regionReport

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see regionReport.

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

Bioconductor version: 3.10

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 "3.6") and enter:


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

Basic genomic regions exploration HTML R Script

Example report using bumphunter results HTML R Script

Introduction to regionReport HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DifferentialExpression, DifferentialMethylation, DifferentialPeakCalling, ImmunoOncology, RNASeq, ReportWriting, Sequencing, Software, Transcription, Visualization

Version 1.20.0

In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)

License Artistic-2.0

Depends R (>= 3.2)

Imports BiocStyle(>= 2.5.19), 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

System Requirements

URL https://github.com/leekgroup/regionReport

Bug Reports https://support.bioconductor.org/t/regionReport/

Suggests BiocManager, biovizBase, bumphunter(>= 1.7.6), derfinderPlot(>= 1.3.2), sessioninfo, DT, DESeq, edgeR, ggbio(>= 1.13.13), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker

Linking To

Enhances

Depends On Me

Imports Me recountWorkflow

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Build Report Build Report

Package Archives

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

Source Package regionReport_1.20.0.tar.gz

Windows Binary regionReport_1.20.1.zip

Mac OS X 10.11 (El Capitan) regionReport_1.20.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/regionReport

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/regionReport

Bioc Package Browser https://code.bioconductor.org/browse/regionReport/

Package Short Url https://bioconductor.org/packages/regionReport/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.10 Source Archive