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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
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Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Bioconductor version: Release (3.4)
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")):
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
| 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 |
Details
| biocViews | Coverage, DifferentialExpression, DifferentialMethylation, DifferentialPeakCalling, RNASeq, ReportWriting, Sequencing, Software, Transcription, Visualization |
| Version | 1.8.2 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2.5 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), methods, 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://support.bioconductor.org/t/regionReport/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | recount |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | regionReport_1.8.2.tar.gz |
| Windows Binary | regionReport_1.8.2.zip |
| Mac OS X 10.9 (Mavericks) | regionReport_1.8.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/regionReport/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/regionReport/ |
| Package Downloads Report | Download Stats |
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