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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("regionReport")
In most cases, you don't need to download the package archive at all.
regionReport
|
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see regionReport.
Generate HTML reports for exploring a set of regions
Bioconductor version: 3.2
Generate HTML reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder.
Author: Leonardo Collado-Torres [aut, cre], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Maintainer: Leonardo Collado-Torres <lcollado at jhu.edu>
Citation (from within R,
enter citation("regionReport")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("regionReport")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("regionReport")
| HTML | Example with data from bumphunter | |
| HTML | Introduction to regionReport | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Coverage, DifferentialExpression, RNASeq, Sequencing, Software, Transcription, Visualization |
| Version | 1.4.1 |
| In Bioconductor since | BioC 3.0 (R-3.1) (1.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2) |
| Imports | bumphunter(>= 1.7.6), derfinder(>= 1.1.0), derfinderPlot(>= 1.3.2), devtools (>= 1.6), GenomeInfoDb, GenomicRanges, ggbio(>= 1.13.13), ggplot2, grid, gridExtra, IRanges, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), mgcv, RColorBrewer, rmarkdown (>= 0.3.3), whisker |
| LinkingTo | |
| Suggests | BiocStyle, biovizBase, Cairo, TxDb.Hsapiens.UCSC.hg19.knownGene |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/leekgroup/regionReport |
| BugReports | https://github.com/leekgroup/regionReport/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | regionReport_1.4.1.tar.gz |
| Windows Binary | regionReport_1.4.1.zip |
| Mac OS X 10.6 (Snow Leopard) | regionReport_1.4.1.tgz |
| Mac OS X 10.9 (Mavericks) | regionReport_1.4.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/regionReport/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/regionReport/ |
| Package Downloads Report | Download Stats |
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