Illumina BaseSpace ATACseq pipeline.

ATACseq workshop, Jachranka 2017

Mouse / human control of cross-contaminations in single-cell ATAC-seq on Fluidigm C1

Analysis repository for Erythropoiesis ATAC/RNA profiling paper

ComplexHeatmap introduction

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

Code for Karakaslar, Katiyar et al., Aging Cell 2023

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

Multi-omics analysis protocols by Lyu.

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.

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

Our comprehensive database integrates data from scRNA seq and sc-ATAC seq, identifying cis-regulatory elements (CREs) through comparison with ENCODE, Epimap, GWAS Catalog, and other datasets. By connecting transcription factors (TFs), CREs, and target genes, cEpiReg unveils hidden regulatory links crucial for understanding AD pathogenesis.

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