A collection of Galaxy-related training material

Multi-omics analysis protocols by Lyu.

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

MAnorm2 for Normalizing and Comparing ChIP-seq Samples

Summer school course materials collection

ReMapEnrich is a R-software package to identify significantly enriched regions from ReMap catalogues or user defined catalogues. ReMapEnrich provide functions to import any in-house catalogue, automate and plot the enrichment analysis for genomic regions.

Supports de cours de l'Ecole de Bioinformatique Aviesan - IFB - Inserm "Initiation au traitement des données de génomique obtenues par séquençage à haut débit"

DEbPeak - Analyze and integrate multi-omics to unravel the regulation of gene expression.

Computational biology/bioinformatics workflows, codes, and concept notes on NGS data

target: An R Package to Predict Combined Function of Transcription Factors

An R package designed to integrate and visualize various levels of epigenomic information, including but not limited to: ChIP, Histone, ATAC, and RNA sequencing. epiRomics is also designed to identify enhancer and enhanceosome regions from these data.

Study gene regulatory network with a combination of ChIP-seq, RNA-seq, and comparative genomics

All code generated for Loupe et al. 2023

ComplexHeatmap introduction

Repository that contains the analysis from Li et al. Cell Regeneration, 2022.

The repository stores files that are used to determine homology between Mus musculus and Danio rerio genomes by analyzing synteny blocks.

Programming in practice based on RNA-seq, scRNA-seq, ATAC-seq, scATAC-seq or ChIP-seq.

Analysis of the phylogeny and domains of OLIG2, as well as its expression in cerebral cells using t-SNE. And a chip-seq analysis to further investigate OLIG2 function.

The documented analysis of the results reported in Akol et al., 2023 as R markdowns, Galaxy histories and jupyter logs..