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  description: PICNIC (Proteins Involved in CoNdensates In Cells) is a machine learning-based
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3384
  validated: 1
  version:
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- accessibility: Open access
  additionDate: '2016-03-24T16:22:28Z'
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    url: http://urgi.versailles.inrae.fr/
  description: "The REPET package integrates bioinformatics pipelines dedicated to\
    \ detect, annotate and analyze transposable elements (TEs) in genomic sequences.\
    \ The main pipelines are (i) TEdenovo, which search for interspersed repeats,\
    \ build consensus sequences and classify them according to TE features, and (ii)\n\
    \ TEannot, which mines a genome with a library of TE sequences, for instance the\
    \ one produced by the TEdenovo pipeline, to provide TE annotations exported into\
    \ GFF3 files."
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  - note: null
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    url: https://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/REPET-V3.0-tutorial
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    note: null
    operation:
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    - data:
        term: Feature table
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      format:
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    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
  homepage: https://urgi.versailles.inrae.fr/Tools/REPET
  homepage_status: 0
  language:
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  - Python
  lastUpdate: '2025-09-09T08:10:41.737859Z'
  license: CECILL-2.0
  link:
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  maturity: Legacy
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  operatingSystem:
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  owner: Institut Francais de Bioinform
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    metadata:
      abstract: ''
      authors: []
      citationCount: 226
      date: '2014-05-02T00:00:00Z'
      journal: PLoS ONE
      title: 'PASTEC: An automatic transposable element classification tool'
    note: null
    pmcid: PMC4008368
    pmid: '24786468'
    type:
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    metadata:
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      authors: []
      citationCount: 355
      date: '2011-02-09T00:00:00Z'
      journal: PLoS ONE
      title: Considering transposable element diversification in de novo annotation
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    note: null
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    pmid: '21304975'
    type:
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    metadata:
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      citationCount: 279
      date: '2005-01-01T00:00:00Z'
      journal: PLoS Computational Biology
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    pmid: '16110336'
    type:
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  - doi: 10.1007/s00239-003-0007-2
    metadata:
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      authors: []
      citationCount: 65
      date: '2003-12-29T00:00:00Z'
      journal: Journal of Molecular Evolution
      title: Detection of New Transposable Element Families in Drosophila melanogaster
        and Anopheles gambiae Genomes
    note: null
    pmcid: null
    pmid: '15008403'
    type:
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    version: null
  - doi: 10.1109/JPROC.2016.2590833
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      citationCount: 18
      date: '2017-03-01T00:00:00Z'
      journal: Proceedings of the IEEE
      title: 'De Novo Annotation of Transposable Elements: Tackling the Fat Genome
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    note: null
    pmcid: null
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    type:
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  relation: []
  toolType:
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  topic:
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  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  validated: 1
  version:
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- accessibility: Open access
  additionDate: '2019-12-23T00:50:02Z'
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  description: The PASTEClassifier (Pseudo Agent System for Transposable Elements
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    features. It browses the whole spectrum of possible classifications at order level
    using Wicker hierarchical system. It is also able to automatically classify other
    repeated elements like SSR (Simple Sequence Repeats), rDNA or potential repeated
    host genes. The output is designed to facilitate manual curation by providing
    to the biologist all characteristics that have been found on each TE sequence.
  documentation:
  - note: null
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  owner: fruitshuang
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      date: '2014-05-02T00:00:00Z'
      journal: PLoS ONE
      title: 'PASTEC: An automatic transposable element classification tool'
    note: null
    pmcid: PMC4008368
    pmid: '24786468'
    type:
    - Method
    version: null
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0157
  validated: 1
  version:
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- accessibility: null
  additionDate: '2024-01-10T12:54:25.092426Z'
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  biotoolsID: urgi
  collectionID:
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  confidence_flag: tool
  cost: Free of charge
  credit:
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    name: Jerome Salse
    note: null
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    url: null
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    note: null
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    typeEntity: Division
    typeRole:
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  description: Comparative genomics-driven translational research tool.
  documentation: []
  download: []
  editPermission:
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  elixirCommunity:
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  function:
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    note: null
    operation:
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    output: []
  homepage: https://urgi.versailles.inrae.fr/synteny
  homepage_status: 0
  language: []
  lastUpdate: '2025-09-09T08:09:00.018602Z'
  license: Other
  link: []
  maturity: null
  name: SyntenyViewer
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: raphael.flores
  publication:
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      journal: Database
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    note: null
    pmcid: PMC10167986
    pmid: '37159239'
    type: []
    version: null
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0102
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Structural variation
    uri: http://edamontology.org/topic_3175
  - term: Paleogenomics
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  - term: Protein expression
    uri: http://edamontology.org/topic_0108
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-09-08T11:36:08.406899Z'
  biotoolsCURIE: biotools:hvrlocator
  biotoolsID: hvrlocator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: HVRLocator is a workflow to identify spanning hypervariable region(s)
    from amplicon sequencing variants or SRA public runs (SRR). It aligns query sequences
    to a reference E. coli full-length 16S rRNA gene and identifies the spanning region
    through alignment.
  documentation: []
  download: []
  editPermission:
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  language:
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  lastUpdate: '2025-09-08T11:37:45.401286Z'
  license: CC0-1.0
  link:
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    type:
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    url: https://cloud.sylabs.io/library/jsaraiva/repo/hvrlocator
  maturity: null
  name: HVRLocator
  operatingSystem:
  - Linux
  otherID: []
  owner: Kasmanas
  publication:
  - doi: 10.1101/2025.07.24.666487
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
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  - Workflow
  topic:
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    uri: http://edamontology.org/topic_0091
  - term: Probes and primers
    uri: http://edamontology.org/topic_0632
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2019-02-13T17:01:40Z'
  biotoolsCURIE: biotools:Jalview
  biotoolsID: Jalview
  collectionID:
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  confidence_flag: null
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    fundrefid: null
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    name: Jim Procter
    note: null
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    rorid: null
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    rorid: null
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    url: https://www.lifesci.dundee.ac.uk/people/geoff-barton
  description: Jalview is a free cross-platform program for multiple sequence alignment
    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:
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  - note: Hands-on exercises, Training courses and Training videos
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  - note: null
    type:
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  - note: null
    type:
    - User manual
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  download:
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    version: null
  - note: null
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    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
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  function:
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    input:
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      format:
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        uri: http://edamontology.org/format_1939
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: GFF2-seq
        uri: http://edamontology.org/format_1938
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: BioJSON (Jalview)
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      - term: PHYLIP format
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      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: RNAML
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      - term: GCG MSF
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      - term: Pileup
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      - term: mmCIF
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      - term: VCF
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      - term: Format
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    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
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        uri: http://edamontology.org/format_1476
    note: 'Other Input formats:

      AMSA (.amsa);

      JnetFile (.concise, .jnet);

      PFAM (.pfam);

      Substitution matrix (.matrix);

      Jalview Project File (.jvp);

      Jalview Feature File (.features, .jvfeatures);

      Jalview Annotations File (.annotations, .jvannotations);

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

      ...

      Other Output formats:

      PFAM (.pfam);

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

      Jalview Project File (.jvp);'
    operation:
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      uri: http://edamontology.org/operation_0564
    - term: Phylogenetic tree analysis
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    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    output:
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      - term: Stockholm format
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      - term: FASTA
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      - term: PHYLIP format
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      - term: BLC
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      - term: GCG MSF
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      - term: Pileup
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      - term: ClustalW format
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    - data:
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      format:
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      - term: HTML
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      - term: EPS
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      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: Format
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  homepage: https://www.jalview.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-09-04T13:26:28.643607Z'
  license: GPL-3.0
  link:
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    type:
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  - note: null
    type:
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    url: https://issues.jalview.org/
  - note: Latest development version
    type:
    - Other
    url: https://www.jalview.org/development/jalview_develop/
  - note: null
    type:
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  - note: Twitter feed
    type:
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  - note: YouTube training videos
    type:
    - Social media
    url: https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw
  maturity: Mature
  name: Jalview
  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: ben_s
  publication:
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    metadata:
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      authors: []
      citationCount: 7499
      date: '2009-05-07T00:00:00Z'
      journal: Bioinformatics
      title: Jalview Version 2-A multiple sequence alignment editor and analysis workbench
    note: null
    pmcid: PMC2672624
    pmid: '19151095'
    type: []
    version: null
  relation:
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    type: uses
  - biotoolsID: chimera
    type: uses
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    type: uses
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    type: uses
  - biotoolsID: bioconda
    type: includedIn
  - biotoolsID: 3d-beacons
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    type: uses
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    type: uses
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    type: uses
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    type: uses
  toolType:
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  - Command-line tool
  topic:
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  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 1
  version:
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- accessibility: Open access
  additionDate: '2025-09-03T08:01:20.173602Z'
  biotoolsCURIE: biotools:cats-rb
  biotoolsID: cats-rb
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
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    name: Kristian Bodulić
    note: null
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    typeEntity: Person
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  description: CATS-rb evaluates transcriptome assemblies using the reference genome
    of the corresponding species
  documentation:
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    type:
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    metadata:
      abstract: The Make 2D-DB tool has been previously developed to help build federated
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      - name: Hoogland C.
      - name: Binz P.-A.
      - name: Appel R.D.
      citationCount: 27
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      journal: Proteomics
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    note: null
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  validated: 1
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  description: Calculator of peptide and glycopeptide masses. It is purposefully kept
    as simple as a basic calculator executing arithmetic operations.
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  toolType:
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  topic:
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  - term: Structural genomics
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  - term: Protein modifications
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  description: A package to identify insertion sequences and similar transposable
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    in entire genomes.
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  toolType:
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- accessibility: Open access
  additionDate: '2017-05-16T12:28:07Z'
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    url: https://www.arrayanalysis.org/
  description: ArrayAnalysis is a web-based application for transcriptomic data analysis.
    It supports the analysis of both microarray and RNA-seq data. The tool may also
    be installed locally as a desktop app, Docker image, or R package.
  documentation:
  - note: null
    type:
    - General
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  publication:
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    metadata:
      abstract: Quality control (QC) is crucial for any scientific method producing
        data. Applying adequate QC introduces new challenges in the genomics field
        where large amounts of data are produced with complex technologies. For DNA
        microarrays, specific algorithms for QC and pre-processing including normalization
        have been developed by the scientific community, especially for expression
        chips of the Affymetrix platform. Many of these have been implemented in the
        statistical scripting language R and are available from the Bioconductor repository.
        However, application is hampered by lack of integrative tools that can be
        used by users of any experience level. To fill this gap, we developed a freely
        available tool for QC and pre-processing of Affymetrix gene expression results,
        extending, integrating and harmonizing functionality of Bioconductor packages.
        The tool can be easily accessed through a wizard-like web portal at http://www.arrayanalysis.org
        or downloaded for local use in R. The portal provides extensive documentation,
        including user guides, interpretation help with real output illustrations
        and detailed technical documentation. It assists newcomers to the field in
        performing state-of-the-art QC and pre-processing while offering data analysts
        an integral open-source package. Providing the scientific community with this
        easily accessible tool will allow improving data quality and reuse and adoption
        of standards.
      authors:
      - name: Eijssen L.M.
      - name: Jaillard M.
      - name: Adriaens M.E.
      - name: Gaj S.
      - name: de Groot P.J.
      - name: Muller M.
      - name: Evelo C.T.
      citationCount: 107
      date: '2013-01-01T00:00:00Z'
      journal: Nucleic acids research
      title: User-friendly solutions for microarray quality control and pre-processing
        on ArrayAnalysis.org.
    note: null
    pmcid: PMC3692049
    pmid: '23620278'
    type: []
    version: null
  - doi: 10.1186/s12864-015-1689-8
    metadata:
      abstract: 'Background: Illumina whole-genome expression bead arrays are a widely
        used platform for transcriptomics. Most of the tools available for the analysis
        of the resulting data are not easily applicable by less experienced users.
        ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive
        interface to the functionality of R and Bioconductor packages for microarray
        data analysis. As a modular open source project, it allows developers to contribute
        modules that provide support for additional types of data or extend workflows.
        Results: To enable data analysis of Illumina bead arrays for a broad user
        community, we have developed a module for ArrayAnalysis.org that provides
        a free and user-friendly web interface for quality control and pre-processing
        for these arrays. This module can be used together with existing modules for
        statistical and pathway analysis to provide a full workflow for Illumina gene
        expression data analysis. Conclusions: The Illumina bead arrays analysis module
        is available at http://www.arrayanalysis.org. A user guide, a tutorial demonstrating
        the analysis of an example dataset, and R scripts are available. The module
        can be used as a starting point for statistical evaluation and pathway analysis
        provided on the website or to generate processed input data for a broad range
        of applications in life sciences research.'
      authors:
      - name: Eijssen L.M.T.
      - name: Goelela V.S.
      - name: Kelder T.
      - name: Adriaens M.E.
      - name: Evelo C.T.
      - name: Radonjic M.
      citationCount: 12
      date: '2015-06-30T00:00:00Z'
      journal: BMC Genomics
      title: A user-friendly workflow for analysis of Illumina gene expression bead
        array data available at the arrayanalysis.org portal
    note: null
    pmcid: PMC4486126
    pmid: '26122086'
    type: []
    version: null
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  topic:
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  - term: Gene expression
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  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2016-12-19T14:24:18Z'
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  description: Convert quality scoring to Sanger in FASTQ files.
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      - term: FASTQ
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    note: null
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    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
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        uri: http://edamontology.org/format_2330
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  lastUpdate: '2025-08-27T10:48:08.675794Z'
  license: null
  link:
  - note: null
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  publication:
  - doi: 10.1093/nar/gkw343
    metadata:
      abstract: High-throughput data production technologies, particularly ‘next-generation’
        DNA sequencing, have ushered in widespread and disruptive changes to biomedical
        research. Making sense of the large datasets produced by these technologies
        requires sophisticated statistical and computational methods, as well as substantial
        computational power. This has led to an acute crisis in life sciences, as
        researchers without informatics training attempt to perform computation-dependent
        analyses. Since 2005, the Galaxy project has worked to address this problem
        by providing a framework that makes advanced computational tools usable by
        non experts. Galaxy seeks to make data-intensive research more accessible,
        transparent and reproducible by providing a Web-based environment in which
        users can perform computational analyses and have all of the details automatically
        tracked for later inspection, publication, or reuse. In this report we highlight
        recently added features enabling biomedical analyses on a large scale.
      authors:
      - name: Afgan E.
      - name: Baker D.
      - name: van den Beek M.
      - name: Blankenberg D.
      - name: Bouvier D.
      - name: Cech M.
      - name: Chilton J.
      - name: Clements D.
      - name: Coraor N.
      - name: Eberhard C.
      - name: Gruning B.
      - name: Guerler A.
      - name: Hillman-Jackson J.
      - name: Kuster G.V.
      - name: Rasche E.
      - name: Soranzo N.
      - name: Turaga N.
      - name: Taylor J.
      - name: Nekrutenko A.
      - name: Goecks J.
      citationCount: 1477
      date: '2016-07-08T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The Galaxy platform for accessible, reproducible and collaborative biomedical
        analyses: 2016 update'
    note: null
    pmcid: null
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    type:
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  - doi: 10.7490/f1000research.1114334.1
    metadata: null
    note: null
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    pmid: null
    type:
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    version: null
  relation: []
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  version:
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- accessibility: Open access
  additionDate: '2025-08-25T14:36:13.568250Z'
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  credit:
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    fundrefid: null
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    url: null
  - email: h.achterberg@erasmusmc.nl
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  description: ‘datmat’ is a Python package aimed to easily gather data from a variety
    of sources and materialize it into a standardized format. It can download projects
    of imaging data from XNAT into the EUCAIM folder structure, and is designed to
    be extendible to support other inputs and outputs.
  documentation:
  - note: null
    type:
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  download:
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  homepage: https://gitlab.com/radiology/infrastructure/data-materialisation/
  homepage_status: 0
  language:
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  lastUpdate: '2025-08-26T09:43:49.092198Z'
  license: Apache-2.0
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  - note: null
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  validated: 0
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- accessibility: Open access
  additionDate: '2025-08-25T14:46:01.217831Z'
  biotoolsCURIE: biotools:img2catalog
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  collectionID: []
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  credit:
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    fundrefid: null
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    note: null
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    name: Health-RI
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  description: This tool, 'img2catalog', is built to extract metadata from imaging
    data repositories, map it to a model class, and export it to a catalog. The tool
    is set up to be modular, but it currently supports extracting metadata from an
    XNAT server, converting it to the Health-RI Core v2 metadata model (https://github.com/Health-RI/health-ri-metadata/tree/v2.0.0),
    based on DCAT-AP v3 and Health-DCAT AP, as defined in Pydantic classes using SeMPyRO
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  - cmd: null
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    note: null
    operation:
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  homepage: https://github.com/Health-RI/img2catalog
  homepage_status: 0
  language:
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  lastUpdate: '2025-08-25T14:46:01.219964Z'
  license: MIT
  link:
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    type:
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    url: https://github.com/Health-RI/img2catalog
  maturity: null
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_4012
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- accessibility: Open access
  additionDate: '2025-08-20T17:28:51.309591Z'
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  - email: null
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    note: null
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    rorid: null
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    url: null
  - email: null
    fundrefid: null
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  description: EssSubgraph is a model algorithm that integrates omics data and network
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      - name: Del Pozo-Valero M.
      - name: Riveiro-Alvarez R.
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      - name: Martin-Merida I.
      - name: Avila-Fernandez A.
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      - name: Nunez-Moreno G.
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      - name: Almoguera B.
      - name: Corton M.
      - name: Ayuso C.
      - name: Minguez P.
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      date: '2022-12-01T00:00:00Z'
      journal: npj Genomic Medicine
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  description: a Python package library that allow to model and detect macromolecular
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        and then annotate cellular functions in microbial genomes. This is done by
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- accessibility: Open access
  additionDate: '2020-01-21T16:40:38Z'
  biotoolsCURIE: biotools:DataDiscovery
  biotoolsID: DataDiscovery
  collectionID:
  - elixir-fr-sdp-2019
  - URGI
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: urgi-support@inrae.fr
    fundrefid: null
    gridid: null
    name: urgi-support
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Support
    url: null
  description: 'DataDiscovery aims at providing researchers a simple and fast access
    to relevant biological data using specific keywords and easy to use filters.


    This tool is expected to be easily customizable for specific filters, environments,
    or data schemas. Its current implementations supported by URGI are: WheatIS, Plant,
    RARe.'
  documentation:
  - note: General terms of use
    type:
    - Terms of use
    url: https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/LEGAL-MENTIONS.md
  - note: How to contribute
    type:
    - Contributions policy
    url: https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#contribute
  - note: How to use
    type:
    - User manual
    url: https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/HELP.md
  - note: How to install
    type:
    - Installation instructions
    url: https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#setup
  download: []
  editPermission:
    authors:
    - urgi-contact
    - cpommier
    - cmichotey
    - erlefloch
    - raphael.flores
    type: group
  elixirCommunity: []
  elixirNode:
  - France
  elixirPlatform:
  - Data
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Keyword
        uri: http://edamontology.org/data_0968
      format: []
    - data:
        term: Ontology data
        uri: http://edamontology.org/data_2353
      format: []
    note: null
    operation:
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Relation extraction
      uri: http://edamontology.org/operation_3625
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    - term: Information retrieval
      uri: http://edamontology.org/operation_3908
    output:
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format: []
    - data:
        term: Data reference
        uri: http://edamontology.org/data_2093
      format: []
    - data:
        term: Identifier
        uri: http://edamontology.org/data_0842
      format: []
  homepage: https://urgi.versailles.inrae.fr/data-discovery/
  homepage_status: 0
  language:
  - JavaScript
  - Java
  - Bash
  lastUpdate: '2025-07-29T13:42:39.375595Z'
  license: BSD-3-Clause
  link:
  - note: GitLab code repository for DataDiscovery
    type:
    - Repository
    url: https://forgemia.inra.fr/urgi-is/data-discovery
  - note: Code repository mirror link for DataDiscovery
    type:
    - Mirror
    url: https://github.com/gnpis/DataDiscovery/
  maturity: Emerging
  name: DataDiscovery
  operatingSystem:
  - Linux
  otherID: []
  owner: nfrancillon
  publication:
  - doi: 10.3835/plantgenome2015.06.0038
    metadata:
      abstract: The genome sequences of many important Triticeae species, including
        bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained
        uncharacterized for a long time because their high repeat content, large sizes,
        and polyploidy. As a result of improvements in sequencing technologies and
        novel analyses strategies, several of these have recently been deciphered.
        These efforts have generated new insights into Triticeae biology and genome
        organization and have important implications for downstream usage by breeders,
        experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu)
        is an EU-funded project aimed at constructing hardware, software, and data
        infrastructure for genome-scale research in the life sciences. Since the Triticeae
        data are intrinsically complex, heterogenous, and distributed, the transPLANT
        consortium has undertaken efforts to develop common data formats and tools
        that enable the exchange and integration of data from distributed resources.
        Here we present an overview of the individual Triticeae genome resources hosted
        by transPLANT partners, introduce the objectives of transPLANT, and outline
        common developments and interfaces supporting integrated data access.
      authors:
      - name: Spannagl M.
      - name: Alaux M.
      - name: Lange M.
      - name: Bolser D.M.
      - name: Bader K.C.
      - name: Letellier T.
      - name: Kimmel E.
      - name: Flores R.
      - name: Pommier C.
      - name: Kerhornou A.
      - name: Walts B.
      - name: Nussbaumer T.
      - name: Grabmuller C.
      - name: Chen J.
      - name: Colmsee C.
      - name: Beier S.
      - name: Mascher M.
      - name: Schmutzer T.
      - name: Arend D.
      - name: Thanki A.
      - name: Ramirez-Gonzalez R.
      - name: Ayling M.
      - name: Ayling S.
      - name: Caccamo M.
      - name: Mayer K.F.X.
      - name: Scholz U.
      - name: Steinbach D.
      - name: Quesneville H.
      - name: Kersey P.J.
      citationCount: 6
      date: '2016-03-01T00:00:00Z'
      journal: Plant Genome
      title: TransPLANT resources for triticeae genomic data
    note: "1-\tSpannagl, M., Alaux, M., Lange, M., Bolser, D. M., Bader, K. C., Letellier,\
      \ T., Kimmel, E., Flores, R.-G., Pommier, C., Kerhornou, A., Walts, B., Nussbaumer,\
      \ T., Grabmuller, C., Chen, J., Colmsee, C., Beier, S., Mascher, M., Schmutzer,\
      \ T., Arend, D., Thanki, A., Ramirez-Gonzalez, R., Ayling, M., Ayling, S., Caccamo,\
      \ M., Mayer, K. F. X., Scholz, U., Steinbach, D., Quesneville, H., Kersey, P.\
      \ (2016). TransPLANT resources for triticeae genomic data. Plant Genome, 9 (1),\
      \ 13 p."
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1038/hortres.2016.56
    metadata:
      abstract: Viticulture, like other fields of agriculture, is currently facing
        important challenges that will be addressed only through sustained, dedicated
        and coordinated research. Although the methods used in biology have evolved
        tremendously in recent years and now involve the routine production of large
        data sets of varied nature, in many domains of study, including grapevine
        research, there is a need to improve the findability, accessibility, interoperability
        and reusability (FAIR-ness) of these data. Considering the heterogeneous nature
        of the data produced, the transnational nature of the scientific community
        and the experience gained elsewhere, we have formed an open working group,
        in the framework of the International Grapevine Genome Program (www.vitaceae.org),
        to construct a coordinated federation of information systems holding grapevine
        data distributed around the world, providing an integrated set of interfaces
        supporting advanced data modeling, rich semantic integration and the next
        generation of data mining tools. To achieve this goal, it will be critical
        to develop, implement and adopt appropriate standards for data annotation
        and formatting. The development of this system, the GrapeIS, linking genotypes
        to phenotypes, and scientific research to agronomical and oeneological data,
        should provide new insights into grape biology, and allow the development
        of new varieties to meet the challenges of biotic and abiotic stress, environmental
        change, and consumer demand.
      authors:
      - name: Adam-Blondon A.-F.
      - name: Alaux M.
      - name: Pommier C.
      - name: Cantu D.
      - name: Cheng Z.-M.
      - name: Cramer G.
      - name: Davies C.
      - name: Delrot S.
      - name: Deluc L.
      - name: Di Gaspero G.
      - name: Grimplet J.
      - name: Fennell A.
      - name: Londo J.
      - name: Kersey P.
      - name: Mattivi F.
      - name: Naithani S.
      - name: Neveu P.
      - name: Nikolski M.
      - name: Pezzotti M.
      - name: Reisch B.
      - name: Topfer R.
      - name: Vivier M.
      - name: Ware D.
      - name: Quesneville H.
      citationCount: 37
      date: '2016-11-23T00:00:00Z'
      journal: Horticulture Research
      title: Towards an open grapevine information system
    note: "2-\tAdam-Blondon, A.-F., Alaux, M., Pommier, C., Cantu, D., Cheng, Z.-M.,\
      \ Cramer, G. R., Davies, C., Delrot, S., Deluc, L., di Gaspero, G., Grimplet,\
      \ J., Fennell, A., Londo, J. P., Kersey, P., Mattivi, F., Naithani, S., Neveu,\
      \ P., Nikolski, M., Pezzotti, M., Reisch, B. I., Topfer, R., Vivier, M., Ware,\
      \ D., Quesneville, H. (2016). Towards an open grapevine information system.\
      \ Horticulture Research, 3, 8 p. , DOI : 10.1038/hortres.2016.56"
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1186/s13059-018-1491-4
    metadata:
      abstract: The Wheat@URGI portal has been developed to provide the international
        community of researchers and breeders with access to the bread wheat reference
        genome sequence produced by the International Wheat Genome Sequencing Consortium.
        Genome browsers, BLAST, and InterMine tools have been established for in-depth
        exploration of the genome sequence together with additional linked datasets
        including physical maps, sequence variations, gene expression, and genetic
        and phenomic data from other international collaborative projects already
        stored in the GnpIS information system. The portal provides enhanced search
        and browser features that will facilitate the deployment of the latest genomics
        resources in wheat improvement.
      authors:
      - name: Alaux M.
      - name: Rogers J.
      - name: Letellier T.
      - name: Flores R.
      - name: Alfama F.
      - name: Pommier C.
      - name: Mohellibi N.
      - name: Durand S.
      - name: Kimmel E.
      - name: Michotey C.
      - name: Guerche C.
      - name: Loaec M.
      - name: Laine M.
      - name: Steinbach D.
      - name: Choulet F.
      - name: Rimbert H.
      - name: Leroy P.
      - name: Guilhot N.
      - name: Salse J.
      - name: Feuillet C.
      - name: Paux E.
      - name: Eversole K.
      - name: Adam-Blondon A.-F.
      - name: Quesneville H.
      citationCount: 181
      date: '2018-08-17T00:00:00Z'
      journal: Genome Biology
      title: Linking the International Wheat Genome Sequencing Consortium bread wheat
        reference genome sequence to wheat genetic and phenomic data
    note: "3-\tAlaux M, Rogers J, Letellier T, Flores R, Alfama  F, Pommier C, Mohellibi\
      \ N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach\
      \ D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, International\
      \ Wheat Genome Sequencing Consortium, Paux E, Eversole K, Adam-Blondon A-F,\
      \ Quesneville H (2018) Linking the International Wheat Genome Sequencing Consortium\
      \ bread wheat reference genome sequence to wheat genetic and phenomic data.\
      \ Genome Biology, 19:111."
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: wheatis
    type: usedBy
  - biotoolsID: RARe
    type: usedBy
  - biotoolsID: Plant_DataDiscovery
    type: usedBy
  toolType:
  - Web API
  - Web application
  - Web service
  - Database portal
  topic:
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Biological databases
    uri: http://edamontology.org/topic_3071
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  validated: 1
  version: []
- accessibility: Restricted access
  additionDate: '2017-03-23T14:24:24Z'
  biotoolsCURIE: biotools:gnpis
  biotoolsID: gnpis
  collectionID:
  - elixir-fr-sdp-2019
  - Animal and Crop Genomics
  confidence_flag: null
  cost: null
  credit:
  - email: urgi-contact@versailles.inra.fr
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: A multispecies integrative information system dedicated to plant and
    fungi pests.. It allows researchers to access genetic, phenotypic and genomic
    data. It is used by both large international projects and the French National
    Research Institute for Agriculture, Food and Environment
  documentation:
  - note: null
    type:
    - General
    url: https://urgi.versailles.inra.fr/gnpis/
  download: []
  editPermission:
    authors:
    - urgi-contact
    - animalandcropgenomics
    - nfrancillon
    - cmichotey
    type: group
  elixirCommunity: []
  elixirNode:
  - France
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genome visualisation
      uri: http://edamontology.org/operation_3208
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    - term: Ontology visualisation
      uri: http://edamontology.org/operation_3559
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format: []
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format: []
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format: []
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    - data:
        term: Ontology data
        uri: http://edamontology.org/data_2353
      format: []
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format: []
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format: []
    - data:
        term: Identifier
        uri: http://edamontology.org/data_0842
      format: []
  homepage: https://urgi.versailles.inrae.fr/gnpis
  homepage_status: 0
  language:
  - JavaScript
  - C#
  lastUpdate: '2025-07-29T13:42:38.871501Z'
  license: CC-BY-4.0
  link: []
  maturity: Mature
  name: Genetic and Genomic Information System (GnpIS)
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: cpommier
  publication:
  - doi: 10.1093/database/bat058
    metadata:
      abstract: Data integration is a key challenge for modern bioinformatics. It
        aims to provide biologists with tools to explore relevant data produced by
        different studies. Large-scale international projects can generate lots of
        heterogeneous and unrelated data. The challenge is to integrate this information
        with other publicly available data. Nucleotide sequencing throughput has been
        improved with new technologies; this increases the need for powerful information
        systems able to store, manage and explore data. GnpIS is a multispecies integrative
        information system dedicated to plant and fungi pests. It bridges genetic
        and genomic data, allowing researchers access to both genetic information
        (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms,
        germplasms and genotypes) and genomic data (e.g. genomic sequences, physical
        maps, genome annotation and expression data) for species of agronomical interest.
        GnpIS is used by both large international projects and plant science departments
        at the French National Institute for Agricultural Research. Here, we illustrate
        its use. © The Author(s) 2013. Published by Oxford University Press.
      authors:
      - name: Steinbach D.
      - name: Alaux M.
      - name: Amselem J.
      - name: Choisne N.
      - name: Durand S.
      - name: Flores R.
      - name: Keliet A.-O.
      - name: Kimmel E.
      - name: Lapalu N.
      - name: Luyten I.
      - name: Michotey C.
      - name: Mohellibi N.
      - name: Pommier C.
      - name: Reboux S.
      - name: Valdenaire D.
      - name: Verdelet D.
      - name: Quesneville H.
      citationCount: 42
      date: '2013-12-01T00:00:00Z'
      journal: Database
      title: 'GnpIS: An information system to integrate genetic and genomic data from
        plants and fungi'
    note: null
    pmcid: PMC3746681
    pmid: '23959375'
    type:
    - Primary
    version: null
  - doi: 10.1007/978-1-4939-6658-5_5
    metadata:
      abstract: GnpIS is an information system designed to help scientists working
        on plants and fungi to decipher the molecular and genetic architecture of
        trait variations by facilitating the navigation through genetic, genomic,
        and phenotypic information. The purpose of the present chapter is to illustrate
        how users can (1) explore datasets from phenotyping experiments in order to
        build new datasets for studying genotype × environment interactions in traits,
        (2) browse into the results of other genetic analysis data such as GWAS to
        generate or check working hypothesis about candidate genes or to identify
        important alleles and germplasms for breeding programs, and (3) explore the
        polymorphism in specific area of the genome using InterMine, JBrowse tools
        embedded in the GnpIS information system.
      authors:
      - name: Adam-Blondon A.-F.
      - name: Alaux M.
      - name: Durand S.
      - name: Letellier T.
      - name: Merceron G.
      - name: Mohellibi N.
      - name: Pommier C.
      - name: Steinbach D.
      - name: Alfama F.
      - name: Amselem J.
      - name: Charruaud D.
      - name: Choisne N.
      - name: Flores R.
      - name: Guerche C.
      - name: Jamilloux V.
      - name: Kimmel E.
      - name: Lapalu N.
      - name: Loaec M.
      - name: Michotey C.
      - name: Quesneville H.
      citationCount: 1
      date: '2017-01-01T00:00:00Z'
      journal: Methods in Molecular Biology
      title: Mining plant genomic and genetic data using the gnpis information system
    note: null
    pmcid: null
    pmid: '27987166'
    type:
    - Primary
    version: null
  - doi: 10.1038/hortres.2016.56
    metadata:
      abstract: Viticulture, like other fields of agriculture, is currently facing
        important challenges that will be addressed only through sustained, dedicated
        and coordinated research. Although the methods used in biology have evolved
        tremendously in recent years and now involve the routine production of large
        data sets of varied nature, in many domains of study, including grapevine
        research, there is a need to improve the findability, accessibility, interoperability
        and reusability (FAIR-ness) of these data. Considering the heterogeneous nature
        of the data produced, the transnational nature of the scientific community
        and the experience gained elsewhere, we have formed an open working group,
        in the framework of the International Grapevine Genome Program (www.vitaceae.org),
        to construct a coordinated federation of information systems holding grapevine
        data distributed around the world, providing an integrated set of interfaces
        supporting advanced data modeling, rich semantic integration and the next
        generation of data mining tools. To achieve this goal, it will be critical
        to develop, implement and adopt appropriate standards for data annotation
        and formatting. The development of this system, the GrapeIS, linking genotypes
        to phenotypes, and scientific research to agronomical and oeneological data,
        should provide new insights into grape biology, and allow the development
        of new varieties to meet the challenges of biotic and abiotic stress, environmental
        change, and consumer demand.
      authors:
      - name: Adam-Blondon A.-F.
      - name: Alaux M.
      - name: Pommier C.
      - name: Cantu D.
      - name: Cheng Z.-M.
      - name: Cramer G.
      - name: Davies C.
      - name: Delrot S.
      - name: Deluc L.
      - name: Di Gaspero G.
      - name: Grimplet J.
      - name: Fennell A.
      - name: Londo J.
      - name: Kersey P.
      - name: Mattivi F.
      - name: Naithani S.
      - name: Neveu P.
      - name: Nikolski M.
      - name: Pezzotti M.
      - name: Reisch B.
      - name: Topfer R.
      - name: Vivier M.
      - name: Ware D.
      - name: Quesneville H.
      citationCount: 37
      date: '2016-11-23T00:00:00Z'
      journal: Horticulture Research
      title: Towards an open grapevine information system
    note: null
    pmcid: PMC5120350
    pmid: '27917288'
    type:
    - Other
    version: null
  - doi: 10.3835/plantgenome2015.06.0038
    metadata:
      abstract: The genome sequences of many important Triticeae species, including
        bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained
        uncharacterized for a long time because their high repeat content, large sizes,
        and polyploidy. As a result of improvements in sequencing technologies and
        novel analyses strategies, several of these have recently been deciphered.
        These efforts have generated new insights into Triticeae biology and genome
        organization and have important implications for downstream usage by breeders,
        experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu)
        is an EU-funded project aimed at constructing hardware, software, and data
        infrastructure for genome-scale research in the life sciences. Since the Triticeae
        data are intrinsically complex, heterogenous, and distributed, the transPLANT
        consortium has undertaken efforts to develop common data formats and tools
        that enable the exchange and integration of data from distributed resources.
        Here we present an overview of the individual Triticeae genome resources hosted
        by transPLANT partners, introduce the objectives of transPLANT, and outline
        common developments and interfaces supporting integrated data access.
      authors:
      - name: Spannagl M.
      - name: Alaux M.
      - name: Lange M.
      - name: Bolser D.M.
      - name: Bader K.C.
      - name: Letellier T.
      - name: Kimmel E.
      - name: Flores R.
      - name: Pommier C.
      - name: Kerhornou A.
      - name: Walts B.
      - name: Nussbaumer T.
      - name: Grabmuller C.
      - name: Chen J.
      - name: Colmsee C.
      - name: Beier S.
      - name: Mascher M.
      - name: Schmutzer T.
      - name: Arend D.
      - name: Thanki A.
      - name: Ramirez-Gonzalez R.
      - name: Ayling M.
      - name: Ayling S.
      - name: Caccamo M.
      - name: Mayer K.F.X.
      - name: Scholz U.
      - name: Steinbach D.
      - name: Quesneville H.
      - name: Kersey P.J.
      citationCount: 6
      date: '2016-03-01T00:00:00Z'
      journal: Plant Genome
      title: TransPLANT resources for triticeae genomic data
    note: null
    pmcid: null
    pmid: '27898761'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  - Database portal
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Genetics
    uri: http://edamontology.org/topic_3053
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  validated: 1
  version:
  - '18.2'
- accessibility: null
  additionDate: '2019-11-27T10:47:08Z'
  biotoolsCURIE: biotools:OakMine
  biotoolsID: OakMine
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Quercus robur annotation database
  documentation:
  - note: null
    type:
    - API documentation
    url: http://intermine.readthedocs.org/en/latest/web-services/
  - note: null
    type:
    - User manual
    url: https://flymine.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors:
    - cmichotey
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format: []
    - data:
        term: Ontology data
        uri: http://edamontology.org/data_2353
      format: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Gene-set enrichment analysis
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        the broader neuroimaging community. © Copyright 2007 by Humana Press Inc.
        All rights of any nature whatsoever are reserved.
      authors:
      - name: Marcus D.S.
      - name: Olsen T.R.
      - name: Ramaratnam M.
      - name: Buckner R.L.
      citationCount: 378
      date: '2007-03-01T00:00:00Z'
      journal: Neuroinformatics
      title: 'The extensible neuroimaging archive toolkit: An informatics platform
        for managing, exploring, and sharing neuroimaging data'
    note: null
    pmcid: null
    pmid: '17426351'
    type:
    - Primary
    version: null
  - doi: 10.1162/jocn.2009.21407
    metadata:
      abstract: The Open Access Series of Imaging Studies is a series of neuroimaging
        data sets that are publicly available for study and analysis. The present
        MRI data set consists of a longitudinal collection of 150 subjects aged 60
        to 96 years all acquired on the same scanner using identical sequences. Each
        subject was scanned on two or more visits, separated by at least 1 year for
        a total of 373 imaging sessions. Subjects were characterized using the Clinical
        Dementia Rating (CDR) as either nondemented or with very mild tomild Alzheimer's
        disease. Seventy-two of the subjects were characterized as nondemented throughout
        the study. Sixty-four of the included subjects were characterized as demented
        at the time of their initial visits and remained so for subsequent scans,
        including 51 individuals with CDR 0.5 similar level of impairment to individuals
        elsewhere considered to have "mild cognitive impairment." Another 14 subjects
        were characterized as nondemented at the time of their initial visit (CDR
        0) and were subsequently characterized as demented at a later visit (CDR >
        0). The subjects were all right-handed and include bothmen (n=62) and women
        (n = 88). For each scanning session, three or four individual T1-weighted
        MRI scans were obtained. Multiple withinsession acquisitions provide extremely
        high contrast to noise, making the data amenable to a wide range of analytic
        approaches including automated computational analysis. Automated calculation
        of whole-brain volume is presented to demonstrate use of the data for measuring
        differences associated with normal aging and Alzheimer's disease. © 2010 Massachusetts
        Institute of Technology.
      authors:
      - name: Marcus D.S.
      - name: Fotenos A.F.
      - name: Csernansky J.G.
      - name: Morris J.C.
      - name: Buckner R.L.
      citationCount: 461
      date: '2010-12-01T00:00:00Z'
      journal: Journal of Cognitive Neuroscience
      title: 'Open access series of imaging studies: Longitudinal MRI data in nondemented
        and demented older adults'
    note: null
    pmcid: PMC2895005
    pmid: '19929323'
    type:
    - Usage
    version: null
  relation:
  - biotoolsID: xnatpy
    type: usedBy
  - biotoolsID: rxnat
    type: usedBy
  - biotoolsID: xnat-pic
    type: usedBy
  - biotoolsID: bigr_xnat
    type: usedBy
  toolType:
  - Web application
  - Web API
  topic:
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Bioimaging
    uri: http://edamontology.org/topic_3383
  - term: Tomography
    uri: http://edamontology.org/topic_3452
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-07-23T10:27:57.572501Z'
  biotoolsCURIE: biotools:etenlnc
  biotoolsID: etenlnc
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: barah@tezu.ernet.in
    fundrefid: null
    gridid: null
    name: Pankaj Barah
    note: Assistant Professor at Department of Molecular Biology and Biotechnology,
      Tezpur University.
    orcidid: https://orcid.org/0000-0001-7039-7996
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Maintainer
    url: https://www.tezu.ernet.in/dmbbt/profile/34
  - email: prangannathofficial@gmai.com
    fundrefid: null
    gridid: null
    name: Prangan Nath
    note: null
    orcidid: https://orcid.org/0000-0002-9451-7822
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  description: ETENLNC (End-To-End-Novel-NonCoding) is a lncRNA identification and
    analysis framework
  documentation:
  - note: A detailed guide on running ETENLNC using the demo data can be found in
      the ETENLNC manual (supplementary to our publication)
    type:
    - Command-line options
    url: https://github.com/EvolOMICS-TU/ETENLNC
  download:
  - note: Sample/demo data for ETENLNC. A detailed guide on running ETENLNC using
      the demo data can be found in the ETENLNC manual (supplementary to our publication).
    type: Biological data
    url: https://zenodo.org/records/14325721?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImVmYTllNWJkLWE4ODUtNGM3OC05YTAxLWM4ZDk5YTljZDZjMCIsImRhdGEiOnt9LCJyYW5kb20iOiI4M2I1YjBlZDQ4MmUyZTIxNDg2YmI0YTFkMWE5MTI1OCJ9.HeB3WrsPduNzMyXjH4x5HfCgmIp4NzYv0P_11XU9lcXC_ZxEaVndP-kD0LDkxwufHVNlroeAhdK33PR51F6jnw
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: bash ETENLNC_docker.sh
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Genome map
        uri: http://edamontology.org/data_1288
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: GTF
        uri: http://edamontology.org/format_2306
      - term: GFF
        uri: http://edamontology.org/format_2305
    note: Run ETENLNC on paired-end raw RNA-Seq (.fastq) data
    operation:
    - term: Read pre-processing
      uri: http://edamontology.org/operation_3219
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    - term: Transcriptome assembly
      uri: http://edamontology.org/operation_3258
    - term: Nucleic acid feature detection
      uri: http://edamontology.org/operation_0415
    - term: RNA-Seq quantification
      uri: http://edamontology.org/operation_3800
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    - term: Heat map generation
      uri: http://edamontology.org/operation_0531
    - term: RNA secondary structure prediction
      uri: http://edamontology.org/operation_0278
    - term: k-mer counting
      uri: http://edamontology.org/operation_3472
    - term: Protein-nucleic acid interaction analysis
      uri: http://edamontology.org/operation_0389
    - term: RNA-binding protein prediction
      uri: http://edamontology.org/operation_3901
    - term: Gene regulatory network prediction
      uri: http://edamontology.org/operation_2437
    output:
    - data:
        term: Nucleic acid sequence record
        uri: http://edamontology.org/data_2887
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Heat map
        uri: http://edamontology.org/data_1636
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format: []
  homepage: https://github.com/EvolOMICS-TU/ETENLNC
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-23T10:27:57.574879Z'
  license: GPL-3.0
  link:
  - note: GitHub Repo
    type:
    - Repository
    url: https://github.com/EvolOMICS-TU/ETENLNC
  maturity: Emerging
  name: ETENLNC
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: prangannath
  publication:
  - doi: 10.1016/j.compbiolchem.2024.108140
    metadata:
      abstract: 'Long non-coding RNAs (lncRNAs) play crucial roles in the regulation
        of gene expression and maintenance of genomic integrity through various interactions
        with DNA, RNA, and proteins. The availability of large-scale sequence data
        from various high-throughput platforms has opened possibilities to identify,
        predict, and functionally annotate lncRNAs. As a result, there is a growing
        demand for an integrative computational framework capable of identifying known
        lncRNAs, predicting novel lncRNAs, and inferring the downstream regulatory
        interactions of lncRNAs at the genome-scale. We present ETENLNC (End-To-End-Novel-Long-NonCoding),
        a user-friendly, integrative, open-source, scalable, and modular computational
        framework for identifying and analyzing lncRNAs from raw RNA-Seq data. ETENLNC
        employs six stringent filtration steps to identify novel lncRNAs, performs
        differential expression analysis of mRNA and lncRNA transcripts, and predicts
        regulatory interactions between lncRNAs, mRNAs, miRNAs, and proteins. We benchmarked
        ETENLNC against six existing tools and optimized it for desktop workstations
        and high-performance computing environments using data from three different
        species. ETENLNC is freely available on GitHub: https://github.com/EvolOMICS-TU/ETENLNC.'
      authors:
      - name: Nath P.
      - name: Bhuyan K.
      - name: Bhattacharyya D.K.
      - name: Barah P.
      citationCount: 2
      date: '2024-10-01T00:00:00Z'
      journal: Computational Biology and Chemistry
      title: 'ETENLNC: An end to end lncRNA identification and analysis framework
        to facilitate construction of known and novel lncRNA regulatory networks'
    note: null
    pmcid: null
    pmid: '38996755'
    type:
    - Primary
    version: '.0'
  relation:
  - biotoolsID: hisat2
    type: uses
  - biotoolsID: salmon
    type: uses
  - biotoolsID: fastqc
    type: uses
  - biotoolsID: fastp
    type: uses
  - biotoolsID: stringtie
    type: uses
  - biotoolsID: gffcompare
    type: uses
  - biotoolsID: cpc2
    type: uses
  - biotoolsID: ncbi_blast_plus
    type: uses
  - biotoolsID: tximport
    type: uses
  - biotoolsID: deseq2
    type: uses
  - biotoolsID: lnctar
    type: uses
  - biotoolsID: capsule-lpi
    type: uses
  - biotoolsID: seekr
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  validated: 0
  version:
  - '1.0'
next: ?page=2
previous: null
