derfinderPlot

DOI: 10.18129/B9.bioc.derfinderPlot  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see derfinderPlot.

Plotting functions for derfinder

Bioconductor version: 3.17

This package provides plotting functions for results from the derfinder package. This helps separate the graphical dependencies required for making these plots from the core functionality of derfinder.

Author: Leonardo Collado-Torres [aut, cre] , Andrew E. Jaffe [aut] , Jeffrey T. Leek [aut, ths]

Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("derfinderPlot")

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("derfinderPlot")

 

HTML	R Script	Introduction to derfinderPlot
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization
Version	1.34.0
In Bioconductor since	BioC 3.0 (R-3.1) (9 years)
License	Artistic-2.0
Depends	R (>= 3.2)
Imports	derfinder(>= 1.1.0), GenomeInfoDb(>= 1.3.3), GenomicFeatures, GenomicRanges(>= 1.17.40), ggbio(>= 1.13.13), ggplot2, graphics, grDevices, IRanges(>= 1.99.28), limma, methods, plyr, RColorBrewer, reshape2, S4Vectors(>= 0.9.38), scales, utils
LinkingTo
Suggests	biovizBase(>= 1.27.2), bumphunter(>= 1.7.6), derfinderData(>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle(>= 2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, covr
SystemRequirements
Enhances
URL	https://github.com/leekgroup/derfinderPlot
BugReports	https://support.bioconductor.org/t/derfinderPlot
Depends On Me
Imports Me	brainflowprobes, recountWorkflow
Suggests Me	derfinder, GenomicState, regionReport
Links To Me
Build Report

Package Archives

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

Source Package	derfinderPlot_1.34.0.tar.gz
Windows Binary	derfinderPlot_1.34.0.zip
macOS Binary (x86_64)	derfinderPlot_1.34.0.tgz
macOS Binary (arm64)	derfinderPlot_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/derfinderPlot
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/derfinderPlot
Bioc Package Browser	https://code.bioconductor.org/browse/derfinderPlot/
Package Short Url	https://bioconductor.org/packages/derfinderPlot/
Package Downloads Report	Download Stats