Side project to find jointly accessible regions in pairs of celltypes
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Updated
Jan 25, 2018 - Shell
Side project to find jointly accessible regions in pairs of celltypes
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
MEGA ATAC-seq Workflow implementation
A Snakemake workflow to split, filter, normalize, integrate and select highly variable features of count matrices resulting from experiments with sequencing readout (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including diagnostic visualizations.
Scripts to run footprinting and motif-flanking accessibility analysis in DNase-seq/ ATAC-seq data
A graphical user interface for distributed data processing of high throughput genomics
Batch annotation and visualization of the peaks identified from ChIP-seq, ChIP-chip, ATAC-seq experiments or any experiments resulted in large number of chromosome ranges
cisVar scripts.
Instructions on how to perform chromatin accessibility data pre-processing and analyses (focusing on bulk ATAC-seq)
Nazzari, et al. (2023) 'Investigation of the effects of phthalates on in vitro thyroid models with RNA-Seq and ATAC-Seq'
Computational biology/bioinformatics workflows, codes, and concept notes on NGS data
nextflow ATACseq pipeline for GG02
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