wiggleplotr
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see wiggleplotr.
Make read coverage plots from BigWig files
Bioconductor version: 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("wiggleplotr")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | AlternativeSplicing, ChIPSeq, Coverage, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Visualization |
Version | 1.28.0 |
In Bioconductor since | BioC 3.5 (R-3.4) (7.5 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 | |
Enhances | |
Depends On Me | |
Imports Me | factR |
Suggests Me | MARVEL |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | wiggleplotr_1.28.0.tar.gz |
Windows Binary (x86_64) | wiggleplotr_1.28.0.zip |
macOS Binary (x86_64) | wiggleplotr_1.28.0.tgz |
macOS Binary (arm64) | wiggleplotr_1.28.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/wiggleplotr |
Source Repository (Developer Access) | git clone [email protected]:packages/wiggleplotr |
Bioc Package Browser | https://code.bioconductor.org/browse/wiggleplotr/ |
Package Short Url | https://bioconductor.org/packages/wiggleplotr/ |
Package Downloads Report | Download Stats |