Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
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Updated
Jul 15, 2024 - Python
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
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.
A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
Instructions on how to perform chromatin accessibility data pre-processing and analyses (focusing on bulk ATAC-seq)
Snakemake pipeline for analysis and normalization of ATAC-seq data starting from fastq.gz files.
A toolkit for working with ATAC-seq data.
Robust Open Chromatin Detection via Convex Optimization: Multisample Consensus Peak Calling
Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.
ChIP-Seq processing pipeline on snakemake
A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.
Variational Auto Encoders for learning binding signatures of transcription factors
Multiome (RNA+ATAC from same cell) data generated by Qinyu Zhang in David Bryder's lab. Paper here: https://doi.org/10.7554/eLife.91826.2
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
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