README.md

In cheejus2/Intron_Vis: visualization of introns in RNA-seq data

IntronVis

IntronVis a package that allows users to visually differentiate between intronic and exonic regions when gene modelling with RNA-seq data.

Installation

You can install the development version from GitHub with:

require("devtools")
install_github("cheejus2/Intron_Vis")
library("Intron_Vis")

Description

IntronVis can be used to view and modifiy Organism and Transcript DB gene track plots with highlighted intronic regions. It is also capable of modifying coverage plots produced from bam files.

To view vignettes:

browseVignettes("IntronVis")

Testing

Make sure that all required packages described in the DESCRIPTION file are installed before use. For the add_intron(plots, introns) function consider using a small data frame such as (df \<- data.frame(a = c(41200000, 41350000), b = c(41200100, 41350100))) to minimize run time. Example data and fields are further described in the comments along with the code.

References

Functions build off of workflow described at: http://bioconductor.org/packages/release/bioc/vignettes/ggbio/inst/doc/ggbio.pdf

Contributing

Pull requests are welcome.

Please update tests as appropriate.

cheejus2/Intron_Vis documentation built on Dec. 8, 2019, 10:35 a.m.