Package: GenomicOZone 1.19.0
Hua Zhong
GenomicOZone: Delineate outstanding genomic zones of differential gene activity
The package clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones across the genome. It enables characterization of effects on multiple genes within adaptive genomic neighborhoods, which could arise from genome reorganization, structural variation, or epigenome alteration. It guarantees cluster optimality, linear runtime to sample size, and reproducibility. One can apply it on genome-wide activity measurements such as copy number, transcriptomic, proteomic, and methylation data.
Authors:
GenomicOZone_1.19.0.tar.gz
GenomicOZone_1.19.0.zip(r-4.5)GenomicOZone_1.19.0.zip(r-4.4)GenomicOZone_1.19.0.zip(r-4.3)
GenomicOZone_1.19.0.tgz(r-4.4-any)GenomicOZone_1.19.0.tgz(r-4.3-any)
GenomicOZone_1.19.0.tar.gz(r-4.5-noble)GenomicOZone_1.19.0.tar.gz(r-4.4-noble)
GenomicOZone_1.19.0.tgz(r-4.4-emscripten)GenomicOZone_1.19.0.tgz(r-4.3-emscripten)
GenomicOZone.pdf |GenomicOZone.html✨
GenomicOZone/json (API)
NEWS
| # Install 'GenomicOZone' in R: |
| install.packages('GenomicOZone', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:GenomicOZone-1.19.0(bioc 3.20)GenomicOZone-1.18.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:7892b777aa
Exports:extract_genesextract_outstanding_zonesextract_zone_expressionextract_zonesGenomicOZoneGOZDataSetplot_chromosomesplot_genomeplot_zones
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobbroombroom.helpersBSgenomebslibcachemcheckmateCkmeans.1d.dpclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggbioggplot2ggstatsgluegraphgridExtragtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglabelledlambda.rlatticelazyevallifecyclelsrmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslOrganismDbipatchworkpillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericspurrrR6rappdirsRBGLrbibutilsRColorBrewerRcppRCurlRdpackreadrreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakertzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Extract annotation of genes, zones, outstanding zones, and expression of zones | extract_genes extract_outputs extract_outstanding_zones extract_zones extract_zone_expression |
| Generate plots of genome, chromosomes and zones. | generate_plots plot_chromosomes plot_genome plot_zones |
| Delineate outstanding genomic zones | GenomicOZone |
| Create an object for outstanding genomic zone analysis | GOZDataSet |
