R toolkit for single cell genomics

A Wes Anderson color palette for R

A list of scRNA-seq analysis tools

Inferring CNV from Single-Cell RNA-Seq

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

NicheNet: predict active ligand-target links between interacting cells

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

🌈 Interactive analysis of metagenomics data

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

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

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

Spatial omics analysis toolbox

IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.

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

A collection of scripts and notes related to genomics and bioinformatics

Haplotype-aware CNV analysis from single-cell RNA-seq

R package for analyzing single-cell RNA-seq data

chromatin Variability Across Regions (of the genome!)

Visualizing transcript structure and annotation using ggplot2

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

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

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

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

SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.

Publication Page for MPAL Paper 2019

Pipeline for exploring metebolic heterogeneity at single-cell resolution