wiggleplotr

DOI: 10.18129/B9.bioc.wiggleplotr    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see wiggleplotr.

Make read coverage plots from BigWig files

Bioconductor version: 3.9

Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.

Author: Kaur Alasoo [aut, cre]

Maintainer: Kaur Alasoo <kaur.alasoo at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("wiggleplotr")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("wiggleplotr")

 

HTML	R Script	Introduction to wiggleplotr
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, ChIPSeq, Coverage, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
License	Apache License 2.0
Depends	R (>= 3.4)
Imports	dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb
LinkingTo
Suggests	knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	wiggleplotr_1.8.0.tar.gz
Windows Binary	wiggleplotr_1.8.0.zip
Mac OS X 10.11 (El Capitan)	wiggleplotr_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/wiggleplotr
Source Repository (Developer Access)	git clone [email protected]:packages/wiggleplotr
Package Short Url	https://bioconductor.org/packages/wiggleplotr/
Package Downloads Report	Download Stats