README.md

In DavisLaboratory/oppar: Outlier profile and pathway analysis in R

oppar

Outlier Profile and Pathway Analysis in R

OPPAR is the R implementation of the modified Cancer Outlier Profile Analysis (mCOPA) method, published by Wang et al. in 2012.

Download Instructions

oppar is now available on Bioconductor

source("https://bioconductor.org/biocLite.R")
biocLite("oppar")

Enter the following lines in R/Rstudio to download and install the source code for the package from Github.

# install.packages("devtools") # if not already installed
library(devtools)
install_github("DavisLaboratory/oppar", build_vignettes = TRUE)
library(oppar)
browseVignettes(package = "oppar") # opens up package vignette 

For a complete example workflow, and to learn about how oppar works, please refer to the package vignette or Wiki.

To report bugs or for any other enquiries, please email [e-mail]

Release notes: The modified gsva function for Gene Set Enrichment Analysis is now available. Several Examples are provided in the Wiki for GSEA. It has also been demonstrated that how oppar can be used in conjuction with other packages such as limma for gene set testing. In addition, examples on how to apply oppar tools are provided in man/help pages. See also help(package = "oppar").

DavisLaboratory/oppar documentation built on May 6, 2019, 1:56 p.m.