betterChromVAR is a much faster, deterministic implementation of the
popular chromVAR (Chromatin
Variation Across Regions) method for computing cell- (or sample-) wise motif
deviations from 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.
We note that only the components of chromVAR used to compute motif deviations were reimplemented here. On a dataset of ~31k cells, ~150k regions, and ~2k motifs, the original chromVAR took 138min to run, the ArchR C++ version 78min, while betterChromVAR ran in ~2min, with outputs correlating to the original by ~0.995.
If unfamiliar with chromVAR, we recommend reading up its documentation before using betterChromVAR.
You can install it from Bioconductor using:
BiocManager::install("betterChromVAR")or install the development version from github with:
BiocManager::install("plger/betterChromVAR")