The Input files

[LuShuYangMing]

Where could we find the raw data such as .rds and .csv files

[microbialman]

Hi files for the module analyses can be found here:
https://github.com/microbialman/IBDTherapyResponsePaper/tree/master/Module_Analyses/Data/Input

[LuShuYangMing]

Hi, I mean the input file is this code from "IBDTherapyResponsePaper/SmartSeq2/notebooks/rnaseq.config.R"
scseq_db="/gfs/work/kralbrecht/18_matthias/scrnaseq-full/csvdb"

[microbialman]

Ah ok, those analyses were contributed from @kevinrue he may be able to help

[kevinrue]

I currently do not have access to those files anymore.
Perhaps @snsansom can find them on the archive of the server where those analyses were run and upload them here?

For what it's worth, I did not upload those files initially for a few reasons:

1. code repositories typically should not track data.
2. I cannot remember off the top of my head, but those csvdb files might have been quite large for GitHub.
3. Raw and processed data are available from data repositorie (GEO, see below)

I am aware of workarounds, like git-lfs, to store large files on GitHub. However, the raw data were upload to public repositories (see https://www.nature.com/articles/s41591-021-01520-5#data-availability), which should be treated as the reference. Notebooks were uploaded for transparency of the code analysis, not containerised reproducibility.

Kind regards
Kevin