wiggleplotr

DOI: 10.18129/B9.bioc.wiggleplotr    

This is the development version of wiggleplotr; for the stable release version, see wiggleplotr.

Make read coverage plots from BigWig files

Bioconductor version: Development (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>

Citation (from within R, enter citation("wiggleplotr")):

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("wiggleplotr", version = "3.9")

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, RNASeq, Sequencing, Software, Transcription, Visualization
Version 1.7.0
In Bioconductor since BioC 3.5 (R-3.4) (1.5 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_1.7.0.tar.gz
Windows Binary wiggleplotr_1.7.0.zip
Mac OS X 10.11 (El Capitan) wiggleplotr_1.7.0.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

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