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    55 repositories

    • genome-annotation-tracker

      Public
      Tracks Eukaryotic genome annotations (gff) from NCBI and Ensembl
      genomegff3annotationsgenesgenomesgff3-files
      Python
      •0•0•0•0•Updated Nov 2, 2025Nov 2, 2025

    • bioproject-genome-tracker

      Public
      Retrieve all the INSDC public assemblies under a BioProject umbrella
      MIT License
      •2•0•0•0•Updated Nov 2, 2025Nov 2, 2025

    • ebp-assemblies-tracker

      Public
      Tracks the assemblies under the Earth Biogenome Project (PRJNA533106) in NCBI Datasets
      Shell
      •
      MIT License
      •0•1•0•0•Updated Nov 1, 2025Nov 1, 2025

    • jbrowse-plugin-annotrieve

      Public
      Plugin to load annotation tracks from the Annotrieve API
      TypeScript
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 27, 2025Oct 27, 2025

    • LyRic

      Public
      Long RNA-seq analysis workflow
      bioinformaticsrnaseqtranscriptomicsgencodeclssnakemake-workflowpacbio-iso-seq
      Python
      •
      GNU General Public License v3.0
      •5•20•7•0•Updated Oct 13, 2025Oct 13, 2025

    • CLS3_GENCODE

      Public
      Charting thousands of novel gene loci in the human and mouse genomes through targeted full-length long-read RNA sequencing
      R
      •2•3•0•0•Updated Sep 8, 2025Sep 8, 2025

    • biogenome-portal

      Public template
      Biogenome data portal
      taxonomytree-structurebiodiversity
      Vue
      •
      MIT License
      •2•6•0•0•Updated Sep 4, 2025Sep 4, 2025

    • cls3-final-files-description

      Public
      0•0•0•0•Updated Jul 30, 2025Jul 30, 2025

    • scientry

      Public template
      Vue
      •0•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • biodiversity-genomics-scripts

      Public
      A bunch of scripts to retrieve biodiversity genomics data (NCBI and Ensembl)
      Python
      •0•0•0•0•Updated Mar 25, 2025Mar 25, 2025

    • gencode-cls-master-table

      Public
      Results of the GENCODE pipeline to produce a collection of full length high quality transcripts
      0•2•0•0•Updated Mar 10, 2025Mar 10, 2025

    • EPIraction

      Public
      Perl
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Feb 27, 2025Feb 27, 2025

    • jbrowse-plugin-refget-api

      Public
      A JBrowse 2 plugin to access servers implementing the refget API of GA4GH
      TypeScript
      •
      Apache License 2.0
      •0•3•0•0•Updated Jan 16, 2025Jan 16, 2025

    • gff2ps

      Public
      A program for visualizing annotations of genomic sequences
      Vue
      •0•1•0•0•Updated Oct 25, 2024Oct 25, 2024

    • rnaseq-course

      Public
      Data for the RNAseq course at CRG
      1•0•0•1•Updated Oct 24, 2024Oct 24, 2024

    • rnaget-beacon-demo

      Public
      Demo of the RNAget extension for BeaconV2
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • grape-nf

      Public
      An automated RNA-seq pipeline using Nextflow
      rna-seqpipelinenextflowngscrgguigo
      Nextflow
      •
      GNU General Public License v3.0
      •10•37•31•1•Updated Sep 21, 2024Sep 21, 2024

    • beacon-v2

      Public
      Unified repository for the GA4GH Beacon v2 API standard
      Creative Commons Zero v1.0 Universal
      •22•0•0•1•Updated Jul 17, 2024Jul 17, 2024

    • ggsashimi

      Public
      Command-line tool for the visualization of splicing events across multiple samples
      Python
      •
      MIT License
      •45•131•9•1•Updated Jun 28, 2024Jun 28, 2024

    • tmerge

      Public
      Merge transcriptome read-to-genome alignments into non-redundant transcript models
      bioinformaticsgenomicsgenomesequencingmergelong-readtranscriptometranscriptomics
      Perl
      •
      MIT License
      •3•18•1•0•Updated May 23, 2024May 23, 2024

    • file-stream-server

      Public
      A little flask API to stream download files given a folder path
      0•0•0•0•Updated May 14, 2024May 14, 2024

    • selenoprofiles-nf

      Public
      selenoprofiles4 nextflow pipeline
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 7, 2024Jan 7, 2024

    • geneidx

      Public
      Nextflow pipeline for genome annotation of protein-coding genes
      genome-annotationgene-predictionnextflow-pipeline
      Nextflow
      •
      GNU General Public License v3.0
      •2•16•2•0•Updated Dec 21, 2023Dec 21, 2023

    • geneid-parameter-files

      Public
      Repo with all the geneid parameter files
      Python
      •0•0•0•0•Updated Nov 28, 2023Nov 28, 2023

    • geneid-param-resolver

      Public
      Given a taxID returns the closest parameter file contained in the repository: https://github.com/guigolab/geneid-parameter-files
      0•0•0•0•Updated Nov 9, 2023Nov 9, 2023

    • sqtlseeker2-nf

      Public
      An automated sQTL mapping pipeline using Nextflow
      R
      •
      GNU General Public License v3.0
      •4•7•2•0•Updated Sep 18, 2023Sep 18, 2023

    • hugo-future-imperfect-slim

      Public
      Multilingual Blogging Theme for Hugo | Check the Wiki for Documentation
      JavaScript
      •
      Other
      •197•0•0•0•Updated Sep 5, 2023Sep 5, 2023

    • sQTLseekeR2

      Public
      R package to detect splicing QTLs (sQTLs)
      R
      •
      GNU General Public License v3.0
      •1•13•1•0•Updated Jul 3, 2023Jul 3, 2023

    • spack

      Public
      A flexible package manager that supports multiple versions, configurations, platforms, and compilers.
      Python
      •
      Other
      •2.4k•0•0•0•Updated Jun 30, 2023Jun 30, 2023

    • rnaget-r-client

      Public
      A R package to query the RNAget compliant servers
      R
      •0•0•0•0•Updated Apr 20, 2023Apr 20, 2023