chromatic is an R package for analyzing chromatin state heterogeneity in high-dimensional epigenomic sequencing assays, such as scATAC-seq. chromatic calculates cell-level chromatin entropy scores based on a cell's usage of different chromatin states (enhancers, promoters, silencers, etc). Chromatin entropy scores can indicate important cell populations and reveal epigenomic remodeling underlying cell state changes across many systems including neurodegeneration, cancer, and development.
chromatic is under active development, and is currently an alpha version. This means that some features of the final package are missing, and current features are subject to change throughout development. The first major release of chromatic will coincide with a forthcoming publication.
# create a new conda environment
conda create -n chromatic -c conda-forge python=3.11 mamba
conda activate chromatic
# install dependencies using mamba
mamba install -c conda-forge -c bioconda \
r-base=4.4 \
r-seurat \
r-signac \
r-devtools \
r-hdf5r \
bioconductor-tfbstools \
bioconductor-rtracklayer \
bioconductor-genomicranges \
bioconductor-motifmatchr \
macs2Now install chromatic within R using devtools.
devtools::install_github('smorabit/chromatic')