# betterChromVAR <!-- badges: start --> <!-- [](https://github.com/plger/betterChromVAR/issues) [](https://github.com/plger/betterChromVAR/pulls) [](https://bioconductor.org/checkResults/release/bioc-LATEST/betterChromVAR) [](https://support.bioconductor.org/tag/betterChromVAR) [](https://bioconductor.org/packages/release/bioc/html/betterChromVAR.html#since) [](https://bioconductor.org/packages/release/bioc/html/betterChromVAR.html#since) --> [](https://bioconductor.org/checkResults/devel/bioc-LATEST/betterChromVAR) [](http://bioconductor.org/checkResults/devel/bioc-LATEST/betterChromVAR/) [](https://github.com/plger/betterChromVAR/actions/workflows/check-bioc.yml) [](https://app.codecov.io/gh/plger/betterChromVAR) <!-- badges: end --> `betterChromVAR` is a much faster, deterministic implementation of the popular [chromVAR](https://greenleaflab.github.io/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](https://greenleaflab.github.io/chromVAR/) before using betterChromVAR. ## Installation instructions You can install it from Bioconductor using: ```r BiocManager::install("betterChromVAR") ``` or install the development version from github with: ```r BiocManager::install("plger/betterChromVAR") ```