derfinderPlot

This is the released version of derfinderPlot; for the devel version, see derfinderPlot.

Plotting functions for derfinder

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DOI: 10.18129/B9.bioc.derfinderPlot

Bioconductor version: Release (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 iD ORCID: 0000-0003-2140-308X , Andrew E. Jaffe [aut] ORCID iD ORCID: 0000-0001-6886-1454 , Jeffrey T. Leek [aut, ths] ORCID iD 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")
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 1.44.0

In Bioconductor since BioC 3.0 (R-3.1) (11 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, regionReport, GenomicState

Links To Me

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Package Archives

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

Source Package derfinderPlot_1.44.0.tar.gz

Windows Binary (x86_64) derfinderPlot_1.44.0.zip (64-bit only)

macOS Binary (x86_64) derfinderPlot_1.44.0.tgz

macOS Binary (arm64) derfinderPlot_1.44.0.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/

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