regionReport

This is the released version of regionReport; for the devel version, see regionReport.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0

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

Bioconductor version: Release (3.23)

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] ORCID: 0000-0003-2140-308X , Andrew E. Jaffe [aut] ORCID: 0000-0001-6886-1454 , Jeffrey T. Leek [aut, ths] ORCID: 0000-0002-2873-2671

Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>

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

Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek. regionReport: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results. doi:10.18129/B9.bioc.regionReport, R package version 1.46.0, https://bioconductor.org/packages/regionReport.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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, QualityControl, RNASeq, ReportWriting, Sequencing, Software, Transcription, Visualization
Version	1.46.0
In Bioconductor since	BioC 3.0 (R-3.1) (12 years)
License	Artistic-2.0
Depends	R (>= 3.2)
Imports	BiocStyle (>= 2.5.19), derfinder (>= 1.25.3), DEFormats, DESeq2, Seqinfo, 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/

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, r-universe

Package Archives

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

Source Package	regionReport_1.46.0.tar.gz
Windows Binary (x86_64)	regionReport_1.46.0.zip
macOS Binary (big-sur-x86_64)	regionReport_1.46.0.tgz
macOS Binary (sonoma-arm64)	regionReport_1.46.0.tgz
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