Comprehensive analysis pipeline for ATAC-seq data including QC, alignment, peak calling, annotation, motif analysis, and gene enrichment. Delivers key insights and reproducible results for chromatin accessibility studies.
This repository to dedicated to notes, scripts, and general miscellaneous items I take during my PhD thesis in computational genetics, gene regulatory evolution
This is an automated workflow pipeline for analyzing bulk ATAC-seq data, implemented primarily in bash scripts, and wrapped in a NextFlow workflow.
Instructions on how to perform chromatin accessibility data pre-processing and analyses (focusing on bulk ATAC-seq)
ATAC-Seq analysis. (Ali T. Abdallah)
Workflow Template
A comprehensive source for Stathopoulos lab code generated and used in data analysis.
Snakemake pipeline for analysis and normalization of ATAC-seq data starting from fastq.gz files.
Pipeline for processing epigenomic NGS data.
CCBR pipeline for preliminary QC and peak calling from ATACseq datasets 🌲
Sanger Cellular Genetics single-cell ATAC-seq pipeline.
Pipeline codes for analyzing various genomics datasets based on MACS3
All-in-one analysis pipeline
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
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