Package: regioneReloaded 1.9.0
Roberto Malinverni
regioneReloaded: RegioneReloaded: Multiple Association for Genomic Region Sets
RegioneReloaded is a package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and the creation of ready-to-publish graphs. It takes over and expands on all the features of its predecessor regioneR. It also incorporates a strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. RegioneReloaded builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs.
Authors:
regioneReloaded_1.9.0.tar.gz
regioneReloaded_1.9.0.zip(r-4.5)regioneReloaded_1.9.0.zip(r-4.4)regioneReloaded_1.9.0.zip(r-4.3)
regioneReloaded_1.9.0.tgz(r-4.4-any)regioneReloaded_1.9.0.tgz(r-4.3-any)
regioneReloaded_1.9.0.tar.gz(r-4.5-noble)regioneReloaded_1.9.0.tar.gz(r-4.4-noble)
regioneReloaded_1.9.0.tgz(r-4.4-emscripten)regioneReloaded_1.9.0.tgz(r-4.3-emscripten)
regioneReloaded.pdf |regioneReloaded.html✨
regioneReloaded/json (API)
NEWS
| # Install 'regioneReloaded' in R: |
| install.packages('regioneReloaded', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rmalinverni/regionereload/issues
- AlienGenome - AlienGenome
- AlienRSList_broad - AlienRSList_broad
- AlienRSList_narrow - AlienRSList_narrow
- cw_Alien_RaR - Cw_Alien_RaR
- cw_Alien_ReG - Cw_Alien_ReG
- cw_Alien_ReG_no_Square - Cw_Alien_ReG_no_Square
- cw_Alien_ReR - Cw_Alien_ReR
- mLZ_regA_ReG - MLZ_regA_ReG
- mLZ_regA_ReG_br - MLZ_regA_ReG_br
- mLZ_regD_ReG - MLZ_regD_ReG
On BioConductor:regioneReloaded-1.9.0(bioc 3.21)regioneReloaded-1.8.0(bioc 3.20)
geneticschipseqdnaseqmethylseqcopynumbervariationclusteringmultiplecomparison
Last updated 2 months agofrom:11e1a346dd. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | OK | Nov 30 2024 |
| R-4.4-mac | OK | Nov 30 2024 |
| R-4.3-win | OK | Nov 30 2024 |
| R-4.3-mac | OK | Nov 30 2024 |
Exports:chooseHclustMetcreateUniversecrosswisePermTestgetHClustgetMatrixgetMultiEvaluationgetParametersgMXRmakeCrosswiseMatrixmakeLZMatrixmLZSmultiLocalZscoreplotCrosswiseDimRedplotCrosswiseMatrixplotLocalZScoreMatrixplotSingleLZplotSinglePTrandomizeRegionsPercsimilarRegionSet
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomecachemcliclustercodetoolscolorspacecpp11crayoncurlDelayedArrayfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggrepelgluegtableherehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplyrpngR6rappdirsRColorBrewerRcppRcppEigenRcppTOMLRCurlregioneRreshape2restfulrreticulateRhtslibrjsonrlangrprojrootRsamtoolsRSpectrartracklayerRtsneS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsumaputf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| AlienGenome | AlienGenome |
| AlienRSList_broad | AlienRSList_broad |
| AlienRSList_narrow | AlienRSList_narrow |
| chooseHclustMet | chooseHclustMet |
| createUniverse | createUniverse |
| crosswisePermTest | crosswisePermTest |
| cw_Alien | cw_Alien |
| cw_Alien_RaR | cw_Alien_RaR |
| cw_Alien_ReG | cw_Alien_ReG |
| cw_Alien_ReG_no_Square | cw_Alien_ReG_no_Square |
| cw_Alien_ReR | cw_Alien_ReR |
| genoMatriXeR Class | genoMatriXeR-class gMXR |
| getHClust | getHClust |
| Get Matrix | getMatrix |
| getMultiEvaluation | getMultiEvaluation |
| getParameters | getParameters |
| makeCrosswiseMatrix | makeCrosswiseMatrix |
| Make Local Z-Score Matrix | makeLZMatrix |
| mLZ_regA_ReG | mLZ_regA_ReG |
| mLZ_regA_ReG_br | mLZ_regA_ReG_br |
| mLZ_regD_ReG | mLZ_regD_ReG |
| multiLocalZscore | multiLocalZscore |
| multiLocalZScore Class | mLZS multiLocalZScore-class |
| plotCrosswiseDimRed | plotCrosswiseDimRed |
| plotCrosswiseMatrix | plotCrosswiseMatrix |
| Plot Local Z-Score Matrix | plotLocalZScoreMatrix |
| plotSingleLZ | plotSingleLZ |
| plotSinglePT | plotSinglePT |
| randomizeRegionsPerc | randomizeRegionsPerc |
| similar RegionSets | similarRegionSet |
