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regionReport

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


Bioconductor version: Release (3.18)

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 "4.3") 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")
Example report using bumphunter results HTML R Script
Introduction to regionReport HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, DifferentialExpression, DifferentialMethylation, DifferentialPeakCalling, ImmunoOncology, QualityControl, RNASeq, ReportWriting, Sequencing, Software, Transcription, Visualization
Version 1.36.0
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(>= 1.25.3), DEFormats, DESeq2, GenomeInfoDb, GenomicRanges, knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment, utils
System Requirements
URL https://github.com/leekgroup/regionReport
Bug Reports https://support.bioconductor.org/t/regionReport/
See More
Suggests BiocManager, biovizBase, bumphunter(>= 1.7.6), derfinderPlot(>= 1.29.1), sessioninfo, DT, edgeR, ggbio(>= 1.35.2), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker
Linking To
Enhances
Depends On Me
Imports Me recountWorkflow
Suggests Me recount
Links To Me
Build Report Build Report

Package Archives

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

Source Package regionReport_1.36.0.tar.gz
Windows Binary regionReport_1.36.0.zip
macOS Binary (x86_64) regionReport_1.36.0.tgz
macOS Binary (arm64) regionReport_1.36.0.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