BiPCA is a Python package for processing high-dimensional omics count data, such as scRNAseq, spatial transcriptomics, scATAC-seq, and many others. BiPCA first scales the rows and columns of the data to make the noise approximately homoscedastic (biwhitening step), which reveals the underlying rank of the data (based on MP distribution). Then, BiPCA performs optimal shrinkage of singular values to recover the biological signal (denoising step).
You can install BiPCA using this command:
pip install -e 'git+https://github.com/KlugerLab/bipca.git#egg=bipca&subdirectory=python'
Alternatively, we recommend installing BiPCA with the accompanied bipca-experiment docker environment. This image reproduces the environment we used to make the BiPCA manuscript. The pre-built docker image can be downloaded using
docker pull jyc34/bipca-experiment:lastest
and to run the docker container:
docker run -it --rm -e USER=john -e USERID=$(id -u) --name bipca -p 8080:8080 -p 8029:8787 -v /data/:/data/ docker.io/jyc34/bipca-experiment:lastest /bin/bash
Here, change /data:/data to <your_local_data_directory>:/data. A jupyter-lab will be launched on host port 8080 and a rstudio will be on port 8029. If you would like to link a local bipca installation (for package development, for instance), you can write -v <your_local_bipca_directory:/bipca.
See for detailed descriptions regarding the docker image usage and the information of the corresponding dockerfile.
- Running BiPCA with a built-in dataset: tutorial-0-quick_start.ipynb
- Running BiPCA with unfiltered dataset from scanpy: tutorial-1-pbmc_scrna_scanpy.ipynb
Codes for the generating the figures used in the manuscript are documented as individual functions in figure.py. For example, run the following to reproduce the marker gene figure:
from bipca.experiments.figures import Figure_marker_genes
fig_obj = Figure_marker_genes(base_plot_directory="./result/",output_dir="./data/",formatstr="png")
fig_obj.plot_figure(save=True)
Figure1_Suppfig1.ipynb regenerates Fig1 and Supplemental fig1 used in the manuscript.