giovp / latent_factors_autoimmune

latent_factors_autoimmune

Repository for the manuscript:

Latent factor modelling of scRNA-seq data uncovers novel pathways dysregulated in cell subsets of autoimmune disease patients

Giovanni Palla* and Enrico Ferrero

Autoimmunity Transplantation and Inflammation Bioinformatics, Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4056, Switzerland
*current address:Institute of Computational Biology, HelmholtzZentrum Muenchen, Munich, Germany

In the latentFactors_pipeline folder you can find the Snakemake pipeline to run the analysis. In the latentFactors_scripts folder you can find the scripts as well as conda environments required by the pipeline.

latent_factors_autoimmune's Issues

Availability of data used by code?

Hi! Excellent paper with very thoughtful consideration of how to leverage latent factor analysis to understand how factors map onto biological pathways.

Our lab is very interested in reproducing some of your methodology. The code as given is very helpful in understanding some of the more fine grained details from the manuscript, but at times the R code is harder to interpret because you're reading in RDS serialized data that other people can't see the structure of, making the code significantly harder to read. For example, if I wanted to better understand assignLoadings.R, having the files in RA_pipeline would make life much easier to simply debug through your code to understand the section of the methods that says "each pathway activity was set as the response variable in a regression setting where the cluster labels function as the predictor". I'm guessing you're actually regressing against the median latent factor scores for the cell label (or similar), but having the data structure you're loading in would let me understand your methods far more completely.

Would it be possible to release some of the data that's loaded in by the scripts, at least in cases where the processed data was generated by you, not the primary data you downloaded from other labs (which of course, I'd expect I'd download myself if I want to reproduce that part of the analysis.)

Thanks for your attention.