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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 (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews AlternativeSplicing, ChIPSeq, Coverage, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Visualization
Version 1.27.0
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
See More
Suggests knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter
Linking To
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Depends On Me
Imports Me factR
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Package Archives

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

Source Package wiggleplotr_1.27.0.tar.gz
Windows Binary wiggleplotr_1.27.0.zip (64-bit only)
macOS Binary (x86_64) wiggleplotr_1.27.0.tgz
macOS Binary (arm64) wiggleplotr_1.27.0.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