# _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. <img src="PTK2B.png" width="450"> ## Installation This repostitory contains the development version of _wiggleplotr_. The latest stable version can be installed directly from [Bioconductor](https://bioconductor.org/packages/wiggleplotr/): ```r ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("wiggleplotr") ``` Alternatively, you can still install the development version using devtools: ```r library("devtools") devtools::install_github("kauralasoo/wiggleplotr") ``` However, the stable Bioconductor version is likely to be the best option for most people. ## Getting started See the [vignette](https://htmlpreview.github.io/?https://github.com/kauralasoo/wiggleplotr/blob/master/vignettes/wiggleplotr.html) for instructions on how to get started. ## Citation If you use this software for research, please cite the following paper in which it was first described: [Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription (Alasoo et al, 2015)](http://www.nature.com/articles/srep12524)