R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

Methods for decontamination of single cell data

ATAC-seq peak-calling and QC analysis pipeline

Pretty heatmaps

Pipeline for processing inDrops sequencing data

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

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

Community-provided extensions to Seurat

A set of scripts for 3' RNA-seq quantification

Framework for Unified Single-Cell Analysis (FUSCA) is a software package for single-cell data analysis developed in R. At the moment, it contains two modules: 1) CellRouter, for reconstruction of c…

R client for the OmniPath web service

Make Complex Heatmaps