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  biotoolsID: pediatric_brain_tumor_segmenter
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  cost: Free of charge
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    fundrefid: null
    gridid: null
    name: Daniel Capellán-Martín
    note: null
    orcidid: https://orcid.org/0000-0002-9743-0845
    rorid: null
    typeEntity: Person
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    url: null
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    fundrefid: null
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    rorid: null
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    url: null
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    url: null
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    name: María Jesus Ledesma-Carbayo
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    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: mlingura@childrensnational.org
    fundrefid: null
    gridid: null
    name: Marius George Linguraru
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
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    url: null
  description: The Pediatric Brain Tumor Segmenter is a software tool developed by
    researchers from Universidad Politécnica de Madrid and Children’s National Hospital
    for the segmentation and analysis of pediatric brain tumors in magnetic resonance
    imaging (MRI). Built in Python, it enables precise quantitative analysis of pediatric
    brain MRIs to support clinical decision-making in both diagnosis and prognosis.
  documentation:
  - note: null
    type:
    - API documentation
    - Citation instructions
    - Terms of use
    - Code of conduct
    - Release notes
    - User manual
    - General
    - Quick start guide
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    operation:
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  homepage: https://segmenter.hope4kids.io/
  homepage_status: 0
  language:
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  lastUpdate: '2025-10-28T18:39:57.123169Z'
  license: CC-BY-NC-SA-4.0
  link:
  - note: Main app webpage
    type:
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    url: https://segmenter.hope4kids.io/
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids
  maturity: Mature
  name: Pediatric Brain Tumor Segmenter
  operatingSystem:
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  owner: dani-capellan
  publication:
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    metadata:
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      authors: []
      citationCount: 2
      date: '2024-01-01T00:00:00Z'
      journal: Lecture Notes in Computer Science (including subseries Lecture Notes
        in Artificial Intelligence and Lecture Notes in Bioinformatics)
      title: Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging
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    pmid: null
    type:
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    version: null
  - doi: 10.1109/ISBI56570.2024.10635469
    metadata:
      abstract: ''
      authors: []
      citationCount: 1
      date: '2024-01-01T00:00:00Z'
      journal: Proceedings - International Symposium on Biomedical Imaging
      title: 'Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble
        with Adaptive Post-Processing'
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  - doi: 10.48550/arXiv.2412.04094
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  - doi: 10.48550/arXiv.2412.04111
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  relation: []
  toolType:
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  topic:
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  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
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- accessibility: null
  additionDate: '2025-10-27T16:27:24.014603Z'
  biotoolsCURIE: biotools:netstart_2.0
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    name: Line Sandvad Nielsen
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    typeEntity: Person
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    fundrefid: null
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    name: Henrik Nielsen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
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    url: null
  description: "Prediction of eukaryotic translation initiation sites using a protein\
    \ language model.\n\nNetStart 2.0 is a deep learning-based model that predicts\
    \ canonical translation initiation sites in mRNA transcripts in species across\
    \ the eukaryotic domain, including vertebrates, invertebrates, plants, fungi,\
    \ and protists. \n\nThe model integrates the ESM-2 protein language model for\
    \ assessing transitions from non-coding to coding regions with local start codon\
    \ sequence context and taxonomical information. It has been trained on sequences\
    \ from 60 phylogenetically diverse eukaryotic species.\n\nIf you need help with\
    \ the bioinformatics programs, see the \"Getting Help\" section at the server\
    \ site at the link."
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  function:
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    note: null
    operation:
    - term: Protein identification
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    - term: Genome annotation
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    - term: Translation initiation site prediction
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    output:
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      format: []
  homepage: https://services.healthtech.dtu.dk/services/NetStart-2.0/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-10-28T17:34:39.042070Z'
  license: null
  link:
  - note: GitHub with code and instructions and to download and run the program locally
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    - Repository
    url: https://github.com/lsandvad/netstart2
  - note: NetStart 2.0 server where sequences can be uploaded directly without having
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    url: https://services.healthtech.dtu.dk/services/NetStart-2.0/
  maturity: null
  name: NetStart
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  owner: linesandvad
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      date: '2025-12-01T00:00:00Z'
      journal: BMC Bioinformatics
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    note: null
    pmcid: PMC12366053
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    type:
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  topic:
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  - term: Gene expression
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  - term: Model organisms
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  validated: 0
  version:
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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
    using geometric reasoning
  documentation:
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    url: https://stripepy.readthedocs.io/
  download:
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    type: Source code
    url: https://github.com/paulsengroup/StripePy/releases
    version: null
  - note: null
    type: Container file
    url: https://hub.docker.com/r/paulsengroup/stripepy
    version: null
  - note: null
    type: Test data
    url: https://doi.org/10.5281/zenodo.14283921
    version: null
  - note: null
    type: Binaries
    url: https://pypi.org/project/stripepy-hic/
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    type: Binaries
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  lastUpdate: '2025-10-28T12:14:50.951141Z'
  license: MIT
  link:
  - note: null
    type:
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    url: https://github.com/paulsengroup/StripePy/issues
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    type:
    - Discussion forum
    url: https://github.com/paulsengroup/StripePy/discussions
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  owner: robomics
  publication:
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    metadata: null
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    type:
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  - doi: 10.1093/bioinformatics/btaf351
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      date: '2025-06-01T00:00:00Z'
      journal: Bioinformatics
      title: 'StripePy: fast and robust characterization of architectural stripes'
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    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
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  - 0.0.2
  - 1.0.0
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- accessibility: null
  additionDate: '2020-01-09T17:51:22Z'
  biotoolsCURIE: biotools:PTM-CrossTalkMapper
  biotoolsID: PTM-CrossTalkMapper
  collectionID: []
  confidence_flag: tool
  cost: null
  credit: []
  description: 'Visualization of the Dynamics of Histone Modifications and Their Crosstalk
    Using PTM-CrossTalkMapper.


    R scripts to create crosstalk maps that visualize multi-layered proteoform data.


    PTM-CrossTalkMapper is a flexible toolkit to visualize multi-layered quantitative
    post-transcriptional modification (PTM) data. The preprint manuscript can be found
    on bioRxiv'
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/veitveit/CrossTalkMapper?tab=readme-ov-file#documentation
  - note: null
    type:
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    url: https://link.springer.com/protocol/10.1007/978-1-0716-2317-6_13
  download: []
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  function:
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    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_3799
    - term: Post-translation modification site prediction
      uri: http://edamontology.org/operation_0417
    - term: PTM localisation
      uri: http://edamontology.org/operation_3755
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://github.com/veitveit/CrossTalkMapper
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-10-27T17:06:26.845284Z'
  license: null
  link: []
  maturity: null
  name: PTM-CrossTalkMapper
  operatingSystem: []
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  owner: Pub2Tools
  publication:
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    metadata:
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      authors: []
      citationCount: 17
      date: '2020-12-01T00:00:00Z'
      journal: Methods
      title: Visualization of the dynamics of histone modifications and their crosstalk
        using PTM-CrossTalkMapper
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Epigenetics
    uri: http://edamontology.org/topic_3295
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Protein modifications
    uri: http://edamontology.org/topic_0601
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  validated: 1
  version: []
- accessibility: null
  additionDate: '2025-10-27T16:15:48.531662Z'
  biotoolsCURIE: biotools:Thor
  biotoolsID: Thor
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: null
    fundrefid: null
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    name: Pengzhi Zhang
    note: null
    orcidid: https://orcid.org/0000-0001-6920-1490
    rorid: null
    typeEntity: Person
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    url: null
  - email: null
    fundrefid: null
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    name: Weiqing Chen
    note: null
    orcidid: https://orcid.org/0000-0003-3539-9210
    rorid: null
    typeEntity: Person
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    url: null
  description: Spatial transcriptomics integrates transcriptomics data with histological
    tissue images, offering deeper insights into cellular organization and molecular
    functions. However, existing computational platforms mainly focus on genomic analysis,
    leaving a gap in the seamless integration of genomic and imaging modalities. Thor
    is a comprehensive spatial transcriptomics analysis tool designed to bridge this
    gap by enabling efficient co-analysis of gene expression profiles and high-resolution
    tissue images. It provides scalable workflows for spatial feature extraction,
    cell segmentation, gene–spatial correlation, and visualization, facilitating multi-omic
    insights into tissue architecture and cellular heterogeneity.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://wanglab.tech/thor/
  download:
  - note: null
    type: Downloads page
    url: https://wanglab.tech/thor
    version: null
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  function:
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    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_0337
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    - term: Imputation
      uri: http://edamontology.org/operation_3557
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    output: []
  homepage: https://github.com/GuangyuWangLab2021/Thor
  homepage_status: 0
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  license: null
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  maturity: null
  name: Thor
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  owner: udayaraja
  publication:
  - doi: 10.21203/RS.3.RS-4909620/V1
    metadata: null
    note: null
    pmcid: PMC11952649
    pmid: '40162205'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-10-27T16:45:48.395441Z'
  biotoolsCURIE: biotools:tetranscripts
  biotoolsID: tetranscripts
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Molly Gale Hammell
    note: null
    orcidid: https://orcid.org/0000-0003-0405-8392
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: TEtranscripts is a software package for including transposable elements
    in differential expression analysis of RNA-seq datasets. It assigns reads to genes
    and transposable elements, performs differential expression testing, and provides
    statistical analysis for transposable element expression.
  documentation:
  - note: null
    type:
    - Installation instructions
    - User manual
    url: https://github.com/mhammell-laboratory/TEtranscripts
  download:
  - note: null
    type: Source code
    url: https://github.com/mhammell-laboratory/TEtranscripts
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  function:
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    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Differential gene expression analysis
      uri: http://edamontology.org/operation_3223
    output:
    - data:
        term: Gene expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://hammelllab.labsites.cshl.edu/software/#TEtranscripts
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-10-27T16:50:09.756484Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/mhammell-laboratory/TEtranscripts
  - note: null
    type:
    - Service
    url: https://www.mghlab.org/software/tetranscripts
  maturity: Mature
  name: TEtranscripts
  operatingSystem:
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  - Linux
  otherID: []
  owner: samuelruizperez
  publication:
  - doi: 10.1093/bioinformatics/btv422
    metadata:
      abstract: ''
      authors: []
      citationCount: 419
      date: '2015-05-25T00:00:00Z'
      journal: Bioinformatics
      title: 'TEtranscripts: A package for including transposable elements in differential
        expression analysis of RNA-seq datasets'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Script
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-10-27T16:45:07.895751Z'
  biotoolsCURIE: biotools:NetworkX
  biotoolsID: NetworkX
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Exploring Network Structure, Dynamics, and Function using NetworkX.


    Software for Complex Networks — NetworkX 3.5.1rc0.dev0 documentation.


    NetworkX is a Python package for the creation, manipulation, and study of the
    structure, dynamics, and functions of complex networks. It provides:.


    With NetworkX you can load and store networks in standard and nonstandard data
    formats, generate many types of random and classic networks, analyze network structure,
    build network models, design new network algorithms, draw networks, and much more.'
  documentation: []
  download: []
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  elixir_badge: 0
  function:
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    input: []
    note: null
    operation:
    - term: Network analysis
      uri: http://edamontology.org/operation_3927
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    output: []
  homepage: https://networkx.org/documentation/latest/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-10-27T16:45:07.898233Z'
  license: BSD-3-Clause
  link: []
  maturity: Mature
  name: NetworkX
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: Julia.Villarroel
  publication:
  - doi: 10.25080/TCWV9851
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Informatics
    uri: http://edamontology.org/topic_0605
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-10-27T16:11:34.389774Z'
  biotoolsCURIE: biotools:string-space
  biotoolsID: string-space
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: larsjuhl.jensen@zs.com
    fundrefid: null
    gridid: null
    name: Dewei Hu
    note: null
    orcidid: https://orcid.org/0009-0005-5823-1498
    rorid: null
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    url: null
  description: 'STRING proteins as complementary embeddings.


    Motivation Representation learning has revolutionized sequence-based prediction
    of protein function and subcellular localization. Protein networks are an important
    source of information complementary to sequences, but the use of protein networks
    has proven to be challenging in the context of machine learning, especially in
    a cross-species setting. Results. We leveraged the STRING database of protein
    networks and orthology relations for 1322 eukaryotes to generate network-based
    cross-species protein embeddings. We did this by first creating species-specific
    network embeddings and subsequently aligning them based on orthology relations
    to facilitate direct cross-species comparisons'
  documentation: []
  download: []
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  elixir_badge: 0
  function:
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    input: []
    note: null
    operation:
    - term: Protein interaction network analysis
      uri: http://edamontology.org/operation_0276
    - term: Protein interaction network prediction
      uri: http://edamontology.org/operation_3094
    - term: Subcellular localisation prediction
      uri: http://edamontology.org/operation_2489
    output: []
  homepage: https://github.com/deweihu96/SPACE
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-10-27T16:11:34.392675Z'
  license: MIT
  link: []
  maturity: null
  name: SPACE
  operatingSystem: []
  otherID: []
  owner: deweihu
  publication:
  - doi: 10.1093/BIOINFORMATICS/BTAF496
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-09-01T00:00:00Z'
      journal: Bioinformatics
      title: 'SPACE: STRING proteins as complementary embeddings'
    note: null
    pmcid: PMC12453690
    pmid: '40924541'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Protein expression
    uri: http://edamontology.org/topic_0108
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-10-27T16:07:12.131271Z'
  biotoolsCURIE: biotools:nucleoatac
  biotoolsID: nucleoatac
  collectionID: []
  confidence_flag: tool
  cost: null
  credit: []
  description: 'Structured nucleosome fingerprints enable high-resolution mapping
    of chromatin architecture within regulatory regions.


    This package is no longer being actively maintained; feel free to post issues
    that others in the community may respond to, but this package will likely not
    be updated further. Additionally, if anyone wants to maintain a fork of the package
    or has developed an alternative package for similar purposes, would be happy to
    link to that repo here.


    2025 Python Packaging Survey is now live!.


    Please cite our paper at Genome Research if you use this tool in your research.


    New Authentication Rolling Out - We''re upgrading our sign-in process to give
    you one account across all Anaconda products! Browser users will see a refreshed
    sign-in flow, while CLI users will experience no changes.


    Home: http://nucleoatac.readthedocs.io/en/latest/.


    Documentation can be found at http://nucleoatac.readthedocs.org/en/latest/.


    Python package for calling nucleosomes using ATAC-Seq data.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://nucleoatac.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Peak calling
      uri: http://edamontology.org/operation_3222
    - term: Transcriptional regulatory element prediction
      uri: http://edamontology.org/operation_0438
    - term: Nucleosome position prediction
      uri: http://edamontology.org/operation_0432
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    output: []
  homepage: https://anaconda.org/bioconda/nucleoatac
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-10-27T16:07:12.133668Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/GreenleafLab/NucleoATAC
  maturity: null
  name: NucleoATAC
  operatingSystem: []
  otherID: []
  owner: satroz
  publication:
  - doi: 10.1101/GR.192294.115
    metadata:
      abstract: ''
      authors: []
      citationCount: 246
      date: '2015-11-01T00:00:00Z'
      journal: Genome Research
      title: Structured nucleosome fingerprints enable high-resolution mapping of
        chromatin architecture within regulatory regions
    note: null
    pmcid: PMC4617971
    pmid: '26314830'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: DNA packaging
    uri: http://edamontology.org/topic_3176
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: ChIP-seq
    uri: http://edamontology.org/topic_3169
  - term: Chromosome conformation capture
    uri: http://edamontology.org/topic_3940
  - term: Protein expression
    uri: http://edamontology.org/topic_0108
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2023-07-26T14:40:01.768324Z'
  biotoolsCURIE: biotools:ms_annika
  biotoolsID: ms_annika
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: viktoria.dorfer@fh-hagenberg.at
    fundrefid: null
    gridid: null
    name: Viktoria Dorfer
    note: null
    orcidid: https://orcid.org/0000-0002-5332-5701
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://bioinformatics.fh-hagenberg.at/
  - email: micha.birklbauer@fh-hagenberg.at
    fundrefid: null
    gridid: null
    name: Micha Birklbauer
    note: null
    orcidid: https://orcid.org/0009-0005-1051-179X
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: http://bioinformatics.fh-hagenberg.at/
  description: MS Annika is a crosslink search engine based on MS Amanda, aimed at
    identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and
    MS3 spectra. It can deal with a wide variety of cross-linkers and provides robust
    and transparent FDR control based on a target-decoy approach. MS Annika is available
    free of charge as a plug-in for Proteome Discoverer.
  documentation:
  - note: null
    type:
    - General
    url: https://hgb-bin-proteomics.github.io/MSAnnika/
  - note: null
    type:
    - User manual
    url: https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/MS_Annika_3.0_UserManual.pdf
  - note: Detailed tutorial how to use MS Annika
    type:
    - Training material
    url: https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/tutorial/MS_Annika_3.0_Tutorial.pdf
  - note: Detailed tutorial how to use MS Annika
    type:
    - Training material
    url: https://www.youtube.com/watch?v=L1lVt35PYv4
  download:
  - note: Latest MS Annika version for Proteome Disoverer 3.2
    type: Software package
    url: https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.2/latest.zip
    version: PD3.2:latest
  - note: Latest MS Annika version for Proteome Disoverer 3.1
    type: Software package
    url: https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.1/latest.zip
    version: PD3.1:latest
  - note: Latest MS Annika version for Proteome Disoverer 3.0
    type: Software package
    url: https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.0/latest.zip
    version: PD3.0:latest
  - note: Latest MS Annika version for Proteome Disoverer 2.5
    type: Software package
    url: https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD2.5/latest.zip
    version: PD2.5:latest
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: Thermo RAW
        uri: http://edamontology.org/format_3712
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Peptide identification
      uri: http://edamontology.org/operation_3631
    - term: Peptide database search
      uri: http://edamontology.org/operation_3646
    - term: PTM localisation
      uri: http://edamontology.org/operation_3755
    - term: PTM identification
      uri: http://edamontology.org/operation_3645
    - term: Target-Decoy
      uri: http://edamontology.org/operation_3649
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://github.com/hgb-bin-proteomics/MSAnnika
  homepage_status: 0
  language:
  - C#
  lastUpdate: '2025-10-26T02:38:48.643054Z'
  license: Freeware
  link:
  - note: MS Annika version archive
    type:
    - Repository
    url: https://github.com/hgb-bin-proteomics/MSAnnika
  maturity: Mature
  name: MS Annika
  operatingSystem:
  - Windows
  otherID: []
  owner: michabirklbauer
  publication:
  - doi: 10.1021/acs.jproteome.0c01000
    metadata:
      abstract: ''
      authors: []
      citationCount: 22
      date: '2021-05-07T00:00:00Z'
      journal: Journal of Proteome Research
      title: 'MS Annika: A New Cross-Linking Search Engine'
    note: MS Annika for cleavable crosslink identification from MS2 spectra
    pmcid: PMC8155564
    pmid: '33852321'
    type:
    - Primary
    version: '1.0'
  - doi: 10.1021/acs.jproteome.3c00325
    metadata:
      abstract: ''
      authors: []
      citationCount: 5
      date: '2023-09-01T00:00:00Z'
      journal: Journal of Proteome Research
      title: MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows
        at High Sensitivity and Specificity
    note: MS Annika 2.0 for cleavable crosslink identification from MS3 spectra
    pmcid: PMC10476269
    pmid: '37566781'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1038/s42004-024-01386-x
    metadata:
      abstract: ''
      authors: []
      citationCount: 2
      date: '2024-12-01T00:00:00Z'
      journal: Communications Chemistry
      title: Proteome-wide non-cleavable crosslink identification with MS Annika 3.0
        reveals the structure of the C. elegans Box C/D complex
    note: MS Annika 3.0 for non-cleavable crosslink identification
    pmcid: PMC11659399
    pmid: '39702463'
    type:
    - Primary
    version: '3.0'
  relation:
  - biotoolsID: ms_amanda
    type: uses
  toolType:
  - Plug-in
  topic:
  - term: Protein folding, stability and design
    uri: http://edamontology.org/topic_0130
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - 'Proteome Discoverer 3.2: MS Annika 3.0 v3.0.7'
  - 'Proteome Discoverer 3.1: MS Annika 3.0 v3.0.7'
  - 'Proteome Discoverer 3.0: MS Annika 2.0 v1.1.4fix'
  - 'Proteome Discoverer 2.5: MS Annika 2.0 v1.1.3'
  - 'Proteome Discoverer 2.4: MS Annika v1.0.0'
  - 'Proteome Discoverer 2.3: MS Annika v1.0.0'
- accessibility: null
  additionDate: '2025-10-25T16:55:18.980477Z'
  biotoolsCURIE: biotools:celltypist
  biotoolsID: celltypist
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: A tool for semi-automatic cell type classification
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/Teichlab/celltypist
  homepage_status: 0
  language: []
  lastUpdate: '2025-10-25T16:55:18.983464Z'
  license: null
  link: []
  maturity: null
  name: celltypist
  operatingSystem: []
  otherID: []
  owner: camlloyd
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2016-11-28T10:07:16Z'
  biotoolsCURIE: biotools:shaman
  biotoolsID: shaman
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Stevenn Volant
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://research.pasteur.fr/en/member/stevenn-volant/
  - email: null
    fundrefid: null
    gridid: null
    name: Hugo Varet
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://research.pasteur.fr/en/member/hugo-varet/
  - email: null
    fundrefid: null
    gridid: null
    name: Pierre Lechat
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://research.pasteur.fr/en/member/pierre-lechat/
  - email: null
    fundrefid: null
    gridid: null
    name: Amine Ghozlane
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://research.pasteur.fr/en/member/amine-ghozlane/
  - email: null
    fundrefid: null
    gridid: null
    name: Institut Pasteur
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://research.pasteur.fr
  - email: null
    fundrefid: null
    gridid: null
    name: C3BI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole: []
    url: https://research.pasteur.fr/en/center/c3bi/
  - email: null
    fundrefid: null
    gridid: null
    name: Bioinformatics and Biostatistics Hub
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole:
    - Provider
    url: https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/
  - email: shaman@pasteur.fr
    fundrefid: null
    gridid: null
    name: SHAMAN team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://research.pasteur.fr/en/software/shaman-shiny-application-for-metagenomic-analysis/
  description: SHiny application for Metagenomic ANalysis including the normalization,
    the differential analysis and mutiple visualization. It is based on DESeq2 R package
    [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in
    [McMurdie and Holmes 2014, Jonsson2016]. It robustly identifies the differential
    abundant genera with the Generalized Linear Model implemented in DESeq2 [Love
    2014].
  documentation:
  - note: null
    type:
    - General
    url: http://shaman.c3bi.pasteur.fr/
  download: []
  editPermission:
    authors:
    - hmenager
    - khillion
    - vashokan
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    note: Quantitative metagenomics Count table & taxonomy Diversity, barplot, boxplot,
      scatterplot, rarefaction curves, heatmap
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    - term: Differential gene expression analysis
      uri: http://edamontology.org/operation_3223
    - term: Species frequency estimation
      uri: http://edamontology.org/operation_3221
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format: []
  homepage: http://shaman.c3bi.pasteur.fr/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-10-23T10:46:59.953305Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/aghozlane/shaman
  maturity: Mature
  name: SHAMAN
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: aghozlane
  publication:
  - doi: 10.1073/pnas.1523899113
    metadata:
      abstract: Listeria monocytogenes is responsible for gastroenteritis in healthy
        individuals and for a severe invasive disease in immunocompromised patients.
        Among the three identified L. monocytogenes evolutionary lineages, lineage
        I strains are overrepresented in epidemic listeriosis outbreaks, but the mechanisms
        underlying the higher virulence potential of strains of this lineage remain
        elusive. Here, we demonstrate that Listeriolysin S (LLS), a virulence factor
        only present in a subset of lineage I strains, is a bacteriocin highly expressed
        in the intestine of orally infected mice that alters the host intestinal microbiota
        and promotes intestinal colonization by L. monocytogenes, as well as deeper
        organ infection. To our knowledge, these results therefore identify LLS as
        the first bacteriocin described in L. monocytogenes and associate modulation
        of host microbiota by L. monocytogenes epidemic strains to increased virulence.
      authors:
      - name: Quereda J.J.
      - name: Dussurget O.
      - name: Nahori M.-A.
      - name: Ghozlane A.
      - name: Volant S.
      - name: Dillies M.-A.
      - name: Regnault B.
      - name: Kennedy S.
      - name: Mondot S.
      - name: Villoing B.
      - name: Cossart P.
      - name: Pizarro-Cerda J.
      citationCount: 87
      date: '2016-05-17T00:00:00Z'
      journal: Proceedings of the National Academy of Sciences of the United States
        of America
      title: Bacteriocin from epidemic Listeria strains alters the host intestinal
        microbiota to favor infection
    note: null
    pmcid: PMC4878514
    pmid: '27140611'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2025-10-23T09:01:44.958137Z'
  biotoolsCURIE: biotools:vivo_platform
  biotoolsID: vivo_platform
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: canudobarreras@unizar.es
    fundrefid: null
    gridid: null
    name: Guillermo Canudo-Barreras
    note: Researcher at Spanish National Research Council (CSIC). Developer.
    orcidid: https://orcid.org/0000-0002-1949-9185
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    - Maintainer
    - Support
    url: null
  - email: eromanos.iacs@aragon.es
    fundrefid: null
    gridid: null
    name: Eduardo Romanos
    note: Researcher at Biomedical Research Center of Aragon (CIBA).
    orcidid: https://orcid.org/0000-0002-9918-3374
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: raquelph@unizar.es
    fundrefid: null
    gridid: null
    name: Raquel P. Herrera
    note: Senior scientist at Spanish National Research Council (CSIC).
    orcidid: https://orcid.org/0000-0002-5244-9569
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: gimeno@unizar.es
    fundrefid: null
    gridid: null
    name: M. Concepción Gimeno
    note: Full professor at Spanish National Research Council (CSIC).
    orcidid: https://orcid.org/0000-0003-0553-0695
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: 'ViVo Platform is a free, open-access web application for the analysis
    of in vivo tumor growth data in mouse models.

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


    By standardizing data processing and incorporating advanced temporal modeling,
    ViVo Platform enhances statistical power and contributes to the 3Rs principle
    by reducing the number of animals needed in preclinical efficacy studies.'
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/gcanudo-barreras/ViVo-Platform/blob/main/README.md
  - note: null
    type:
    - User manual
    url: https://github.com/gcanudo-barreras/ViVo-Platform/blob/main/ViVo_USER_MANUAL.md
  - note: Full methodology
    type:
    - Other
    url: https://www.biorxiv.org/content/10.1101/2025.10.14.682266v1
  - note: null
    type:
    - Release notes
    url: https://github.com/gcanudo-barreras/ViVo-Platform/releases/tag/v1.0-beta
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data analysis
      uri: http://edamontology.org/operation_2945
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output: []
  - cmd: null
    input:
    - data:
        term: Physiology parameter
        uri: http://edamontology.org/data_3722
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Morphology parameter
        uri: http://edamontology.org/data_3723
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: CSV
        uri: http://edamontology.org/format_3752
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://gcanudo-barreras.github.io/ViVo-Platform/
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2025-10-23T09:09:29.560348Z'
  license: MIT
  link:
  - note: null
    type:
    - Service
    url: https://gcanudo-barreras.github.io/ViVo-Platform/
  - note: bioRxiv preprint
    type:
    - Other
    url: https://www.biorxiv.org/content/10.1101/2025.10.14.682266v1
  - note: null
    type:
    - Repository
    url: https://github.com/gcanudo-barreras/ViVo-Platform
  maturity: Emerging
  name: ViVo Platform
  operatingSystem: []
  otherID: []
  owner: gcanudo-barreras
  publication:
  - doi: 10.1101/2025.10.14.682266
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Method
    version: Research Beta 1.0
  relation: []
  toolType:
  - Web application
  topic:
  - term: Preclinical and clinical studies
    uri: http://edamontology.org/topic_3379
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Laboratory animal science
    uri: http://edamontology.org/topic_3386
  - term: Bioinformatics
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