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Bioconductor - derfinderPlot (development version)

derfinderPlot

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

Plotting functions for derfinder

Bioconductor version: Development (3.22)

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")): Installation

To install this package, start R (version "4.5") 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")
Details biocViews DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization Version 1.43.0 In Bioconductor since BioC 3.0 (R-3.1) (10.5 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 System Requirements URL https://github.com/leekgroup/derfinderPlot Bug Reports https://support.bioconductor.org/t/derfinderPlot See More 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, regionReport, GenomicState Links To Me Build Report Build Report Package Archives

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

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