BPCells#
The BPCells python bindings are still experimental and the API is subject to change.
The existing functionality is mainly focused on allowing read/write access to BPCells file formats for integer matrices and scATAC fragments. Future updates will add the data-processing functions present in the R interface (e.g. streaming normalization, PCA, or ATAC-seq peak/tile matrix creation). This will provide Python access to the shared C++ core code.
Notably, plotting functionality is not currently planned for implementation, as it is written primarily in R and relies on R plotting libraries not present in Python. There are a few other helper functions in R BPCells that are implemented in pure R and thus are unlikely to be added in Python in the near future. If any of this functionality is of interest to you, we would welcome your contributions – you would be able to write most of the code in pure Python. Reach out via github/email if interested.
Installation#
BPCells can be directly installed via pip:
python -m pip install bpcells