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derfinderPlot

This is the development version of derfinderPlot; for the stable release version, see derfinderPlot.

Plotting functions for derfinder

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Introduction to derfinderPlot HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization
Version 1.35.0
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
Linking To
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
System Requirements
Enhances
URL https://github.com/leekgroup/derfinderPlot
Bug Reports https://support.bioconductor.org/t/derfinderPlot
See More
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_1.35.0.tar.gz
Windows Binary derfinderPlot_1.35.0.zip
macOS Binary (x86_64) derfinderPlot_1.35.0.tgz
macOS Binary (arm64) derfinderPlot_1.35.0.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