Installation
Basic installation
Python 3.7 (or later) is required. Consider using virtual environments with Miniconda or Anaconda.
To install, run
pip install commot
Alternatively, you can install the latest version from GitHub
git clone https://github.com/zcang/COMMOT.git
cd COMMOT
pip install .
Optional dependency
One of the downstream analysis function commot.tl.communication_deg_detection()
relies on tradeSeq [1] to find signaling DE genes.
To use this function, tradeSeq and some extra python packages need to be installed.
To install commot with extra packages, run
pip install commot[tradeSeq]
Currently, the R-python interface was tested to only work with R-3.6.3 and tradeSeq-1.0.1. Consider the following approach to install R-3.6.3 together with other R versions, for example, on Ubuntu 20.04, run
export R_VERSION=3.6.3
curl -O https://cdn.rstudio.com/r/ubuntu-2004/pkgs/r-${R_VERSION}_1_amd64.deb
sudo gdebi r-${R_VERSION}_1_amd64.deb
sudo ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R
sudo ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript
To switch between R versions, export R_VERSION
to the desired version, remove the symbolic links /usr/local/bin/R
and /usr/local/bin/Rscript
, and run the last two lines again. Once R-3.6.3 is installed, install tradeSeq-1.0.1 by running
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tradeSeq")
We are working on an easier solution of this.
Installation on Windows
rvlib
rvlib
may need to be installed prior. Install it by
conda install -c conda-forge rvlib
pygeos
For Python 3.8+, pygeos
may need to be uninstalled after installing commot
due to incompatibilities with Shapely
rasterio
For Python 3.7, rasterio
may require installation using the appropriate whl files. See this discussion for installation instructions.
References
[1] Van den Berge, Koen, et al. “Trajectory-based differential expression analysis for single-cell sequencing data.” Nature communications 11.1 (2020): 1-13.