Wipperman, M.F., Bhattarai, S.K., Vorkas, C.K. et al. Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis. Nat Commun 12, 1141 (2021).
https://www.nature.com/articles/s41467-021-21475-y doi: https://doi.org/10.1038/s41467-021-21475-y
Please download the data from following dropbox folder to run the scripts:
Up to date scripts can be accessed here: scripts on Shakti's GitHub
The R scripts can be executed in following order: (based on order of paper figures)
a)Fig_2
b)Fig_3
c)Fig_4
d)Fig_5A
e)Fig_5B
f)FGSEA
g)comb_gsva (GSVA for all RNA Samples)
h)cross_val_fc_cc
i)rf_model_FC_CC (RF Model for Hallmark Pathways using FC and CC samples)
j)lme_pathways
k)diff_rf (Diff RF Model)
l)Supp (Supplementary files)
Where's the 16S and RNAseq raw data?
The raw data used for the papers can be downloaded from the National Library of Medicine. The data is under BioProject ID: PRJNA445968.