Jose Espinosa-Carrasco's repositories
crisprseq
A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
stimulus
Main pipeline here: https://github.com/mathysgrapotte/stimulus
atacseq-workshop-limoges
ATAC-seq tutorial to be used during Limoges Course (November 2022)
bioconda-recipes
Conda recipes for the bioconda channel.
joseespinosa
Bio readme
multi-package-containers
Testing building mulled containers for multi-requirement tools.
multiplesequencealign
Main pipeline here: github.com/nf-core/multiplesequencealign
nf-core-atacseq
Main pipeline here: https://nf-co.re/atacseq
nf-core-chipseq
Main pipeline here:
nf-core-fetchngs
Main pipeline here:
nf-core-hic
Analysis of Chromosome Conformation Capture data (Hi-C)
nf-core-methylseq
Original nf-core pipeline here:
nf-core-modules
Main repository here:
nf-core-nanoseq
Original nf-core pipeline here:
nf-core-proteinfold
Main pipeline here:
nf-core-rnaseq
Main pipeline here:
nf-core-sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
nf-core-smrnaseq
Main pipeline here:
nf-core-tools
Main repository here:
nf-wrap
Nextflow wrapper built around nf-core/modules
reportho
nf-core pipeline for comparative analysis of ortholog predictions
shared_notes
A place to share notes with collaborators
tcoffee
A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
test-datasets
Test data to be used for automated testing with the nf-core pipelines
test_hmmratac
Test hmmratac for nf-core/atacseq
testpipeline
A small example pipeline used to test new nf-core infrastructure and common code.