Data from Lewis, Barnes, Blighe et al., Cell Rep. 2019 Aug 27; 28(9): 2455–2470.e5.

R package to visualize gene expression data based on weighted kernel density estimation

The integration of single cell rank-based gene set enrichment analysis

Single-cell RNA-seq Gene Expression Recovery

Count HLA alleles in single-cell RNA-seq data

Benchmarking analysis of data integration tools

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity

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

Learning Single-Cell Perturbation Responses using Neural Optimal Transport

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

Single cell trajectory detection

ENCODE ATAC-seq pipeline

NicheNet: predict active ligand-target links between interacting cells

Single-cell analysis in Python. Scales to >1M cells.

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

Studio Ghibli colour palettes

A Wes Anderson color palette for R

R toolkit for single cell genomics

CellRank: dynamics from multi-view single-cell data

RNA Velocity generalized through dynamical modeling