R package for integrating and analyzing multiple single-cell datasets

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

Multi-Omics Factor Analysis

Analysis Pipeline for Single Cell ATAC-seq

Multi-Omics Factor Analysis

🎯 ChIP peak Annotation, Comparison and Visualization

R package for the joint analysis of multiple single-cell RNA-seq datasets

Automated cell type classification

Publication Page for Satpathy*, Granja* et al 2019

TCGA-Assembler 2

Empirical Bayes binomial estimation

R package to analyze large-scale pharmacogenomic datasets.

R script for the covid balf data analysis

Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)

supporting code for the multinomial single cell RNA-Seq paper

A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications

An unsupervised approach for the integrative analysis of single-cell multi-omics data

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

R code for single-cell analysis of intestinal epithelial cells

R functions to make LDSC annotations

HMM Domain called and additional code used in the Chen et, Nature Genetics, 2021 paper