A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.
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Updated
Jun 6, 2024 - Python
A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.
CWL based Bioinformatics Workflows
An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.
An R shiny web server for linking of ATAC-seq to gene expression data
Snakemake pipeline for analysis and normalization of ATAC-seq data starting from fastq.gz files.
A Snakemake workflow for performing and visualizing differential expression analyses (DEA) on NGS data powered by the R package limma.
Single cell ATAC and RNA seq data analysis
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
A differential and enrichment analyses pipeline for bulk ATAC-seq (and RNA-seq)
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.
WDL workflow language program, developed for singlecell rna sequencing data analysis, maintained by @sunhao(OOAAHH)
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
nextflow ATACseq pipeline for GG02
An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
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.
MACS -- Model-based Analysis of ChIP-Seq
Robust Open Chromatin Detection via Convex Optimization: Multisample Consensus Peak Calling
🎯 ChIP peak Annotation, Comparison and Visualization
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