R toolkit for single cell genomics

Machine Learning in R

Convert statistical analysis objects from R into tidy format

📊 A universal enrichment tool for interpreting omics data

R Interface to Keras

Inferring CNV from Single-Cell RNA-Seq

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

A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution methods

R package for performing 2-sample MR using MR-Base database

A repository of my Coursera latex code and notes

Analysis Pipeline for Single Cell ATAC-seq

Useful functions to make your scRNA-seq plot more cool!

Multi-subject Single Cell Deconvolution

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

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

Gene set variation analysis

Automated, probabilistic assignment of cell types in scRNA-seq data

Support files for a data visualization course and book

Spatial Transcriptomics Capture Location Deconvolution

Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data

The github repository for mathematical biostatistics bootcamp 2

Gene set scoring for single-cell data

PHESANT - PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank

An implement R package to visualize GSEA results

Multi-Omics integration and VIsualization in Cancer Subtyping

AUCell: score single cells with gene regulatory networks

SingleCellNet: classify single cells across species and platforms