Package: regionReport 1.47.0

Leonardo Collado-Torres

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

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.

Authors:Leonardo Collado-Torres [aut, cre], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]

regionReport_1.47.0.tar.gz
regionReport_1.47.0.zip(r-4.7)regionReport_1.47.0.zip(r-4.6)regionReport_1.47.0.zip(r-4.5)
regionReport_1.47.0.tgz(r-4.6-any)regionReport_1.47.0.tgz(r-4.5-any)
regionReport_1.47.0.tar.gz(r-4.7-any)regionReport_1.47.0.tar.gz(r-4.6-any)
regionReport_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
regionReport/json (API)

# Install 'regionReport' in R:
install.packages('regionReport', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/leekgroup/regionreport/issues

On BioConductor:regionReport-1.47.0(bioc 3.24)regionReport-1.46.0(bioc 3.23)

differentialexpressionsequencingrnaseqsoftwarevisualizationtranscriptioncoveragereportwritingdifferentialmethylationdifferentialpeakcallingimmunooncologyqualitycontrolbioconductorderfinderdeseq2edgerregionreportrmarkdown

7.25 score 9 stars 49 scripts 2 mentions 9 exports 144 dependencies

Last updated from:62a3b7a182. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE295
linux-devel-x86_64NOTE758
source / vignettesOK379
linux-release-x86_64NOTE780
macos-release-arm64NOTE409
macos-oldrel-arm64NOTE456
windows-develNOTE773
windows-releaseNOTE782
windows-oldrelNOTE788
wasm-releaseOK269

Exports:derfinderReportDESeq2ReportedgeReportrenderReporttemplateDensitytemplateHistogramtemplateManhattantemplatePvalueDensitytemplatePvalueHistogram

Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHbibtexBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiocStyleBiostringsbitbit64bitopsblobbookdownBSgenomebslibbumphuntercachemcheckmatecigarillocliclustercodetoolscolorspacecommonmarkcpp11crayoncurldata.tableDBIDEFormatsDelayedArrayderfinderderfinderHelperDESeq2digestdoRNGedgeRevaluatefarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrknitrBootstraplabelinglambda.rlatticelifecyclelimmalitedownlocfitlubridatemagrittrmarkdownMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpkgconfigplyrpngqvalueR6rappdirsRColorBrewerRcppRcppArmadilloRCurlRefManageRreshape2restfulrRhtslibrjsonrlangrmarkdownrngtoolsrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsystimechangetinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml

Example report using bumphunter results
r Biocpkg('bumphunter') example | Reproducibility
Rendered frombumphunterExample.Rmdusingknitr::rmarkdown

Last update: 2025-07-27
Started: 2015-07-01

Introduction to regionReport
Basics | Install r Biocpkg('regionReport') | Required knowledge | Asking for help | Citing r Biocpkg('regionReport') | HTML reports for a set differential region results | Using r Biocpkg('regionReport') for r Biocpkg('DESeq2') results | Example | Using r Biocpkg('regionReport') for r Biocpkg('edgeR') results | Using r Biocpkg('regionReport') for region results | Examples | General case | r Biocpkg('derfinder') single base-level case | Run r Biocpkg('derfinder') | Create report | Notes | Reproducibility | Bibliography
Rendered fromregionReport.Rmdusingknitr::rmarkdown

Last update: 2025-01-14
Started: 2014-09-24