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derfinderPlot

Plotting functions for derfinder


Bioconductor version: Release (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")

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 1.36.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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 brainflowprobes, recountWorkflow
Suggests Me derfinder, GenomicState, regionReport
Links To Me
Build Report Build Report

Package Archives

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

Source Package derfinderPlot_1.36.0.tar.gz
Windows Binary derfinderPlot_1.36.0.zip (64-bit only)
macOS Binary (x86_64) derfinderPlot_1.36.0.tgz
macOS Binary (arm64) derfinderPlot_1.36.0.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