derfinderPlot

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0

Plotting functions for derfinder

Bioconductor version: Development (3.24)

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] ORCID: 0000-0003-2140-308X , Andrew E. Jaffe [aut] ORCID: 0000-0001-6886-1454 , Jeffrey T. Leek [aut, ths] ORCID: 0000-0002-2873-2671

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

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

Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek. derfinderPlot: Plotting functions for derfinder. doi:10.18129/B9.bioc.derfinderPlot, R package version 1.47.0, https://bioconductor.org/packages/derfinderPlot.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization
Version	1.47.0
In Bioconductor since	BioC 3.0 (R-3.1) (12 years)
License	Artistic-2.0
Depends	R (>= 3.2)
Imports	derfinder (>= 1.1.0), Seqinfo, GenomeInfoDb (>= 1.45.9), 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
System Requirements
URL	https://github.com/leekgroup/derfinderPlot
Bug Reports	https://support.bioconductor.org/t/derfinderPlot

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
Linking To
Enhances
Depends On Me
Imports Me	recountWorkflow
Suggests Me	derfinder, GenomicState, regionReport
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	derfinderPlot_1.47.0.tar.gz
Windows Binary (x86_64)	derfinderPlot_1.47.0.zip
macOS Binary (big-sur-x86_64)	derfinderPlot_1.47.0.tgz
macOS Binary (sonoma-arm64)	derfinderPlot_1.47.0.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