Package: regionReport 1.41.1

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_1.41.1.tar.gz
regionReport_1.41.1.zip(r-4.5)regionReport_1.41.1.zip(r-4.4)regionReport_1.41.1.zip(r-4.3)
regionReport_1.41.1.tgz(r-4.4-any)regionReport_1.41.1.tgz(r-4.3-any)
regionReport_1.41.1.tar.gz(r-4.5-noble)regionReport_1.41.1.tar.gz(r-4.4-noble)
regionReport_1.41.0.tgz(r-4.4-emscripten)regionReport_1.41.1.tgz(r-4.3-emscripten)
regionReport.pdf |regionReport.html✨
regionReport/json (API)
NEWS

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

Peer review:

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

On BioConductor:regionReport-1.41.0(bioc 3.21)regionReport-1.40.0(bioc 3.20)

differentialexpressionsequencingrnaseqsoftwarevisualizationtranscriptioncoveragereportwritingdifferentialmethylationdifferentialpeakcallingimmunooncologyqualitycontrolbioconductorderfinderdeseq2edgerregionreportrmarkdown

7.19 score 9 stars 43 scripts 314 downloads 2 mentions 9 exports 150 dependencies

Last updated 8 days agofrom:f885790a2f. Checks:1 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 15 2025
R-4.5-winNOTEJan 15 2025
R-4.5-linuxNOTEJan 15 2025
R-4.4-winNOTEJan 15 2025
R-4.4-macNOTEJan 15 2025
R-4.3-winNOTEJan 15 2025
R-4.3-macNOTEJan 15 2025

Exports:derfinderReportDESeq2ReportedgeReportrenderReporttemplateDensitytemplateHistogramtemplateManhattantemplatePvalueDensitytemplatePvalueHistogram

Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHbibtexBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiocStyleBiostringsbitbit64bitopsblobbookdownBSgenomebslibbumphuntercachemcheckmatecliclustercodetoolscolorspacecommonmarkcpp11crayoncurldata.tableDBIDEFormatsDelayedArrayderfinderderfinderHelperDESeq2digestdoRNGedgeRevaluatefansifarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrknitrBootstraplabelinglambda.rlatticelifecyclelimmalocfitlubridatemagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrplyrpngqvalueR6rappdirsRColorBrewerRcppRcppArmadilloRCurlRefManageRreshape2restfulrRhtslibrjsonrlangrmarkdownrngtoolsrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletimechangetinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryaml

Example report using bumphunter results

Leonardo Collado-Torres

Rendered frombumphunterExample.Rmdusingknitr::rmarkdownon Jan 15 2025.

Last update: 2020-04-18
Started: 2015-07-01

Introduction to regionReport

Leonardo Collado-Torres

Rendered fromregionReport.Rmdusingknitr::rmarkdownon Jan 15 2025.

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