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. See the
package documentation
and the related preprint.
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")