biobenkj/compartmentalizer: Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

Compartmap performs direct inference of higher-order chromatin from scRNA-seq, scATAC-seq, and methylation arrays. This package implements a James-Stein estimator for computing single-cell level higher-order chromatin domains. Further, we utilize random matrix theory as a method to de-noise correlation matrices to achieve a similar "plaid-like" patterning as observed in Hi-C and scHi-C data.

Getting started

Package details

Bioconductor views ATACSeq Epigenetics Genetics RNASeq SingleCell
LicenseGPL-3 + file LICENSE
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
biobenkj/compartmentalizer documentation built on Oct. 13, 2023, 5:26 p.m.