regionReport: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Version 1.10.0

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.

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
Version1.10.0
URL https://github.com/leekgroup/regionReport
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("regionReport")

Getting started

Package overview
README.md
Example report using bumphunter results
Introduction to regionReport

Popular man pages

derfinderReport: Generate a HTML/PDF report exploring the basic results from...
DESeq2Report: Generate a HTML/PDF report exploring DESeq2 results
edgeReport: Generate a HTML/PDF report exploring edgeR results
load_install: Attempt to load the namespace of a package and install it if...
regionReport-package: Generate HTML or PDF reports for a set of regions or...
renderReport: Generate a HTML/PDF report exploring a set of genomic regions
with_wd: Temporarily evaluate an expression in a directory
See all...

All man pages Function index File listing

Man pages

derfinderReport: Generate a HTML/PDF report exploring the basic results from...
DESeq2Report: Generate a HTML/PDF report exploring DESeq2 results
edgeReport: Generate a HTML/PDF report exploring edgeR results
load_install: Attempt to load the namespace of a package and install it if...
regionReport-package: Generate HTML or PDF reports for a set of regions or...
renderReport: Generate a HTML/PDF report exploring a set of genomic regions
with_wd: Temporarily evaluate an expression in a directory

Functions

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
regionReport documentation built on May 20, 2017, 10:09 p.m.

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

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

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