This directory contains the code and outputs for runnning gene program inference on the objects contained in the datasets directory. Subdirectories are first broken up by dataset, with each containing the outputs of the 3 inference methods: factor_analysis, cNMF and Topyfic.
The main outputs of inference are again h5mu files mirroring the input format, but with the addition of the inferred gene programs. These files are then used as input to the evaluation and dashboard steps. See the main README.md for more information on the input and output formats for inference.
Currently, the inference method procedure is not completely standardized across each method. You will likely need to dig into the code for each method to get it running on a new dataset. This is a known issue and will be addressed in future releases.