wiggleplotr

wiggleplotr is a tool to visualise RNA-seq read overage overlapping gene annotations. A key feature of wiggleplotr is that it is able rescale all introns of a gene to fixed length, making it easier to see differences in read coverage between neighbouring exons that can otherwise be too far away. Since wiggleplotr takes standard BigWig files as input, it can also be used to visualise read overage from other sequencing-based assays such as ATAC-seq and ChIP-seq.

This repository contains a modified version of wiggleplotr. The original stable version can be installed directly from Bioconductor:

Installation

## try http:// if https:// URLs are not supported
library("devtools")
devtools::install_github("mflamand/wiggleplotr")

There are 3 main differences with the original package:

• Gene structures are displayed in black only (instead of shades of blue), but UTR regions will be slimer than CDS.
• New option in plotCoverage for type = "line_sd", which allows plotting of average+/-standard deviation of coverage as a line + ribbon plot
• Can now optionally inout a list of Granges to be displayed below the gene structure (for example for CLIP sites)

Getting started

See the vignette for instructions on how to get started.

Citation

If you use wiggleplotr for research, please cite the Bioconductor package directly: Alasoo K (2019). wiggleplotr: Make read coverage plots from BigWig files. R package version 1.8.0.