betterChromVAR is a much faster, deterministic implementation of the
popular chromVAR (Chromatin
Variation Across Regions) method, used to infer TF activity from (bulk
or single-cell) ATAC-seq data and motif annotations. The functions
additionally have extra options and also include an ATAC-seq normalization
method based on the general chromVAR logic.
On a dataset of ~31k cells, ~150k regions, and ~2k motifs, the original chromVAR took 138min to run, the ArchR version 78min, while betterChromVAR ran in ~2min, with outputs correlating to the original by ~0.995.
You can install it from Bioconductor using:
BiocManager::install("betterChromVAR")or install the development version from github with:
BiocManager::install("plger/betterChromVAR")