R toolkit for single cell genomics

Make Complex Heatmaps

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

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

NicheNet: predict active ligand-target links between interacting cells

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

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

radar charts with ggplot2

Draw heatmap simply using a tidy data frame

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.

RNA velocity estimation in R

Clone of the Bioconductor repository for the SingleR package.

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕

LIANA: a LIgand-receptor ANalysis frAmework

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".

R client for the OmniPath web service

Inference of cell-cell communication from single-cell RNAseq data

an integrative analysis tool for analysing large-scale single cell RNA-sequencing data

FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis

Unsupervised Inference of Developmental Directions for Single Cells

SLICER algorithm for inferring cell trajectories. See details in Welch et al., Genome Biology 2016: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0975-3

Trajectory Inference with growing neural Gas

Brain and Organoid Manifold Alignment