This is a collection of Jupyter notebooks to showcase how to use the ReactomeGSA R package.
Most of these notebooks contain rather large analyses take quite a while to run. Shorter tutorials that also cover the complete functionality of the ReactomeGSA package are released as vignettes of the R package.
You can find these vignettes as pre-compiled HTML files at the ReactomeGSA Bioconductor page (or here for the latest development version).
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TCGA Cancer Analysis: An analysis of B cell rich vs. poor cancer samples from the TCGA studies on melanoma, ovarian, lung (adenocarcinoma and squamous cell carcinoma), and breast cancer as well as the corresponding CPTAC proteomics studies on breast and ovarian cancer.
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GEO Atopic Dermatitis Example: This notebook shows how to analyse datasets from GEO using ReactomeGSA. Most importantly we showcase how to combine the use of GEOQuery with ReactomeGSA. Finally, this notebook also contains an example of how to perform a time course analysis.
- B cell subtype analysis: An analysis of B cells extracted from the single-cell RNA-sequencing dataset published by Jerby-Arnon et al. (Cell, 2018). ReactomeGSA allowed us to quickly compare different pathway functions in the identified B cell subtypes.