Skip to content
new version of categoryCompare that is a complete rewrite
R
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R
exec
executable_related
inst
man
tests
vignettes
.Rbuildignore
.Rinstignore
.gitignore
BUGS
DESCRIPTION
LICENSE
NAMESPACE
NEWS
categoryCompare2.Rproj
readme.md
test_data_gen.R
test_data_gen2.R
tests.R

readme.md

categoryCompare2

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.

API

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 S4 or R6 based objects and methods, but we expect that the function calls themselves will remain the same.

To Do

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 GOCats Python library for summarizing ontologies
  • Better exploration of features that are linked to specific annotations, including the original data associated with the features

Documentation

The Vignette provides a description of the thinking behind this package as well as a toy example for demonstration purposes.

Installation

Installation of this package from Github requires the devtools package.

install.packages("devtools")
library(devtools)
install_github("rmflight/categoryCompare2")

Citation

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

You can’t perform that action at this time.