regionReport: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("regionReport")
AuthorLeonardo Collado-Torres [aut, cre], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Bioconductor views Coverage DifferentialExpression DifferentialMethylation DifferentialPeakCalling RNASeq ReportWriting Sequencing Software Transcription Visualization
Date of publicationNone
MaintainerLeonardo Collado-Torres <lcollado@jhu.edu>
LicenseArtistic-2.0
Version1.8.2
https://github.com/leekgroup/regionReport

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/DESeq2Report.R R/derfinderReport.R R/edgeReport.R R/regionReport-package.R R/renderReport.R R/utils.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/DESeq2Exploration
inst/DESeq2Exploration/DESeq2Exploration.Rmd
inst/basicExploration
inst/basicExploration/basicExploration.Rmd
inst/doc
inst/doc/bumphunterExample.R
inst/doc/bumphunterExample.Rmd
inst/doc/bumphunterExample.html
inst/doc/bumphunterExampleOutput.R
inst/doc/bumphunterExampleOutput.Rmd
inst/doc/bumphunterExampleOutput.html
inst/doc/regionReport.R
inst/doc/regionReport.Rmd
inst/doc/regionReport.html
inst/regionExploration
inst/regionExploration/regionExploration.Rmd
man
man/DESeq2Report.Rd man/derfinderReport.Rd man/edgeReport.Rd man/load_install.Rd man/regionReport-package.Rd man/renderReport.Rd man/with_wd.Rd
vignettes
vignettes/Makefile
vignettes/bumphunterExample.Rmd
vignettes/bumphunterExampleOutput.Rmd
vignettes/bumphunterExampleOutput.bib
vignettes/fakeVignettes
vignettes/fakeVignettes/bumphunterExampleOutput.Rmd
vignettes/regionReport.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.