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neurorestore / DE-analysis

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Lack of files #1

Open vdsukhov opened 2 years ago

vdsukhov commented 2 years ago

Hello! I noticed that some scripts refer to files that are not included in the repository. Example: file DE-analysis/R/run_bulk_DE/outer-run-DE.R has lines:

source("R/functions/submit_job.R")
source("R/functions/detect_system.R")

Could you add this files to repository, please?

skinnider commented 2 years ago

Hi @vdsukhov, these are just functions used to run the jobs on the HPC clusters that we used in this work. They are not necessary to reproduce the results and will almost certainly not work for you on your own HPC configuration.

vdsukhov commented 2 years ago

@skinnider thanks. So, basically I just need to call run_DE method from Libra package with data from grid0 (variable from DE-analysis/R/run_bulk_DE/outer-run-DE.R)?

skinnider commented 2 years ago

Yes, that's what you would need to do if you were trying to reproduce our analysis. Are you trying to apply Libra to your own data? You will find a clearer description of how to do this at the Libra repository (https://github.com/neurorestore/Libra).

vdsukhov commented 2 years ago

@skinnider Yes, I'm trying to reproduce some of your analysis, especially repeat steps of differential expression analysis

vdsukhov commented 2 years ago

Can this function (Libra::run_de) be used for bulk datasets or it just works with single-cell data?

skinnider commented 2 years ago

For our paper, the code that was used for bulk datasets is in R/analysis/run_bulk_DE, and the relevant function is at https://github.com/neurorestore/DE-analysis/blob/master/R/functions/run_DE.R#L387.