Installation | Quick start- load datasets from hard drive | Quick start- load datasets from AnnotationHub | Quick start- load user defined GenomicRanges (GRanges) datasets | Frequently asked questions | How to add additional datasets from AnnotationHub? | How to add custom GenomicRanges datasets? | How to add datasets stored as .gff files? | How to add datasets stored as tabular files? | What type of overlaps are reported? | How to change dataset names? | Session info
Package: OGRE 1.17.0
Sven Berres
OGRE: Calculate, visualize and analyse overlap between genomic regions
OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs, or reads from sequencing experiments. Key numbers help analyse the extend of overlaps which can also be visualized at a genomic level.
Authors:
OGRE_1.17.0.tar.gz
OGRE_1.17.0.zip(r-4.7)OGRE_1.17.0.zip(r-4.6)OGRE_1.17.0.zip(r-4.5)
OGRE_1.17.0.tgz(r-4.6-any)OGRE_1.17.0.tgz(r-4.5-any)
OGRE_1.17.0.tar.gz(r-4.7-any)OGRE_1.17.0.tar.gz(r-4.6-any)
OGRE_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OGRE/json (API)
| # Install 'OGRE' in R: |
| install.packages('OGRE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/svenbioinf/ogre/issues
On BioConductor:OGRE-1.17.0(bioc 3.24)OGRE-1.16.0(bioc 3.23)
softwareworkflowstepbiologicalquestionannotationmetagenomicsvisualizationsequencing
Last updated from:5f45d91f63. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 257 | ||
| linux-devel-x86_64 | OK | 612 | ||
| source / vignettes | OK | 357 | ||
| linux-release-x86_64 | OK | 564 | ||
| macos-release-arm64 | OK | 563 | ||
| macos-oldrel-arm64 | OK | 287 | ||
| windows-devel | OK | 463 | ||
| windows-release | OK | 509 | ||
| windows-oldrel | OK | 473 | ||
| wasm-release | OK | 207 |
Exports:addDataSetFromHubaddGRangescovPlotextendGRangesextractPromotersfOverlapsgvizPlotlistPredefinedDataSetsloadAnnotationsmakeExampleGRangesmakeExampleOGREDataSetOGREDataSetOGREDataSetFromDirplotHistreadDataSetFromFolderSHRECsubsetGRangessummarizeOverlapsumPlot
Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrDTensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslotelpillarpkgconfigpngprettyunitsprogresspromisesProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoshinyshinyBSshinydashboardshinyFilessnowsourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2xtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| OGRE package to calculate, analyze and visiualize overlap between annotated genomic region datasets | OGRE-package |
| Add dataSet from AnnotationHub | addDataSetFromHub |
| Add GenomicRanges | addGRanges |
| Coverage plot | covPlot |
| Extend a GRanges object | extendGRanges |
| Extract promoter | extractPromoters |
| Find overlaps | fOverlaps |
| Generate Gviz plot | gvizPlot |
| List predefined datasets | listPredefinedDataSets |
| Load annotation datasets | loadAnnotations |
| Make an example GRanges dataset | makeExampleGRanges |
| Make a example OGRE dataset | makeExampleOGREDataSet |
| BuildOGREDataSet | OGREDataSet |
| BuildOGREDataSetFromDir | OGREDataSetFromDir |
| Plot histogram | plotHist |
| Read dataset(s) from folder | readDataSetFromFolder |
| SHREC SHiny interface for REgion Comparison | SHREC |
| Subset a GRanges object | subsetGRanges |
| Calculates min/max/average overlap | summarizeOverlap |
| Generate summary plot | sumPlot |
