Cell Layers: Uncovering clustering structure in unsupervised single-cell transcriptomic analysis

Cell Layers is an interactive Sankey tool for the quantitative investigation of gene expression, coexpression, biological processes, and cluster integrity across clustering resolutions.

For more information, please visit our Read the Docs.

Installation

The CellLayers Python module can be installed via pip. Please note, the Python module requires the cluster metric and enrichment data to be generated independently or via our R library SetupCellLayers.

$ pip install CellLayers==0.2.1

The SetupCellLayers R library can be installed via devtools.

> library(devtools)
> options(timeout=9999999)
> devtools::install_github("apblair/CellLayers/SetupCellLayers")
> library(SetupCellLayers)

Both CellLayers and SetupCellLayers are fully containerized via Docker and Singularity, which are extended from the jupyter/datascience-notebook image. Please run the command below to start jupyter lab and then navigate to http://localhost:10000:

$ docker pull apblair/cell-layers:v0.2
$ docker run -it --rm -p 10000:8888 -v "${PWD}":/home/jovyan/work apblair/cell-layers:v0.2

Please note, if you are using an M1 Mac you might need to enable the "Big Sur virtualization.framework" under the "Experimental Features" in your Docker Desktop.

To run the singularity container on a HPC, like UCSF's Wynton HPC please run the commands below to start jupyter lab and then navigate to http://localhost:9595:

$ singularity pull --arch amd64 library://apblair/single-cell-tools/cell-layers:v0-2
$ singularity exec cell-layers_v0-2.sif start.sh jupyter lab --port=9595

Tutorial

Please see the notebooks folder for a tutorial on how to reproduce Fig.1 using SetupCellLayers and CellLayers.

Reference

Cell Layers: Uncovering clustering structure in unsupervised single-cell transcriptomic analysis Andrew P. Blair, Robert K. Hu, Elie N. Farah, Neil C. Chi, Katherine S. Pollard, Pawel F. Przytycki*, Irfan S. Kathiriya*, Benoit G. Bruneau* bioRxiv 2020.11.29.400614; doi: https://doi.org/10.1101/2020.11.29.400614

Accepted: Bioinformatics Advances

Please consider citing Cell Layers if you used the application or code snippets for your project.

Authors Contributions

A.P.B. conceived and initiated the project. R.H assisted in analysis. B.G.B., P.F.P, and I.S.K. supervised A.P.B. I.S.K. provided datasets. K.S.P. advised. All authors commented on the manuscript.

Acknowledgments

We thank the Cytoscape and scNetViz developers Alex Pico and Scooter Morris for their input on Plotly, Dan Carlin for his input on multi-resolution analysis, members of the CIRM Heart of Cells group, Gladstone Bioinformatics core, and Bruneau lab for discussions and comments.

Funding

This work has been supported by the California Institute of Regenerative Medicine (RB4-05901 to B.G.B), Additional Ventures (to B.G.B and K.S.P), National Institutes of Health (5U01HL157989-02 to B.G.B and K.S.P), UCSF Department of Anesthesia and Perioperative Care (to I.S.K.), and the Younger family fund (to B.G.B).