derfinderPlot

DOI: 10.18129/B9.bioc.derfinderPlot  

Plotting functions for derfinder

Bioconductor version: Release (3.16)

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 "4.2") 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	1.32.0
In Bioconductor since	BioC 3.0 (R-3.1) (8.5 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_1.32.0.tar.gz
Windows Binary	derfinderPlot_1.32.0.zip
macOS Binary (x86_64)	derfinderPlot_1.32.0.tgz
macOS Binary (arm64)	derfinderPlot_1.32.0.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