regionReport

DOI:10.18129/B9.bioc.regionReport

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, seeregionReport.

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

Bioconductor version: 3.8

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

Installation

To install this package, start R (version "3.5") and enter:

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

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

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("regionReport")

HTML	R Script	Basic genomic regions exploration
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,RNASeq,ReportWriting,Sequencing,Software,Transcription,Visualization
Version	1.16.1
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 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
LinkingTo
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
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

Followbob 体育网址 instructions to use this package in your R session.

Source Package	regionReport_1.16.1.tar.gz
Windows Binary	regionReport_1.16.1.zip
Mac OS X 10.11 (El Capitan)	regionReport_1.16.1.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	//www.anjoumacpherson.com/packages/regionReport/
Package Downloads Report	Download Stats