Package: regionReport 1.46.0

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_1.46.0.tar.gz
regionReport_1.46.0.zip(r-4.7)regionReport_1.46.0.zip(r-4.6)regionReport_1.46.0.zip(r-4.5)
regionReport_1.46.0.tgz(r-4.6-any)regionReport_1.46.0.tgz(r-4.5-any)
regionReport_1.46.0.tar.gz(r-4.7-any)regionReport_1.46.0.tar.gz(r-4.6-any)
regionReport_1.46.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
regionReport/json (API)
NEWS

# Install 'regionReport' in R:
install.packages('regionReport', repos = c('https://bioc-release.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

7.27 score 9 stars 52 scripts 508 downloads 2 mentions 9 exports 144 dependencies

Last updated from:0b5727526b (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE292
linux-devel-x86_64NOTE752
source / vignettesOK454
linux-release-x86_64NOTE763
macos-release-arm64NOTE632
macos-oldrel-arm64NOTE475
windows-develNOTE832
windows-releaseNOTE906
windows-oldrelNOTE763
wasm-releaseOK246

Exports:derfinderReportDESeq2ReportedgeReportrenderReporttemplateDensitytemplateHistogramtemplateManhattantemplatePvalueDensitytemplatePvalueHistogram

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

Example report using bumphunter results

Leonardo Collado-Torres

Rendered frombumphunterExample.Rmdusingknitr::rmarkdownon May 31 2026.

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

Introduction to regionReport

Leonardo Collado-Torres

Rendered fromregionReport.Rmdusingknitr::rmarkdownon May 31 2026.

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