Inferring CNV from Single-Cell RNA-Seq

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

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

Fast Gene Set Enrichment Analysis

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

Community-provided extensions to Seurat

Interpretation of cell states using reference single-cell maps

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

LIANA: a LIgand-receptor ANalysis frAmework

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.

Snakemake workflow to benchmark scRNA-seq data simulators