Installation

We recommend running deconvATAC within virtual environments, such as Conda, to prevent conflicts.

Create conda environment

conda create -n deconvATAC python=3.9 r-base=4.3.0
conda activate deconvATAC

Installing deconvATAC

First, clone the directory:

git clone https://github.com/theislab/deconvATAC.git

Install the package:

cd deconvATAC
pip install .

If you encounter issues with glibc during the installation you can try to install it using conda:

conda create -n deconvATAC python=3.9 r-base=4.3.0 gcc_linux-64 gxx_linux-64

Installing optional dependencies

deconvATAC is only installed with the packages needed for the simulation, highly variable peak selection, and metrics. For running the deconvolution methods, we recommend to work with a different environment for each method to prevent dependency conflicts, with deconvATAC installed in each. You can install the dependencies needed for the python-based deconvolution methods with:

pip install .[cell2location] # note: for zsh shell, please use brackets: '.[cell2location]'
pip install .[tangram]
pip install .[destvi]

RCTD

For installing RCTD, please use the following

conda install bioconda::r-spacexr

In your R terminal, install

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("S4Vectors")
BiocManager::install("SingleCellExperiment")

SpatialDWLS

For SpatialDWLS, the Giotto package needs to be installed. Please follow the installation guidelines in the Giotto documentation for installation of the package.