A curated list of awesome R packages, frameworks and software.

dplyr: A grammar of data manipulation

🎓 A collection of interactive courses for the swirl R package.

Turn your R code into a web API.

Static Code Analysis for R

NicheNet: predict active ligand-target links between interacting cells

Publication-ready volcano plots with enhanced colouring and labeling

Multi-Omics Factor Analysis

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

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

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

Interpretation of cell states using reference single-cell maps

Simple simulation of single-cell RNA sequencing data

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

Haplotype-aware CNV analysis from single-cell RNA-seq

Automated cell type classification

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length …

A R framework for pipeline benchmarking, with application to single-cell RNAseq

R package for bcbio single-cell RNA-seq analysis.