To install from CRAN

This should download the rnaseqWrapper package and all of its smaller dependencies:


However, the three larger dependencies, including two from Bioconductor, are not automatically installed, though you will be prompted to install them if you call a function that needs them. To install them on your own use:



Note that these are large packages, and may take a while to install.

To install from this development version


### Install dependencies ###


## note that DESeq, topGO and seqinr are only "suggested" and only needed for certain functions

### Install this package ###

Version notes

To start using

Load the package


List functions available in rnaseqWrapper


Available functions

I will write some sort of vignette in the near(ish) future (I hope). For now, here is a brief description of the functions, broken down by area.

Merge count data

Run DESeq

Make basic calculations on data

These represent the most commonly done/used calculations on basic read/FPKM data, and (hopefully) make it easier to calculate them

A distance function

A slight tweak to a plot

Reading in variant files

These are just two common variant formats, but most of the other possible formats won't need to be modified for downstream use in the package.

Variant Analysis

These functions should work on nearly any input format of variant information, and (I hope) represent the most commonly used basic analyses. All but calculateThirdPosBias require a reference file, and even calculateThirdPosBias is only sort of worthwhile without one

Miscellaneous info

For more usage information, or to report bugs and enhancement requests, please contact the authors. This package was very recently converted from in-house scripts, so some idiosyncrasies may persist.