Analysis for IST publication

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This repository contains the analysis on public and in-house datasets necessary to reproduce the results in the IST (In Silico Treatment) publication. IST is a computational method to assess the translatability between animal models and human disease data at the pathway and gene level. The manuscript and the package vignette will guide the user on IST's capabilities and user manual.

Repo structure

The organisation is:

• 0_rawdata: internal/external gene expression data (quantified, differential analysis)
• 1_preprocessing: data fetching, wrangling and preparation for IST runs
• 2_IPF: IPF animal models and treatments
• 3_NASH: NASH animal models and treatments
• 9_misc: miscellaneous supporting material (figures, logos, etc)
• 9_temp: folder for testing code, not included in publication

Each report comes with a companion folder with the exported results. If the report name is 3_report.Rmd, the output folder will be 3_report_output/, so it is always caught by .gitignore.

Important file locations are defined in the config.yml file and fecthed using the config R package.

Requirements

The IST R package, also published with the manuscript.

Package dependencies are described in the renv.lock file using the renv R package via renv::snapshot().

Reproduce analysis

The Makefile contains automated instructions to rerun the whole repo. You can reproduce regenerate the whole analysis by running:

make all

To run specific parts from the tree structure, there are more specific commands:

make preprocessing
make ipf
make nash