All RNA-seq data are available from the Gene Expression Omnibus database (accession numbers GSE110949, GSE118056) or EBI Single Cell Expression Atlas (accession number E-GEOD-86618).
The datasets must be downloaded as saved in the directory data in H5 format (from Scanpy).
The output directory contains: -the Reaction Activity Scores values for all the datasets and the denoisers -the metabolic fluxes computering using Flux Balance Analysis (FBA)
To run the codes you need to install:
- Scanpy
- Cobrapy
- MAGIC denoiser
- ENHANCE scripts
- SAVER (R-based)
We provided an R script to run the SAVER denoiser.
The notebook "workflow" can be used to compute both RAS from transcriptional data and single cell Flux Balance Analysis