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.
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see regionReport.
Bioconductor version: 3.3
Generate HTML or PDF 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. You can also create reports for DESeq2 or edgeR results.
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")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("regionReport")
HTML | R Script | Basic genomic regions exploration |
HTML | R Script | Example report using bumphunter results |
HTML | R Script | Introduction to regionReport |
Reference Manual | ||
Text | NEWS |
biocViews | Coverage, DifferentialExpression, DifferentialMethylation, DifferentialPeakCalling, RNASeq, ReportWriting, Sequencing, Software, Transcription, Visualization |
Version | 1.6.5 |
In Bioconductor since | BioC 3.0 (R-3.1) (2 years) |
License | Artistic-2.0 |
Depends | R (>= 3.2) |
Imports | derfinder(>= 1.1.0), DEFormats, DESeq2, GenomeInfoDb, GenomicRanges, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment |
LinkingTo | |
Suggests | BiocStyle, biovizBase, bumphunter(>= 1.7.6), Cairo, derfinderPlot(>= 1.3.2), devtools (>= 1.6), DT, DESeq, edgeR, ggbio(>= 1.13.13), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker |
SystemRequirements | |
Enhances | |
URL | https://github.com/leekgroup/regionReport |
BugReports | https://github.com/leekgroup/regionReport/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | regionReport_1.6.5.tar.gz |
Windows Binary | regionReport_1.6.5.zip |
Mac OS X 10.9 (Mavericks) | regionReport_1.6.5.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/regionReport/tree/release-3.3 |
Package Short Url | http://bioconductor.org/packages/regionReport/ |
Package Downloads Report | Download Stats |
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