wiggleplotr

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see wiggleplotr.

Make read coverage plots from BigWig files

Bioconductor version: 3.10

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 (!require("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")

Introduction to wiggleplotr HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AlternativeSplicing, ChIPSeq, Coverage, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Visualization

Version 1.10.1

In Bioconductor since BioC 3.5 (R-3.4) (7 years)

License Apache License 2.0

Depends R (>= 3.6)

Imports dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb

System Requirements

URL

Suggests knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter

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Package Archives

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

Source Package wiggleplotr_1.10.1.tar.gz

Windows Binary wiggleplotr_1.10.1.zip (32- & 64-bit)

Mac OS X 10.11 (El Capitan) wiggleplotr_1.10.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/wiggleplotr

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/wiggleplotr

Bioc Package Browser https://code.bioconductor.org/browse/wiggleplotr/

Package Short Url https://bioconductor.org/packages/wiggleplotr/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.10 Source Archive