derfinderPlot

DOI: 10.18129/B9.bioc.derfinderPlot    

Plotting functions for derfinder

Bioconductor version: Release (3.14)

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>

Citation (from within R, enter citation("derfinderPlot")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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 1.28.1
In Bioconductor since BioC 3.0 (R-3.1) (7 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_1.28.1.tar.gz
Windows Binary derfinderPlot_1.28.1.zip
macOS 10.13 (High Sierra) derfinderPlot_1.28.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/derfinderPlot
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/derfinderPlot
Package Short Url https://bioconductor.org/packages/derfinderPlot/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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