wiggleplotr

DOI: 10.18129/B9.bioc.wiggleplotr    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see wiggleplotr.

Make read coverage plots from BigWig files

Bioconductor version: 3.8

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 "3.5") 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	1.6.1
In Bioconductor since	BioC 3.5 (R-3.4) (2 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
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Build Report

Package Archives

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

Source Package	wiggleplotr_1.6.1.tar.gz
Windows Binary	wiggleplotr_1.6.1.zip
Mac OS X 10.11 (El Capitan)	wiggleplotr_1.6.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/wiggleplotr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/wiggleplotr
Package Short Url	http://bioconductor.org/packages/wiggleplotr/
Package Downloads Report	Download Stats