BAQLaVa Manuscript code (additional data and figure generation code)

All final data is provided within the BAQLaVa manuscript supplementary data file, however, a large amount of intermediate files and code are generated to produce the final data and figures. This repository corresponds to all data & code required to move from intermediates to final BAQLaVa data files and figures.

Directory Structure

All code is available in this repo. Many datafiles were much too large to host directly. As such, all data has been packaged corresponding to its respective code subdirectory. Data files should be downloaded from the following locations:

HMP2:

https://huttenhower.sph.harvard.edu/baqlava-manuscript-data/maaslin3.tar.gz

https://huttenhower.sph.harvard.edu/baqlava-manuscript-data/trait_enrichment.tar.gz

Host_prediction:

https://huttenhower.sph.harvard.edu/baqlava-manuscript-data/host_prediction.tar.gz

Validation_and_benchmarking:

https://huttenhower.sph.harvard.edu/baqlava-manuscript-data/baqlava_benchmarking_workflow.tar.gz

https://huttenhower.sph.harvard.edu/baqlava-manuscript-data/baqlava_showcase_workflow.tar.gz

https://huttenhower.sph.harvard.edu/baqlava-manuscript-data/parameter_tuning_workflow.tar.gz