@@ -12,33 +12,21 @@ Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC ma

 as follows:

 ```

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

-biocLite("CoGAPS")

+install.packages("BiocManager")

+BiocManager::install("CoGAPS")

 ```

 The most up-to-date version of *CoGAPS* can be installed directly from the 

 *FertigLab* Github Repository:

 ```

-## Method 1 using biocLite

-biocLite("FertigLab/CoGAPS", dependencies = TRUE, build_vignettes = TRUE)

+## Method 1 using BiocManager

+BiocManager::install("FertigLab/CoGAPS")

 ## Method 2 using devtools package

 devtools::install_github("FertigLab/CoGAPS")

 ```

-There is also an option to install the development version of *CoGAPS*, 

-while this version has the latest experimental features, it is not guaranteed

-to be stable.

-

-```

-## Method 1 using biocLite

-biocLite("FertigLab/CoGAPS", ref="develop", dependencies = TRUE, build_vignettes = TRUE)

-

-## Method 2 using devtools package

-devtools::install_github("FertigLab/CoGAPS", ref="develop")

-```

-

 # Using CoGAPS

 Follow the vignette here: http://htmlpreview.github.io/?https://github.com/FertigLab/CoGAPS/blob/develop/vignettes/CoGAPS.html