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archr

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

atacseq_pipeline

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.

cellsnake

Cellsnake tool main repo

coolbox

Jupyter notebook based genomic data visualization toolkit.

cooler

A cool place to store your Hi-C

eaglec

A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps

hic_pipeline

An easy-to-use Hi-C data processing software supporting distributed computation.

hichipper

A preprocessing and QC pipeline for HiChIP data

issaac-seq

mcibox

pmcb-tobridge

PMCB-SCB scRNA-seq pipeline

sccare-seq

A single-cell multimodal omics method for simultaneously detecting chromatin architecture and mRNA expression by sequencing (scCARE-seq)

scifirna-seq

scrna-seq_notes

A list of scRNA-seq analysis tools

seqtk

Toolkit for processing sequences in FASTA/Q formats

seurat

R toolkit for single cell genomics

signac

R toolkit for the analysis of single-cell chromatin data

snapatac2

Single-cell epigenomics analysis tools

snaphic

SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data

star

RNA-seq aligner