R toolkit for single cell genomics

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

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

High dimensional weighted gene co-expression network analysis

R toolkit for the analysis of single-cell chromatin data

Multi-Omics Factor Analysis

A toolkit for single-cell immune profiling

Community-provided extensions to Seurat

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

Multi-subject Single Cell Deconvolution

Pretty heatmaps

Tools and methods for analysis of single cell assay data in R

Shiny Interactive Web Apps for Single-Cell Data

Conversion between scRNA-seq objects

adegenet: a R package for the multivariate analysis of genetic markers

MrBiomics: Composable modules and recipes automate bioinformatics for multi-omics analyses

recipes that save time

SingleCellNet: classify single cells across species and platforms

iCellR is an interactive R package designed to facilitate the analysis and visualization of high-throughput single-cell sequencing data. It supports a variety of single-cell technologies, including…

Metacell - Single-cell mRNA Analysis

scPred package for cell type prediction from scRNA-seq data

Coarse-graining of large single-cell RNA-seq data into metacells

An elegant package to visualize gene structures

An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline

InstaPrism is an R package for fast implementation of BayesPrism

ShinyCell2 is a lightweight R package for building interactive, shareable apps to explore single-cell multi-omics, scATAC-seq and spatial transcriptomics data with customizable, publication-ready v…