Introduction | regioneR and regioneReloaded | Normalized Z-Score | Installation | Quick start | Example dataset: the Alien Genome | Multi Permutation Test with regioneReloaded | Crosswise Analysis and the genoMatriXeR object | Parameters | multiOverlaps | Matrix | Evaluation functions | Randomization functions | Matrix Calculation and visualization | Plot Single permutation test | Plot Dimensionality Reduction | Multi Local Zscore | Single Local ZScore | Analyses of non-square matrices | Session Info
Package: regioneReloaded 1.15.0
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_1.15.0.tar.gz
regioneReloaded_1.15.0.zip(r-4.7)regioneReloaded_1.15.0.zip(r-4.6)regioneReloaded_1.15.0.zip(r-4.5)
regioneReloaded_1.15.0.tgz(r-4.6-any)regioneReloaded_1.15.0.tgz(r-4.5-any)
regioneReloaded_1.15.0.tar.gz(r-4.7-any)regioneReloaded_1.15.0.tar.gz(r-4.6-any)
regioneReloaded_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
regioneReloaded/json (API)
| # 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
Datasets:
- 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-1.15.0(bioc 3.24)regioneReloaded-1.14.0(bioc 3.23)
geneticschipseqdnaseqmethylseqcopynumbervariationclusteringmultiplecomparison
Last updated from:d229c87868. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 198 | ||
| linux-devel-x86_64 | NOTE | 481 | ||
| source / vignettes | OK | 293 | ||
| linux-release-x86_64 | NOTE | 453 | ||
| macos-release-arm64 | NOTE | 247 | ||
| macos-oldrel-arm64 | NOTE | 238 | ||
| windows-devel | NOTE | 431 | ||
| windows-release | NOTE | 398 | ||
| windows-oldrel | NOTE | 404 | ||
| wasm-release | OK | 156 |
Exports:chooseHclustMetcreateUniversecrosswisePermTestgetHClustgetMatrixgetMultiEvaluationgetParametersgMXRmakeCrosswiseMatrixmakeLZMatrixmLZSmultiLocalZscoreplotCrosswiseDimRedplotCrosswiseMatrixplotLocalZScoreMatrixplotSingleLZplotSinglePTrandomizeRegionsPercsimilarRegionSet
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomecachemcigarillocliclustercodetoolscpp11crayoncurlDelayedArrayfarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2ggrepelgluegtableherehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslplyrpngR6rappdirsRColorBrewerRcppRcppEigenRcppTOMLRCurlregioneRreshape2restfulrreticulateRhtslibrjsonrlangrprojrootRsamtoolsRSpectrartracklayerRtsneS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsysUCSC.utilsumapvctrsviridisLitewithrXMLXVectoryaml
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 |
