wiggleplotr
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see wiggleplotr.
Make read coverage plots from BigWig files
Bioconductor version: 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("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 | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, ChIPSeq, Coverage, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Visualization |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 years) |
| License | Apache License 2.0 |
| Depends | R (>= 3.4) |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | wiggleplotr_1.8.0.tar.gz |
| Windows Binary | wiggleplotr_1.8.0.zip |
| Mac OS X 10.11 (El Capitan) | wiggleplotr_1.8.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |