========================================================== vivlib

by @vivekbhr

Useful functions and wrappers around RNAseq analysis

vivlib is a set of useful functions for RNA-Seq analysis built around featureCounts and edgeR/DESeq2. It includes exploring featureCounts output, performing edgeR/DESeq2, annotating the outputs and some downstream analysis. Some useful operations on BAM files and bed files are also included.

Installation

You can install vivlib using either biocLite from bioconductor or using install_github command from devtools package.

Using biocLite :

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

Functions

To get a list of available functions, install vivlib and do :

library(vivlib)
ls(pos = "package:vivlib")

Disclaimer

Although most functions in the latest release have been tested, the package is always under active (but infrequent) development.