Name Mode Size
..
getGenotypePalette.Rd 100644 1 kb
makeManhattanPlot.Rd 100644 1 kb
ncoa7_cdss.Rd 100644 1 kb
ncoa7_exons.Rd 100644 1 kb
ncoa7_metadata.Rd 100644 1 kb
pasteFactors.Rd 100644 0 kb
plotCoverage.Rd 100644 5 kb
plotCoverageFromEnsembldb.Rd 100644 1 kb
plotCoverageFromUCSC.Rd 100644 2 kb
plotTranscripts.Rd 100644 2 kb
plotTranscriptsFromEnsembldb.Rd 100644 1 kb
plotTranscriptsFromUCSC.Rd 100644 1 kb
wiggleplotr.Rd 100644 1 kb
README.md
# _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 if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("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 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.](https://doi.org/doi:10.18129/B9.bioc.wiggleplotr)