Guigo Lab

All

54 repositories

genome-annotation-tracker
Public
Tracks Eukaryotic genome annotations (gff) from NCBI and Ensembl
genome gff3 annotations genes genomes gff3-files
Shell
•0•0•0•0•Updated Jul 14, 2025Jul 14, 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 Jul 13, 2025Jul 13, 2025
bioproject-genome-tracker
Public
Retrieve all the INSDC public assemblies under a BioProject umbrella
MIT License
•2•0•0•0•Updated Jul 13, 2025Jul 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 Jul 8, 2025Jul 8, 2025
biogenome-portal
Public
Biogenome data portal
taxonomy tree-structure biodiversity
Vue
•
MIT License
•2•6•0•0•Updated Jul 3, 2025Jul 3, 2025
scientry
Public
Vue
•0•0•0•0•Updated Jun 25, 2025Jun 25, 2025
cls3-final-files-description
Public
0•0•0•0•Updated Jun 3, 2025Jun 3, 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
•0•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
LyRic
Public
Long RNA-seq analysis workflow
bioinformatics rnaseq transcriptomics gencode cls snakemake-workflow pacbio-iso-seq
Python
•
GNU General Public License v3.0
•4•18•7•1•Updated Dec 5, 2024Dec 5, 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
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-seq pipeline nextflow ngs crg guigo
Nextflow
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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
•44•130•9•0•Updated Jun 28, 2024Jun 28, 2024
tmerge
Public
Merge transcriptome read-to-genome alignments into non-redundant transcript models
bioinformatics genomics genome sequencing merge long-read transcriptome transcriptomics
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-annotation gene-prediction nextflow-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•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
•198•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•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
•2.4k•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
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