A Bioconductor package for meta analysis of high-throughput datasets using enriched feature annotations instead of just the features themselves.
Note that this is a rewrite of the categoryCompare package. For more information about how things have changed and why, please see this poster.
This version is mostly complete and works for many full analyses. The user facing API is expected to be close to fixed, especially for the core functionality. Some methods need actual
R6 based objects and methods, but we expect that the function calls themselves will remain the same.
Things that are still needed include:
- Wrapper for initial analysis when given feature data and annotations
- Example for importing the users own annotations
- Integration of
GOCatsPython library for summarizing ontologies
- Better exploration of features that are linked to specific annotations, including the original data associated with the features
The Vignette provides a description of the thinking behind this package as well as a toy example for demonstration purposes.
Installation of this package from Github requires the devtools package.
install.packages("devtools") library(devtools) install_github("rmflight/categoryCompare2")
Flight RM, Harrison BJ, Mohammad F, Bunge MB, Moon LDF, Petruska JC and Rouchka EC (2014). .CATEGORYCOMPARE, an analytical tool based on feature annotations. Frontiers in Genetics. link