - Perl
  - Python
  lastUpdate: '2025-11-29T17:30:01.186940Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    - Issue tracker
    url: https://github.com/abhishektiwari/hbat
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/hbat-1-1-hydrogen-bond-analysis-tool.html
  maturity: Mature
  name: HBAT
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: abhishektiwari
  publication:
  - doi: 10.3233/ISI-2007-00337
    metadata: null
    note: Peer-reviewed paper for HBAT 1.0
    pmcid: null
    pmid: '18467777'
    type:
    - Primary
    version: null
  - doi: 10.5281/zenodo.17645321
    metadata: null
    note: Preprint for HBAT 2.x software
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  validated: 1
  version:
  - 2.x
  - 1.1, 1.0
- accessibility: Open access
  additionDate: '2025-11-28T17:29:53.564906Z'
  biotoolsCURIE: biotools:gc-meox-tms
  biotoolsID: gc-meox-tms
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: RECETOX SpecDatRI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole:
    - Maintainer
    - Provider
    - Primary contact
    - Developer
    url: https://www.recetox.muni.cz/en/services/data-services-2/spectrometric-data-processing-and-analysis
  description: 'This package performs in-silico MeOX + TMS derivatization (as described
    e.g. in https://doi.org/10.1021/acs.analchem.7b01010):


    Methoximation: ketone R(C=O)R'' and aldehyde (-HC=O) carbonyl groups are substituted
    with -C=NOCH3

    Trimethylsilylation: the acidic hydrogen in -OH, -SH, -COOH, -NH2, -NHR, =NH,
    the hydrogen is substituted with -Si(CH3)3 The substitution doesn''t always have
    to happen; its probability is currently hardcoded in the package. Typically, multiple
    substitution attempts are run on each input molecule, and all distinct results
    are gathered.

    Known limitation is methoximation on cycles which should be broken. This is not
    implemented yet.'
  documentation:
  - note: null
    type:
    - Installation instructions
    - Command-line options
    url: https://github.com/RECETOX/gc-meox-tms/blob/master/README.md
  - note: null
    type:
    - Quick start guide
    - Training material
    url: https://github.com/RECETOX/gc-meox-tms/blob/master/example/derivatization.ipynb
  download:
  - note: null
    type: Software package
    url: https://github.com/RECETOX/gc-meox-tms.git
    version: v1.0.1
  editPermission:
    authors:
    - recetox-specdatri
    type: group
  elixirCommunity:
  - Metabolomics
  elixirNode:
  - Czech Republic
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: add_derivatization_groups()
    input:
    - data:
        term: SMILES string
        uri: http://edamontology.org/data_2301
      format: []
    note: Produces MeOX/TMS derivatives of given compounds
    operation:
    - term: Sequence editing
      uri: http://edamontology.org/operation_0231
    output:
    - data:
        term: SMILES string
        uri: http://edamontology.org/data_2301
      format: []
  homepage: https://github.com/RECETOX/gc-meox-tms
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-28T17:42:43.031944Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/RECETOX/gc-meox-tms
  - note: null
    type:
    - Issue tracker
    url: https://github.com/RECETOX/gc-meox-tms/issues
  maturity: Mature
  name: gc-meox-tms
  operatingSystem: []
  otherID: []
  owner: Ondrej_Bucek
  publication:
  - doi: 10.1021/acs.analchem.7b01010
    metadata:
      abstract: ''
      authors: []
      citationCount: 44
      date: '2017-06-20T00:00:00Z'
      journal: Analytical Chemistry
      title: Integrated Strategy for Unknown EI-MS Identification Using Quality Control
        Calibration Curve, Multivariate Analysis, EI-MS Spectral Database, and Retention
        Index Prediction
    note: The package is based on this publication
    pmcid: null
    pmid: '28520403'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Analytical chemistry
    uri: http://edamontology.org/topic_3370
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-11-04T18:24:22.573039Z'
  biotoolsCURIE: biotools:brain_metastasis_segmenter
  biotoolsID: brain_metastasis_segmenter
  collectionID:
  - EUCAIM
  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
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Developer
    - 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:
    - Developer
    - 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:
    - Contributor
    - 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:
    - Primary contact
    - Contributor
    url: null
  - email: mlingura@childrensnational.org
    fundrefid: null
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  - email: jose.almeida@research.fchampalimaud.org
    fundrefid: null
    gridid: null
    name: José Guilherme de Almeida
    note: null
    orcidid: https://orcid.org/0000-0002-1887-0157
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: https://josegcpa.net
  - email: null
    fundrefid: null
    gridid: null
    name: Nickolas Papanikolaou
    note: null
    orcidid: https://orcid.org/0000-0003-3298-2072
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Nuno Rodrigues
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: 'This tool automatically segments the the prostate into two zones:
    the central and transition zones (TZ+CZ) and the peripheral zone (PZ). It takes
    as input a T2-weighted image and produces a segmentation in the same input format.


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


      If the input is DICOM, `--is_dicom` should be used.'
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --shm-size=1gb -v $(pwd)/example_dataset:/data/input:ro -v $(pwd)/test_output:/data/output:rw
      --gpus="all" test-eucaim:latest nnunet-predict-batch {{--data_json /data/input/<dataset_json>.json|--data_dir
      /data/input --output_dir /data/output}}
    input:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: "Batch image annotation for DICOM and Nifti images using dataset JSON and\
      \ data directory supports two methods: using a dataset JSON and using a data\
      \ directory. \n\nThe dataset JSON-based method relies on having a dataset JSON\
      \ which has a list of dictionaries that follow this structure: `{\"study_path\"\
      : str, \"series_folders\": [[str]], \"output_dir\": str}`. These are analogous\
      \ to the previous modes. Be mindful that paths should be specified accordingly\
      \ for the Docker file-system. The dataset JSON should be specified using `--data_json`.\n\
      \nThe data directory-based method relies on having a directory structured as\
      \ patient/study/series, where each series follows an nnU-Net-like convention\
      \ (i.e. `<series_id>_0000`, `<series_id>_0001`, etc.). In this case, it should\
      \ be `<series-id>_0000`. The data directory should be specified using `--data_dir`\
      \ and requires the specification of an `--output_dir`.\n\nIf the input is DICOM,\
      \ `--is_dicom` should be specified."
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/champ-prostate-zone-segmentation
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-28T12:18:55.232382Z'
  license: CC-BY-NC-4.0
  link:
  - note: This is the nnunet_serve repository, containing the generic nnU-Net building
      and serving functionalities used by the Computational Clinical Imaging Group
      at Champalimaud Foundation. This should also be used as documentation.
    type:
    - Repository
    url: https://github.com/josegcpa/nnunet_serve
  - note: The EUCAIM model card for this model, containing details on model training,
      data and libraries.
    type:
    - Other
    url: https://docs.google.com/spreadsheets/d/1bcdhs9Xg2MxAH0WDGz08SjEVMFr3e-TP/edit?usp=sharing&ouid=111102743696297094705&rtpof=true&sd=true
  maturity: Emerging
  name: Prostate zone segmentation tool
  operatingSystem:
  - Linux
  otherID: []
  owner: josegcpa
  publication:
  - doi: 10.1016/j.compbiomed.2024.108216
    metadata:
      abstract: ''
      authors: []
      citationCount: 9
      date: '2024-03-01T00:00:00Z'
      journal: Computers in Biology and Medicine
      title: Analysis of domain shift in whole prostate gland, zonal and lesions segmentation
        and detection, using multicentric retrospective data
    note: null
    pmcid: null
    pmid: '38442555'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: nnunet
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-10-29T08:08:30.731334Z'
  biotoolsCURIE: biotools:lethe_dicom_anonymizer
  biotoolsID: lethe_dicom_anonymizer
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Computational BioMedicine Laboratory, Foundation for Research and Technology
      Hellas (FORTH)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.ics.forth.gr/cbml/?lang=en
  description: "A DICOM Anonymization pipeline in a Docker container. This pipeline\
    \ is designed to anonymize DICOM files according to the EUCAIM standard and includes\
    \ the following steps:\n\nStep 1 (Optional): Perform OCR on DICOM pixel data to\
    \ remove sensitive information (burned-in information).\nStep 2: Deidentify DICOM\
    \ metadata using the RSNA CTP Anonymizer and the EUCAIM anonymization script.\
    \ \nStep 3 (Optional): Deidentify clinical data provided in CSV files so that\
    \ the referenced patient id is anonymized the same way CTP does in Step 2."
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/cbml-forth/lethe_anon_pipeline/blob/main/README.md
  download: []
  editPermission:
    authors:
    - ssfak
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Anonymisation
      uri: http://edamontology.org/operation_3283
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/lethe-dicom-anonymizer/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-28T07:49:09.801303Z'
  license: EUPL-1.1
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/cbml-forth/lethe_anon_pipeline
  maturity: null
  name: Lethe DICOM Anonymizer
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: vkalokyri
  publication: []
  relation: []
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  - term: Data protection
    uri: http://edamontology.org/topic_4044
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version:
  - 0.9.12
- accessibility: null
  additionDate: '2025-05-30T17:07:05.725785Z'
  biotoolsCURIE: biotools:ct_slice_thickness_normalization
  biotoolsID: ct_slice_thickness_normalization
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Quibim
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: http://quibim.com
  - email: xavierrafael@quibim.com
    fundrefid: null
    gridid: null
    name: Xavier Rafael-Palou
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: anajimenez@quibim.com
    fundrefid: null
    gridid: null
    name: Ana Jiménez
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  description: This tool standardizes slice thickness in CT scans by resampling them
    to a common slice spacing. It is intended as a preprocessing step to harmonize
    CT data, improving consistency across scans acquired with varying slice thicknesses.
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.google.com/file/d/12lCxh-RHZbAYjoyoPIcOB9qBXQgz5Fb3/view?usp=drive_link
  - note: null
    type:
    - General
    url: https://quibim.com/products/qp-lung/
  download: []
  editPermission:
    authors:
    - celia_martin
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: jobman submit -i ct_slice_thickness_harmonization -- <INPUT_DIR> <OUTPUT_DIR>
      <MODEL> <INPUT_TYPE>
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: 'The application accepts 4 parameters:

      The input path to a DICOM directory

      The output directory where harmonized DICOM will be saved.

      The model to use (options: lung)

      The type of input (options: series -folder containing .dcm files of a DICOM
      image- or study -folder containing series)'
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://quibim.com/products/qp-lung/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-27T16:07:40.483173Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/quibim
  maturity: Emerging
  name: CT Slice thickness harmonization
  operatingSystem:
  - Linux
  otherID: []
  owner: xrafael
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version:
  - '0.1'
- accessibility: null
  additionDate: '2025-05-30T16:38:57.306019Z'
  biotoolsCURIE: biotools:mri_image_intensity_normalization
  biotoolsID: mri_image_intensity_normalization
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Quibim
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: http://quibim.com
  - email: xavierrafael@quibim.com
    fundrefid: null
    gridid: null
    name: Xavier Rafael-Palou
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ana Jiménez
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  description: 'The purpose of this tool is to harmonize the intensity dynamic ranges
    of MR T2W prostate images through a deep learning model that transforms the input
    image into an harmonized one closer to a curated reference set of high-quality
    contrast MR T2W.

    prostate images.'
  documentation:
  - note: null
    type:
    - General
    url: https://quibim.com/news/understanding-mri-image-harmonization/
  - note: null
    type:
    - User manual
    url: https://drive.google.com/file/d/19dagjHPCp8XUjwB02hNsBfD-QF19wAFS/view?usp=drive_link
  download: []
  editPermission:
    authors:
    - celia_martin
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: jobman submit -i mri_image_intensity_harmonization -- <INPUT_DIR> <OUTPUT_DIR>
      <MODEL> <BATCH>
    input:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: 'The application accepts 4 parameters:

      - The input path to a DICOM directory

      - The output directory where the harmonized DICOM will be saved.

      - The model to use (options: prostate)

      - The batch execution mode (options: series that is the folder with .dcm files
      of a DICOM image, or study which is the folder containing the series.'
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://quibim.com/news/understanding-mri-image-harmonization/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-27T16:06:53.546832Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/quibim/
  maturity: Emerging
  name: MRI Image intensity harmonization
  operatingSystem:
  - Linux
  otherID: []
  owner: xrafael
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version:
  - '0.1'
- accessibility: null
  additionDate: '2017-04-15T08:42:53Z'
  biotoolsCURIE: biotools:trimal
  biotoolsID: trimal
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: salcagu@gmail.com
    fundrefid: null
    gridid: null
    name: Salvador Capella-Gutierrez
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: tgabaldon@crg.es
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://gabaldonlab.crg.es/
  description: Tool for the automated removal of spurious sequences or poorly aligned
    regions from a multiple sequence alignment.
  documentation:
  - note: Old versions
    type:
    - General
    url: http://trimal.cgenomics.org/
  - note: null
    type:
    - General
    url: https://trimal.readthedocs.io
  download:
  - note: null
    type: Source code
    url: https://github.com/inab/trimal
    version: 1.5.1
  - note: null
    type: Source code
    url: https://github.com/inab/trimal/tree/2.0_RC
    version: 2.0-RC
  editPermission:
    authors:
    - nico_bsc
    - sergitobara
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format: []
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Alignment
        uri: http://edamontology.org/data_1916
      format:
      - term: phylipnon
        uri: http://edamontology.org/format_1998
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://trimal.readthedocs.io
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-11-26T09:30:50.611915Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/inab/trimal
  maturity: Mature
  name: trimAl
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: scapella
  publication:
  - doi: 10.1093/bioinformatics/btp348
    metadata:
      abstract: ''
      authors: []
      citationCount: 8679
      date: '2009-08-01T00:00:00Z'
      journal: Bioinformatics
      title: 'trimAl: A tool for automated alignment trimming in large-scale phylogenetic
        analyses'
    note: null
    pmcid: PMC2712344
    pmid: '19505945'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 1
  version:
  - 1.5.1
  - 2.0-RC
- accessibility: null
  additionDate: '2025-06-30T15:03:36.801398Z'
  biotoolsCURIE: biotools:lexicmap
  biotoolsID: lexicmap
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: shenwei356@gmail.com
    fundrefid: null
    gridid: null
    name: Wei Shen
    note: null
    orcidid: https://orcid.org/0000-0002-8099-8258
    rorid: null
    typeEntity: null
    typeRole: []
    url: http://shenwei.me
  description: LexicMap is a nucleotide sequence alignment tool for efficiently querying
    gene, plasmid, viral, or long-read sequences (>100 bp) against up to millions
    of prokaryotic genomes.
  documentation:
  - note: null
    type:
    - User manual
    url: https://bioinf.shenwei.me/LexicMap/
  download: []
  editPermission:
    authors:
    - shenwei356
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://bioinf.shenwei.me/LexicMap/
  homepage_status: 0
  language:
  - Other
  lastUpdate: '2025-11-17T12:41:11.971171Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/shenwei356/LexicMap
  maturity: null
  name: LexicMap
  operatingSystem: []
  otherID: []
  owner: smeds
  publication:
  - doi: 10.1101/2024.08.30.610459
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic: []
  validated: 0
  version:
  - v0.7.0
  - v0.6.1
  - v0.6.0
  - v0.5.0
  - v0.4.0
  - v0.3.0
  - v0.2.0
  - v0.1.0
- accessibility: null
  additionDate: '2025-11-17T10:03:13.644804Z'
  biotoolsCURIE: biotools:protein-quest
  biotoolsID: protein-quest
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Python package to search/retrieve/filter proteins and protein structures.
  documentation:
  - note: null
    type:
    - General
    url: http://www.bonvinlab.org/protein-quest/
  download:
  - note: null
    type: Software package
    url: https://pypi.org/project/protein-quest
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
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  elixir_badge: 0
  function: []
  homepage: http://www.bonvinlab.org/protein-quest/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-17T10:05:01.348125Z'
  license: Apache-2.0
  link:
  - note: null
    type:
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