Repositories list

• genome-annotation-tracker

  Public
  Tracks Eukaryotic genome annotations (gff) from NCBI and Ensembl

  genomegff3annotations+ 3genesgenomesgff3-files

  0•0•0•0•Updated Dec 23, 2024Dec 23, 2024

• bioproject-genome-tracker

  Public
  Retrieve all the INSDC public assemblies under a BioProject umbrella

  MIT License

  •2•0•0•0•Updated Dec 22, 2024Dec 22, 2024

• CLS3_GENCODE

  Public
  Charting thousands of novel gene loci in the human and mouse genomes through targeted full-length long-read RNA sequencing

  R

  •1•1•0•0•Updated Dec 16, 2024Dec 16, 2024

• LyRic

  Public
  Long RNA-seq analysis workflow

  bioinformaticsrnaseqtranscriptomics+ 4gencodeclssnakemake-workflowpacbio-iso-seq

  Python

  •

  GNU General Public License v3.0

  •4•14•6•1•Updated Dec 5, 2024Dec 5, 2024

• biogenome-portal

  Public
  Biogenome data portal

  taxonomytree-structurebiodiversity

  Vue

  •

  MIT License

  •2•6•0•0•Updated Nov 29, 2024Nov 29, 2024

• gff2ps

  Public
  A program for visualizing annotations of genomic sequences

  Vue

  •0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

• rnaseq-course

  Public
  Data for the RNAseq course at CRG

  1•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• cls3-final-files-description

  Public
  0•0•0•0•Updated Oct 15, 2024Oct 15, 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-seqpipelinenextflow+ 3ngscrgguigo

  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

  •42•123•14•0•Updated Jun 28, 2024Jun 28, 2024

• 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 Jun 7, 2024Jun 7, 2024

• tmerge

  Public
  Merge transcriptome read-to-genome alignments into non-redundant transcript models

  bioinformaticsgenomicsgenome+ 5sequencingmergelong-readtranscriptometranscriptomics

  Perl

  •

  MIT License

  •3•13•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

  •1•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

• EPIraction

  Public
  Perl

  •0•0•0•0•Updated Nov 7, 2023Nov 7, 2023

• sqtlseeker2-nf

  Public
  An automated sQTL mapping pipeline using Nextflow

  R

  •

  GNU General Public License v3.0

  •4•6•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

  •196•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

  •0•12•1•0•Updated Jul 3, 2023Jul 3, 2023

• spack

  Public
  A flexible package manager that supports multiple versions, configurations, platforms, and compilers.

  Python

  •

  Other

  •2.3k•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

• rnaget-py-client

  Public
  A python client to query the RNAget compliant servers

  Python

  •

  MIT License

  •0•0•1•0•Updated Apr 6, 2023Apr 6, 2023

• rnaget-client

  Public
  Demo client for the GA4GH rnaget API

  rna-seqga4ghlarge-scale-genomics

  Go

  •

  MIT License

  •0•0•0•0•Updated Jan 30, 2023Jan 30, 2023

• geneid

  Public
  Predict genic elements as splice sites, exons or genes, along eukaryotic DNA sequences

  C

  •6•17•2•0•Updated Jan 19, 2023Jan 19, 2023

• git-tech-session

  Public
  Lab tech session on Git, GiHub and GitHub Actions

  Python

  •7•0•0•1•Updated Jan 18, 2023Jan 18, 2023

• 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•1•0•Updated Dec 18, 2022Dec 18, 2022