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BPCells

BPCells is a package for high performance single cell analysis on RNA-seq and ATAC-seq datasets. It can analyze a 1.3M cell dataset with 2GB of RAM in around 10 minutes (benchmarks). This makes analysis of million-cell datasets practical on a laptop.

BPCells provides:

  • Efficient storage of single cell datasets via bitpacking compression
  • Fast, disk-backed RNA-seq and ATAC-seq data processing powered by C++
  • Downstream analysis such as marker genes, and clustering
  • Interoperability with AnnData, 10x datasets, R sparse matrices, and GRanges

Additionally, BPCells exposes its optimized data processing infrastructure for use in scaling 3rd party single cell tools (e.g. Seurat)

Learn more

Installation

BPCells is easiest to install directly from github:

remotes::install_github("bnprks/BPCells/r")

Before installing, you must have the HDF5 library installed and accessible on your system. HDF5 can be installed from your choice of package manager.

You will also need a C/C++ compiler either gcc >=8.0 (>=9.1 recommended), or clang >= 7.0 (>= 9.0 recommended). This corresponds to versions from late-2018 and newer. Older versions may work in some cases so long as they have basic C++17 support, but they are not officially supported.

Linux

Obtaining the HDF5 dependency is usually pretty straightforward on Linux - apt: sudo apt-get install libhdf5-dev - yum: sudo yum install hdf5-devel - conda: conda install -c anaconda hdf5 - Note: Linux users should prefer their distro’s package manager (e.g. apt or yum) when possible, as it appears to give a slightly more reliable installation experience.

Windows

Compiling R packages from source on Windows requires installing R tools for Windows. See Issue #9 for more discussion.

MacOS

For MacOS, installing HDF5 through homebrew seems to be most reliable: brew install hdf5.

Mac-specific troubleshooting:

  • Macs with ARM CPUs: a common error is to have an ARM-based HDF5 install but an x86-based R install. This will cause errors when BPCells tries to access HDF5 during installation.
    • Check your R installation by running sessionInfo(), and seeing if it lists ARM or x86 under “Platform”.
    • The easiest option is to use ARM R because homebrew will default to an ARM hdf5 installation
    • It is possible (though tricky) to install an x86 copy of homebrew in order to access an x86 version of hdf5
  • Older Macs (10.14 Mojave or older): The default compiler on old Macs does not support needed C++17 filesystem features. See issue #3 for tips getting a newer compiler set up via homebrew.

General Installation troubleshooting

BPCells tries to print informative error messages during compilation to help diagnose the problem. For a more verbose set of information, run Sys.setenv(BPCELLS_DEBUG_INSTALL="true") prior to remotes::install_github("bnprks/BPCells/r"). If you still can’t solve the issue with that additional information, feel free to file a Github issue, being sure to use a collapsible section for the verbose installation log.

Contributing

BPCells is an open source project, and we welcome quality contributions. If you are interested in contributing and have experience with C++, along with Python or R, feel free to reach out with ideas you would like to implement yourself. I’m happy to provide pointers for how to get started, my time permitting.

If you are unfamiliar with C++ it will be difficult for you to contribute code, but detailed bug reports with reproducible examples are still a useful way to help out. Github issues are the best forum for this.

If you maintain a single cell analysis package and want to use BPCells to improve your scalability, I’m happy to provide advice. We have had a couple of labs try this so far, with promising success. Email is the best way to get in touch for this (look in the DESCRIPTION file on github for contact info). Python developers welcome, though the full python package will likely not be available until after summer 2023.