derfinderPlot
This is the development version of derfinderPlot; for the stable release version, see derfinderPlot.
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]
, Andrew E. Jaffe [aut]
, Jeffrey T. Leek [aut, ths]
Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>
citation("derfinderPlot")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text |
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 |
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.
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/derfinderPlot/ |
| Package Short Url | https://bioconductor.org/packages/derfinderPlot/ |
| Package Downloads Report | Download Stats |