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  confidence_flag: null
  cost: Free of charge
  credit:
  - email: swim@fishka.bio
    fundrefid: null
    gridid: null
    name: Fishka Bio
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://fishka.bio
  description: "Browser-based viewer for GenBank and GenPept files. Renders an interactive\
    \ linear and circular feature map, the annotated source text, and the nucleotide/protein\
    \ sequence side by side. \n\nTranslates CDS features using the record's own genetic\
    \ code and translation qualifiers, flags where the stored /translation disagrees\
    \ with a plain translation, and adds optional computed layers: ORF prediction\
    \ and restriction-site mapping. Handles multi-record files. Runs entirely in the\
    \ browser — files are never uploaded."
  documentation: []
  download:
  - note: Offline build — the same application as a self-contained archive, runs from
      local files with no server
    type: Downloads page
    url: https://fishka.bio/download
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence record
        uri: http://edamontology.org/data_0849
      format:
      - term: GenBank format
        uri: http://edamontology.org/format_1936
      - term: genpept
        uri: http://edamontology.org/format_1937
    note: null
    operation:
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    - term: Restriction site recognition
      uri: http://edamontology.org/operation_0431
    - term: Coding region prediction
      uri: http://edamontology.org/operation_0436
    - term: DNA translation
      uri: http://edamontology.org/operation_0371
    output:
    - data:
        term: Sequence record
        uri: http://edamontology.org/data_0849
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://fishka.bio/gbatlas
  homepage_status: 0
  language:
  - TypeScript
  lastUpdate: '2026-07-20T00:49:52.782035Z'
  license: Freeware
  link:
  - note: fishka.bio — the tool collection gbatlas belongs to
    type:
    - Software catalogue
    url: https://fishka.bio
  maturity: Mature
  name: gbatlas
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: fishka
  publication:
  - doi: 10.5281/zenodo.21444547
    metadata: null
    note: Software deposit (concept DOI — resolves to the latest version) covering
      the fishka.bio tools, including gbatlas.
    pmcid: null
    pmid: null
    type:
    - Other
    version: 2026.07.19
  relation: []
  toolType:
  - Web application
  - Desktop application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Nucleic acid sites, features and motifs
    uri: http://edamontology.org/topic_3511
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-02-29T15:44:00.705364Z'
  biotoolsCURIE: biotools:kMetaShot
  biotoolsID: kMetaShot
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: giuseppe.defazio@uniba.it
    fundrefid: null
    gridid: null
    name: Giuseppe Defazio
    note: Post-Doc Researcher at University of Bari
    orcidid: https://orcid.org/0000-0002-9356-5224
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://persone.ict.uniba.it/rubrica/@@cerca?advanced_search=False&sort_on=&SearchableText=defazio
  description: The application of 2nd and 3rd generation High Throughput Sequencing
    (HTS) technologies has deeply reshaped experimental method to investigate microbial
    communities and obtain a taxonomic and functional profile of the invetigated community.
    Shotgun Metagenomics allow to quickly obtain a representation of microorganisms
    genomes characterizing a particular environment. In order to obtain a fast e reliable
    taxonomic classification of microorganisms genomes we present kMetaShot, an alignment-free
    taxonomic classifier based on k-mer/minimizer counting.
  documentation:
  - note: null
    type:
    - Other
    url: https://github.com/gdefazio/kMetaShot
  download: []
  editPermission:
    authors:
    - bfosso
    - gpesole
    type: group
  elixirCommunity:
  - Marine Metagenomics
  elixirNode:
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  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://github.com/gdefazio/kMetaShot
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-07-17T09:37:14.810675Z'
  license: GPL-3.0
  link: []
  maturity: Emerging
  name: kMetaShot
  operatingSystem:
  - Linux
  otherID: []
  owner: gdefazio
  publication:
  - doi: 10.1093/bib/bbae680
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-07-13T07:29:39.957646Z'
  biotoolsCURIE: biotools:transcriptoscope
  biotoolsID: transcriptoscope
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Abubakar Abdulkadir
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    - Documentor
    - Primary contact
    url: https://github.com/Shettima123
  - email: null
    fundrefid: null
    gridid: null
    name: Dr. Rosby's Lab
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    - Support
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Southern University A and M
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: Local Windows-friendly R Shiny application for RNA-seq differential
    expression using DESeq2, normalized-expression testing, over-representation analysis,
    fgsea-ranked pathway analysis, and WGCNA coexpression-network analysis. It supports
    input validation, additive and interaction designs, built-in human, fruit-fly,
    and yeast annotations, publication-quality plots, and reproducibility bundles
    containing results, settings, and executable R and R Markdown rerun code.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/README.md
  - note: null
    type:
    - Installation instructions
    - Quick start guide
    url: https://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/INSTALL_WINDOWS.md
  - note: null
    type:
    - Release notes
    url: https://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/RELEASE_NOTES.md
  - note: null
    type:
    - Citation instructions
    url: https://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/CITATION.cff
  - note: Support and issue-reporting instructions.
    type:
    - General
    url: https://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/SUPPORT.md
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  - note: Standalone x64 Windows installer that bundles R and the required package
      library.
    type: Binaries
    url: https://github.com/Shettima123/TranscriptoScope/releases/download/v0.5.0/TranscriptoScope_Windows_Store_v0.5.0.exe
    version: 0.5.0
  - note: Manual Windows package for users who already have R.
    type: Software package
    url: https://github.com/Shettima123/TranscriptoScope/releases/download/v0.5.0/TranscriptoScope_Windows_v0.5.0.zip
    version: 0.5.0
  - note: null
    type: Source code
    url: https://github.com/Shettima123/TranscriptoScope/archive/refs/tags/v0.5.0.zip
    version: 0.5.0
  - note: null
    type: Downloads page
    url: https://github.com/Shettima123/TranscriptoScope/releases/tag/v0.5.0
    version: 0.5.0
  editPermission:
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: RNA-Seq analysis
      uri: http://edamontology.org/operation_3680
    - term: Pathway analysis
      uri: http://edamontology.org/operation_3928
    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    - term: Weighted correlation network analysis
      uri: http://edamontology.org/operation_3766
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    output: []
  homepage: https://github.com/Shettima123/TranscriptoScope
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-07-17T09:02:32.913006Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/Shettima123/TranscriptoScope
  - note: null
    type:
    - Issue tracker
    url: https://github.com/Shettima123/TranscriptoScope/issues
  maturity: Mature
  name: TranscriptoScope
  operatingSystem:
  - Windows
  otherID: []
  owner: Abubakar
  publication:
  - doi: 10.5281/zenodo.21409091
    metadata: null
    note: Version-specific archived software release.
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 0.5.0
  relation: []
  toolType:
  - Workbench
  - Desktop application
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version:
  - 0.5.0
- accessibility: Open access
  additionDate: '2025-06-30T08:52:48.500476Z'
  biotoolsCURIE: biotools:fair_eva_4_eucaim
  biotoolsID: fair_eva_4_eucaim
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Fernando Aguilar
    note: 'Creator and devloper of the main package FAIR EVA.

      This software started to be developed within IFCA-Advanced-Computing receives
      funding from the European Union’s Horizon 2020 research and innovation programme
      under grant agreement No 857647.'
    orcidid: https://orcid.org/0000-0001-9462-4831
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    - Documentor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: David Rodríguez
    note: Developer of the EUCAIM plugin.
    orcidid: https://orcid.org/0000-0002-9160-5106
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Inés Victoria
    note: Developer of the EUCAIM plugin.
    orcidid: https://orcid.org/0009-0003-7950-3937
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: 'FAIR EVA: Evaluator, Validator & Advisor has been developed to check
    the FAIRness level of digital objects from different repositories or data portals.
    It requires the object identifier (preferably persistent and unique identifier)
    and the repository to check. It also provides a generic and agnostic way to check
    digital objects.

    This software started to be developed within IFCA-Advanced-Computing receives
    funding from the European Union’s Horizon 2020 research and innovation programme
    under grant agreement No 857647.'
  documentation:
  - note: Documentation for the main package, EUCAIM plugin specific documentation
      not included.
    type:
    - General
    url: https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md
  - note: Wiki page with FAIR EVA for EUCAIM specific instructions.
    type:
    - User manual
    url: https://gitlabpages.ifca.es/fair-eva-guide-608baa/
  download: []
  editPermission:
    authors:
    - ines.ifca
    - davrodgon
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: fair-eva-cli batch -p eucaim_legacy
    input:
    - data:
        term: Database ID
        uri: http://edamontology.org/data_1048
      format: []
    note: null
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
  homepage: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-07-16T12:49:00.960818Z'
  license: Apache-2.0
  link:
  - note: Repository for FAIR EVA, without the EUCAIM specific plugin
    type:
    - Repository
    url: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  - note: Repository for FAIR-EVA for eucaim plugin. Currently not public.
    type:
    - Repository
    url: https://gitlab.ifca.es/eucaim/fair_eucaim
  maturity: Mature
  name: FAIR EVA for EUCAIM
  operatingSystem:
  - Linux
  otherID: []
  owner: davrodgon
  publication:
  - doi: 10.1038/s41597-023-02652-8
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Plug-in
  - Web service
  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version:
  - EUCAIM_plugin_0.3
  - EUCAIM_plugin_0.3.1
  - EUCAIM_plugin_0.4.0
  - EUCAIM_0.4.2
  - v0.6.1
- accessibility: Open access
  additionDate: '2026-02-26T12:47:29.542367Z'
  biotoolsCURIE: biotools:inflexa
  biotoolsID: inflexa
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: support@inflexa.ai
    fundrefid: null
    gridid: null
    name: Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: null
  description: Inflexa is an open-source, agentic orchestration platform for computational
    biology and translational medicine. It is designed to assist researchers in analyzing
    multi-omics, cheminformatics, and imaging data by reading published literature,
    designing multi-step analysis plans, and executing experiments with full reproducibility.
  documentation: []
  download:
  - note: null
    type: Binaries
    url: https://github.com/inflexa-ai/inflexa/releases
    version: null
  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: []
  homepage: https://inflexa.ai
  homepage_status: 0
  language:
  - Python
  - TypeScript
  - Go
  lastUpdate: '2026-07-16T09:46:41.686377Z'
  license: Apache-2.0
  link:
  - note: GitHub repo
    type:
    - Repository
    url: https://github.com/inflexa-ai/inflexa
  - note: Pharmacogenomic Drug Screen in Mouse Cerebrocortical Cultures (Re-analysis
      of GSE110256)
    type:
    - Other
    url: https://public.inflexa.ai/GSE110256/pharmacogenomic-mouse-cerebrocortical-cultures
  - note: Genome-wide Dissection of IL-33 and IL-4Rα Blockade in HDM-driven Airway
      Inflammation (Re-analysis of GSE282861)
    type:
    - Other
    url: https://public.inflexa.ai/GSE282861/il-33-il-4ra-blockade-hdm-airway-inflammation
  - note: How Genetic Ancestry Shapes Breast Cancer Biology (Re-analysis of Roelands
      et al. 2021 (npj Breast Cancer) )
    type:
    - Other
    url: https://public.inflexa.ai/33558495/breast-cancer-african-arab-european-ancestry
  - note: ATG7 Deficiency Reshapes Microglia Biology in Alzheimer’s Disease (Re-analysis
      of GSE286094 / GSE286095)
    type:
    - Other
    url: https://public.inflexa.ai/GSE286094-GSE286095/atg7-deficiency-reshapes-microglia-biology-alzheimers-disease
  - note: Atopic Dermatitis Transcriptome Under Dupilumab and Cyclosporine (Re-analysis
      of GSE157194)
    type:
    - Other
    url: https://public.inflexa.ai/GSE157194/atopic-dermatitis-dupilumab-cyclosporine
  maturity: null
  name: Inflexa
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: radu.tanasa
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Cheminformatics
    uri: http://edamontology.org/topic_2258
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Natural language processing
    uri: http://edamontology.org/topic_0218
  - term: Omics
    uri: http://edamontology.org/topic_3391
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-07-16T05:56:10.804636Z'
  biotoolsCURIE: biotools:reactr
  biotoolsID: reactr
  collectionID:
  - Bioconda
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Reactr is an modularized, Snakemake workflow for automated, species-agnostic
    characterization of gene families from sequence to experimental design. Given
    a query protein sequence and NCBI taxonomy IDs (or RefSeq assembly accessions),
    reactr retrieves genomic data and runs comprehensive analysis across 4 integrated
    tiers: (1) evolutionary analysis, including homolog detection, domain-based clustering,
    multiple sequence alignment, and phylogenetic inference; (2) synteny and selection
    analysis, detecting collinear blocks and calculating Ka/Ks ratios; (3) structural
    and regulatory characterization, including motif discovery, chromosomal mapping,
    biochemical property prediction, subcellular localization prediction, and promoter
    analysis; and (4) experimental design tools, generating PCR primers and scored
    CRISPR gRNAs for lab validation. Reactr bridges computational prediction and experimental
    validation, thus enabling rapid transition from genomic discovery to functional
    studies.'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: '`snakemake -s LoadDatasets.smk --cores 8`'
    input: []
    note: Loads genomic data and prepares it for query analysis
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output: []
  - cmd: '`snakemake -s MainPipeline.smk`'
    input: []
    note: Runs query analysis
    operation:
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    - term: Comparison
      uri: http://edamontology.org/operation_2424
    - term: Generation
      uri: http://edamontology.org/operation_3429
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    - term: Alignment
      uri: http://edamontology.org/operation_2928
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    - term: Data analysis
      uri: http://edamontology.org/operation_2945
    - term: Protein property calculation
      uri: http://edamontology.org/operation_0250
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Validation
      uri: http://edamontology.org/operation_2428
    - term: Classification
      uri: http://edamontology.org/operation_2990
    output: []
  homepage: https://zenodo.org/records/21125109
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-07-16T06:16:23.845202Z'
  license: MIT
  link: []
  maturity: null
  name: REACTR
  operatingSystem:
  - Mac
  otherID: []
  owner: anteel
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - '3'
- accessibility: Open access (with restrictions)
  additionDate: '2026-06-17T13:48:11.660514Z'
  biotoolsCURIE: biotools:dante-tr
  biotoolsID: dante-tr
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: jaroslav.budis@geneton.sk
    fundrefid: null
    gridid: null
    name: Jaroslav Budiš
    note: null
    orcidid: https://orcid.org/0000-0002-8667-6655
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    url: null
  - email: andrej.balaz@geneton.sk
    fundrefid: null
    gridid: null
    name: Andrej Baláž
    note: null
    orcidid: https://orcid.org/0000-0002-3113-3389
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: marcel.kucharik@geneton.sk
    fundrefid: null
    gridid: null
    name: Marcel Kucharik
    note: null
    orcidid: https://orcid.org/0000-0002-5373-8282
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  - email: ingrid.lojova@savba.sk
    fundrefid: null
    gridid: null
    name: Ingrid Lojová
    note: null
    orcidid: https://orcid.org/0000-0001-7659-0850
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: jan.radvanszky@savba.sk
    fundrefid: null
    gridid: null
    name: Ján Radvánszky
    note: null
    orcidid: https://orcid.org/0000-0001-9657-1198
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  description: 'DANTE is a software tool for genotyping and characterizing tandem
    repeats (TRs) from both second- and third-generation sequencing data. It supports
    the analysis of short-read massively parallel sequencing (sr-MPS) and long-read
    massively parallel sequencing (lr-MPS), enabling accurate repeat characterization
    across a wide range of loci.


    A key feature of DANTE is its ability to determine genotypes at nucleotide resolution,
    including the characterization and phasing of complex repeat motifs. For sr-MPS
    data, the tool determines allele size and sequence composition of alleles for
    which spanning reads are generated. In addition, it identifies alleles that exceed
    the sequencing read length by estimating their presence from partial read evidence
    and supports the visualisation of the sequence composition of partial reads. For
    lr-MPS data, where complete repeat regions are typically sequenced, DANTE determines
    the allele size and sequence composition of identified alleles.'
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/dante-tr/dante-tr/blob/main/README.md
  download:
  - note: null
    type: Source code
    url: https://github.com/dante-tr/dante-tr
    version: null
  editPermission:
    authors: []
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
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      abstract: We present SequenceMatrix, software that is designed to facilitate
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        Linux operating systems. The software is freely available from © The Willi
        Hennig Society 2010. © The Willi Hennig Society 2010.
      authors:
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      - name: Lohman D.J.
      - name: Meier R.
      citationCount: 1348
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      journal: Cladistics
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  description: 'Regional Association of Methylome variability with the Exposome and
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next: ?page=2
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