R toolkit for single cell genomics

Tools to make an R developer's life easier

Additional themes, scales, and geoms for ggplot2

Paginate the HTML Output of R Markdown with CSS for Print

Organize your project into a research website

A list of scRNA-seq analysis tools

Fast, sensitive and accurate integration of single-cell data with Harmony

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

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

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

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

R package for integrating and analyzing multiple single-cell datasets

A toolkit for single-cell immune profiling

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

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

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

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

Generate high quality, publication ready visualizations for single cell transcriptomics data.

Shiny Interactive Web Apps for Single-Cell Data

Easy single cell analysis platform for enrichment

Interactively analyze single cell genomic data

Collection of public scRNA-Seq datasets used by our group

Gene set scoring for single-cell data

Seurat meets tidyverse. The best of both worlds.

Quantifying metabolism activity at the single-cell resolution

marker-based purification of cell types from single-cell RNA-seq datasets

BANKSY: spatial clustering