derfinderPlot

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see derfinderPlot.

Plotting functions for derfinder

Bioconductor version: 3.14

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 "4.1") 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 1.28.1

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

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

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