Projects in Awesome Lists tagged with atac-seq
A curated list of projects in awesome lists tagged with atac-seq .
https://github.com/macs3-project/MACS
MACS -- Model-based Analysis of ChIP-Seq
atac-seq chip-seq dnase-seq macs peak-caller poisson-equation python
Last synced: 19 Apr 2025
https://github.com/maxplanck-ie/snakepipes
Customizable workflows based on snakemake and python for the analysis of NGS data
atac-seq bisulfite-sequencing chip-seq hi-c ngs rna-seq snakemake workflow
Last synced: 07 May 2025
https://github.com/nf-core/atacseq
ATAC-seq peak-calling and QC analysis pipeline
atac-seq chromatin-accessibiity nextflow nf-core pipeline workflow
Last synced: 10 May 2025
https://github.com/pinellolab/scATAC-benchmarking
Benchmarking computational single cell ATAC-seq methods
atac-seq bash benchmark jupyternotebook python r reproducible singlecell
Last synced: 11 May 2025
https://github.com/GreenleafLab/chromVAR
chromatin Variability Across Regions (of the genome!)
atac-seq bioinformatics dnase-seq r
Last synced: 10 May 2025
https://github.com/vanheeringen-lab/seq2science
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.
atac-seq bioinformatics bioinformatics-pipeline chip-seq fastq ngs pipeline reproducible-research rna-seq snakemake sra workflows
Last synced: 19 Dec 2024
https://github.com/LiuLabUB/HMMRATAC
HMMRATAC peak caller for ATAC-seq data
atac-seq machine-learning peak-caller peak-detection sequencing
Last synced: 10 May 2025
https://github.com/crazyhottommy/pyflow-ATACseq
ATAC-seq snakemake pipeline
Last synced: 10 May 2025
https://github.com/crazyhottommy/pyflow-atacseq
ATAC-seq snakemake pipeline
Last synced: 06 May 2025
https://github.com/tobiasrausch/atacseq
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
atac-seq atac-seq-pipeline chromatin next-generation-sequencing nucleosome-positioning peak-detection sequencing
Last synced: 13 Apr 2025
https://github.com/ParkerLab/ataqv
A toolkit for QC and visualization of ATAC-seq results.
atac-seq quality-control software tool visualization
Last synced: 10 May 2025
https://github.com/epigen/atacseq_pipeline
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
atac-seq bash bioinformatics biomedical-data-science ngs pipeline python snakemake workflow
Last synced: 15 Apr 2025
https://github.com/epigen/enrichment_analysis
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
atac-seq bioinformatics biomedical-data-science chip-seq enrichment-analysis gene-set-enrichment gene-sets genomic-regions motif-enrichment-analysis pipeline rna-seq snakemake visualization workflow
Last synced: 15 Apr 2025
https://github.com/ManchesterBioinference/Scasat
Scasat is a single cell ATAC-seq preprocessing and analysis pipeline
atac-seq pipelines single-cell
Last synced: 10 May 2025
https://github.com/epigen/dea_limma
A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.
atac-seq bioinformatics biomedical-data-science chip-seq differential-expression-analysis limma limma-trend limma-voom r rna-seq scrna-seq snakemake statistics visualization volcano-plot workflow
Last synced: 15 Apr 2025
https://github.com/epigen/genome_tracks
A Snakemake workflow and MrBiomics module 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.
atac-seq bioinformatics biomedical-data-science genome-browser genome-track genomic-regions pipeline python rna-seq scrna-seq snakemake visualization workflow
Last synced: 15 Apr 2025
https://github.com/epigen/open_pipelines
Pipelines for NGS data preprocessing by the Bock lab and friends
atac-seq bioinformatics chip-seq looper ngs-pipeline pipeline pypiper rna-seq
Last synced: 15 Apr 2025
https://github.com/epigen/spilterlize_integrate
A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.
atac-seq batch-effect bioinformatics biomedical-data-science chip-seq confounding-effects count-matrix dimensionality-reduction integration ngs normalization pipeline rna-seq snakemake visualization workflow
Last synced: 15 Apr 2025
https://github.com/SUwonglab/scABC
atac-seq single-cell single-cell-atac-seq
Last synced: 10 May 2025
https://github.com/afrendeiro/toolkit
A toolkit for NGS analysis with Python
atac-seq bioinformatics chip-seq looper ngs ngs-analysis project-management pypiper rna-seq
Last synced: 12 Apr 2025
https://github.com/alleninstitute/aifi-swanson-teaseq
Code related to Swanson, et. al. for TEA-seq, ICICLE-seq, and scATAC-seq data processing, analysis, and visualization
atac-seq icicle-seq scatac-seq tea-seq
Last synced: 11 Apr 2025
https://github.com/aryarm/as_analysis
A complete Snakemake pipeline for detecting allele specific expression in RNA-seq
allele-specific-expression atac-seq rna-seq snakemake whole-genome-sequencing
Last synced: 11 Apr 2025
https://github.com/sa-lee/fluentgenomics
plyranges and tximeta case study
atac-seq bioconductor genomics rna-seq workflow
Last synced: 15 Mar 2025
https://github.com/olegs/bioinformatics
Reviews on NGS data analysis methods
atac-seq chip-seq differential-chip-seq
Last synced: 12 Mar 2025
https://github.com/jetbrains-research/sc-atacseq-explorer
Single cell ATAC-Seq preprocessing for single cell explorer
atac-seq explorer pipeline single-cell t-sne
Last synced: 20 Nov 2024
https://github.com/jetbrains-research/chipseq-smk-pipeline
ChIP-Seq processing pipeline on snakemake
atac-seq chip-seq peak-calling pipeline quality-control snakemake visualization
Last synced: 20 Nov 2024
https://github.com/mayurdivate/guavasourcecode
Source code repository for GUAVA (ATAC-seq data analysis tool).
atac-seq bioinformatics guava pipeline tool
Last synced: 16 May 2025
https://github.com/epigen/macrophage-regulation
Integrated time series analysis and high-content CRISPR screening delineates the dynamics of macrophage immune regulation
atac-seq bioinformatics crispr crop-seq epigenomics immunology perturb-seq perturbations rna-seq scrna-seq systems-biology systems-immunology time-series transcriptomics
Last synced: 15 May 2025
https://github.com/biomystery/ataccnv
A tool to call CNV (Copy Number Variation) from bulk ATAC-Seq data
Last synced: 04 Mar 2025
https://github.com/UcarLab/BiFET
A robust statistical test for TF footprint data analyses
atac-seq bioconductor chromatin-accessibiity dnase-seq footprinting r statistical-tests transcription-factor-binding
Last synced: 10 May 2025
https://github.com/zsteve/nf-atac
ATAC-seq pipeline written in Nextflow
atac-seq bioinformatics epigenomics nextflow ngs pipeline
Last synced: 29 Mar 2025
https://github.com/kzkedzierska/atac
ATAC-seq snakemake pipeline
atac-seq snakemake snakemake-workflow
Last synced: 11 Mar 2025
https://github.com/cometsong/atac_seq_nxf
ATAC_Seq Analysis Pipeline using Nextflow framework.
atac-seq bioinformatics nextflow pipeline
Last synced: 14 Mar 2025
https://github.com/lanl/slur-m-py
SLUR(M)-py (pronounced slurpy): A SLURM Powered Pythonic Pipeline for Parallel Processing of 3D (Epi)genomic Profiles
Last synced: 29 Mar 2025
https://github.com/alleninstitute/lowcat
Low coverage accessibility and transcriptomics
Last synced: 29 Mar 2025
https://github.com/jcaperella29/jc_bioinformatics_hub
A personal hub to showcase my bioinformatics applications including RNA-Seq, ATAC-Seq, and miRNA-Seq analysis tools. Powered by simple HTML, CSS, and JavaScript with a biotech-themed design.
atac-seq bioinformatics biotech data-analysis github-pages portal rna-seq webapp
Last synced: 15 May 2025
