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A collection of R tools for benchmarking single-sample GSA methods

First version: May 25th, 2020
Last review: May 25th, 2020

What is single-sample GSA?

Single Sample Gene Set Analysis(ss-GSA) is a specific type of Gene Set Analysis, used to calculate each individual sample’s pathway score for comparison among those individuals in normal and disease status. ss-GSA methods are concentrated on individual samples.

Contents

  • The R folder contains functions that used to manage data format, read .GMT files, get microarray data, run each ss-GSA tools and computing sensitivity, specificity and precision(SSP for short).
  • The data folder contains target pathways of each disease, and the phenotype data information of benchmark datasets.
  • The man folder contains descriptions and examples of each R functions.
  • The results folder contains .RDS files about scores results and SSP results.
  • The workflows folder contains the workflow of using each method with the example dataset(here is part data of GSE10245).

References

See our paper:

XIE, C., JAUHARI, S., MORA, A. (2020), Popularity and performance of bioinformatics software -The case of gene set analysis