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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
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Build Report Build Report

Package Archives

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

Source Package regionReport_1.36.0.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