Installing pyroe with conda

Alevin-fry is a highly accurate and performant method to process single-cell or single-nuclei RNA-seq data. For downstream processing, its output can be parsed into R with the fishpond::loadFry() function. For analysis using python, the pyroe module is available.

It can be installed either using pip or conda, and the latter will install additional dependencies (e.g. bedtools) and include the load_fry() as well.

To install pyroe with conda, I first followed bioconda’s instructions to add and configure the required channels:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

and then installed pyroe

conda install pyroe

Now I can convert alevin-fry output to one of the following formats: zarr, csvs, h5ad or loom.

pyroe convert --help

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