regionReport

DOI: 10.18129/B9.bioc.regionReport    

This is the development version of regionReport; for the stable release version, see regionReport.

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

Bioconductor version: Development (3.13)

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 <lcolladotor at gmail.com>

Citation (from within R, enter citation("regionReport")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("regionReport")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("regionReport")

 

HTML R Script Example report using bumphunter results
HTML R Script Introduction to regionReport
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, DifferentialExpression, DifferentialMethylation, DifferentialPeakCalling, ImmunoOncology, QualityControl, RNASeq, ReportWriting, Sequencing, Software, Transcription, Visualization
Version 1.25.0
In Bioconductor since BioC 3.0 (R-3.1) (6 years)
License Artistic-2.0
Depends R (>= 3.2)
Imports BiocStyle(>= 2.5.19), derfinder(>= 1.2.5), DEFormats, DESeq2, GenomeInfoDb, GenomicRanges, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment, utils
LinkingTo
Suggests BiocManager, biovizBase, bumphunter(>= 1.7.6), derfinderPlot(>= 1.3.2), sessioninfo, DT, edgeR, ggbio(>= 1.35.2), 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 recountWorkflow
Suggests Me recount
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package regionReport_1.25.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/regionReport
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/regionReport
Package Short Url https://bioconductor.org/packages/regionReport/
Package Downloads Report Download Stats

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