A list of scRNA-seq analysis tools

Inferring CNV from Single-Cell RNA-Seq

R package for integrating and analyzing multiple single-cell datasets

R package implementation of Milo for testing for differential abundance in KNN graphs

A toolkit for single-cell immune profiling

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

Analysis Pipeline for Single Cell ATAC-seq

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

Interactively analyze single cell genomic data

Multi-sample multi-group scRNA-seq analysis tools

Spatial Transcriptomics Capture Location Deconvolution

Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.

Metacell - Single-cell mRNA Analysis

Reproducibility repository accompanying Wilk, Rustagi, Zhao, et al. "A single-cell atlas of the peripheral immune response to severe COVID-19"

writes RMarkdown (.Rmd) files to MDX (.mdx) format. Used for R ➡️ RMarkdown ➡️ Markdown ➡️ MDX ➡️ JS ➡️ Gatsby blog

Package for analysis and experimental design of multiplexed imaging data

Tools and assets for easy gene identifier conversion