R toolkit for single cell genomics

A Grammar of Animated Graphics

RStudio add-in to make plots interactively with ggplot2

Make Complex Heatmaps

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file form…

Collection of various algorithms implemented in R.

A Framework for Building Robust Shiny Apps

Organize your project into a research website

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

Inferring CNV from Single-Cell RNA-Seq

NicheNet: predict active ligand-target links between interacting cells

R package for detecting doublets in single-cell RNA sequencing data

A package to help convert different single-cell data formats to each other

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

R package for integrating and analyzing multiple single-cell datasets

R toolkit for the analysis of single-cell chromatin data

Combination matrix axis for 'ggplot2' to create 'UpSet' plots

Table of software for the analysis of single-cell RNA-seq data.

Analysis Pipeline for Single Cell ATAC-seq

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

Statistical Analysis of Network Data with R, 2nd Edition

Multi-subject Single Cell Deconvolution

Multi-Omics Factor Analysis

R package for modeling single cell UMI expression data using regularized negative binomial regression

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Publication-quality sequence logos in R

make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.

RNA velocity estimation in R