Gene set variation analysis for microarray and RNA-seq data

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

Docker CE

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

Uniform Manifold Approximation and Projection

Code to build the ensembl and ensembl genomes marts

R package for integrating and analyzing multiple single-cell datasets

Google AI Research

Personal website of Yihui Xie

R toolkit for single cell genomics

Comparison of methods for trajectory inference on single-cell data 🥇

R/broman: A package with Karl Broman's personal R code

Survival Analysis and Visualization

Genome Annotation Library - A perl toolkit for working with SO compliant genome annotations

Create Blogs and Websites with R Markdown

Clustering on Network of Samples

R Markdown: The Definitive Guide (published by Chapman & Hall/CRC in July 2018)

List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

R for data science: a book