Package: RcmdrPlugin.BiclustGUI 1.1.3.1

RcmdrPlugin.BiclustGUI: 'Rcmdr' Plug-in GUI for Biclustering

A plug-in for R Commander ('Rcmdr'). The package is a Graphical User Interface (GUI) in which several biclustering methods can be executed, followed by diagnostics and plots of the results. Further, the GUI also has the possibility to connect the methods to more general diagnostic packages for biclustering. Biclustering methods from 'biclust', 'fabia', 's4vd', 'iBBiG', 'isa2', 'BiBitR', 'rqubic' and 'BicARE' are implemented. Additionally, 'superbiclust' and 'BcDiag' are also implemented to be able to further investigate results. The GUI also provides a couple of extra utilities to export, save, search through and plot the results. 'RcmdrPlugin.BiclustGUI' also provides a very specific framework for biclustering in which new methods, diagnostics and plots can be added. Scripts were prepared so that R-package developers can freely design their own dialogs in the GUI which can then be added by the maintainer of 'RcmdrPlugin.BiclustGUI'. These scripts do not required any knowledge of 'tcltk' and 'Rcmdr' and are easy to fill in. (Note: rqubic currently requires manual installation through BiocManager::install('rqubic').)

Authors:De Troyer Ewoud, Otava Martin

RcmdrPlugin.BiclustGUI_1.1.3.1.tar.gz
RcmdrPlugin.BiclustGUI_1.1.3.1.zip(r-4.5)RcmdrPlugin.BiclustGUI_1.1.3.1.zip(r-4.4)RcmdrPlugin.BiclustGUI_1.1.3.1.zip(r-4.3)
RcmdrPlugin.BiclustGUI_1.1.3.1.tgz(r-4.4-any)RcmdrPlugin.BiclustGUI_1.1.3.1.tgz(r-4.3-any)
RcmdrPlugin.BiclustGUI_1.1.3.1.tar.gz(r-4.5-noble)RcmdrPlugin.BiclustGUI_1.1.3.1.tar.gz(r-4.4-noble)
RcmdrPlugin.BiclustGUI_1.1.3.1.tgz(r-4.4-emscripten)RcmdrPlugin.BiclustGUI_1.1.3.1.tgz(r-4.3-emscripten)
RcmdrPlugin.BiclustGUI.pdf |RcmdrPlugin.BiclustGUI.html✨
RcmdrPlugin.BiclustGUI/json (API)
NEWS

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

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 1 scripts 855 downloads 134 exports 180 dependencies

Last updated 2 years agofrom:e25feeaf8b. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 18 2024
R-4.5-winNOTEOct 18 2024
R-4.5-linuxNOTEOct 18 2024
R-4.4-winNOTEOct 18 2024
R-4.4-macNOTEOct 18 2024
R-4.3-winNOTEOct 18 2024
R-4.3-macNOTEOct 18 2024

Exports:.add.frame.AssignEnvBiclustGUI.bicare2biclust.binary.activematrix.check.build.button.function.build.command.argument.checkplotgridpref.combine.rows.correctdataforresult.eval.command.fabia2biclust.find.frame.GetEnvBiclustGUI.give.doublequote.grid.matrix.initialize.grid.config.initialize.grid.rows.initialize.new.frames.is.binary.matrix.isbiclustGUIresult.isBiclustresult.isListofBiclustGUIresults.make.correct.frame.makeResultList.makesearchdata.makeSuperbiclustResultList.order.button.frames.output.sparse.txt.putbefore.rcmdr.warning.tobiclust.tobiclust_transf.transform.vector2text.update.biclustering.objectas.ExprSetBCDIAG_isa2biclustbcdiag_WINDOWbcdiaghighlight_WINDOWbcdiagwrite_WINDOWbibit_WINbibit3_BC_GUIbibit3_WINBiBitDendrogram.GUIbibitworkflow_WINBiBitWorkflow.GUIbicare_WINDOWbicare.genesetenrichmentbicare.GUIbicare.makereportbicare.pdatabicare.residuplotbicare.samplesenrichmentbicarebiclust_WINDOWbiclust.bimax.GUIbiclust.quest.GUIbiclust.robust.fusebiclust.robust.fuse.GUIbiclustbimax_WINbiclustCC_WINbiclustextraplots_WINDOWbiclustGUI_helpbiclustguiwebsitelinkbiclustplaid_WINbiclustquest_WINbiclustspectral_WINbiclustXMotif_WINchooseresultsGUIclearresults_WINDOWcluster_templateClusterRowCoverage.GUIColNoiseBC.GUIexport.Biclustexport.fabiaexport.fabia.threshLexportFURBY_WINDOWexportTXT_WINDOWextractbicluster_WINDOWExtractBiclustersGUIExtractBiclustersGUI_generalfabia.biplotfabiabiclust_WINDOWfabialaplace_WINfabiapostprojection_WINfabiaSPARSE_WINfabiasparsenessprojection_WINFindBiclustersfindbiclusters_WINDOWgreenredHeatmapBC.GUIheatmapJI_WINDOWiBBiG_WINimage_WINDOWindexedBicisa.extractisa.GUIisa.scoreplotsisa.summaryisadefault_WINisadefault_WIN_TEMPORARYisaextraplots_WINDOWjaccard_WINDOWMaxBC_WINDOWnewtool_templateopenGUIScriptsopenGUIVignetteparallelCoordinates2parallelCoordinates3plotgridpref_WINDOWplotSuper.GUIredgreenrepeatanalysis.GUIresetworkflow.GUIrobust.fuse.supportrobust.resetrqubic_WINDOWrqubic.GUIs4vd_WINsaveload_WINDOWsaveworkflow.GUIsearch_WINDOWSearchMethodDataSetwdshinylinkstandaloneshinylinkwebsitespfabia.GUIssvd_WINsummaryBICAREsummaryworkflow.GUIsuperbiclust_WINDOWsuperbiclust.GUIsuperbiclust.robust.GUIUpdate.GUIviridiswriteBic.GUI

Dependencies:abindadditivityTestsade4annotateAnnotationDbiaskpassbackportsbase64encBcDiagBiBitRBicAREbiclustBiobaseBiocGenericsBiostringsbitbit64bitopsblobbootbroombslibcachemcarcarDatacaToolscellrangercheckmateclassclicliprclustercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdendextendDerivdigestdoBydplyre1071effectsestimabilityevaluatefabiafansifarverfastmapflexclustfontawesomeforcatsforeachforeignFormulafsgenericsGenomeInfoDbGenomeInfoDbDataggplot2glueGO.dbgplotsgraphgridExtraGSEABasegtablegtoolshavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttriBBiGinsightIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamitoolsmodelrmodeltoolsmulttestmunsellnlmenloptrnnetnortestnumDerivopensslpbkrtestpillarpixmappkgconfigplogrpngprettyunitsprogressproxypurrrquantregR6randomcoloRrappdirsRcmdrRcmdrMiscRColorBrewerRcppRcppArmadilloRcppEigenreadrreadstata13readxlrelimprematchrlangrmarkdownrpartRSQLiterstudioapiRtsnes4vdS4VectorssandwichsassscalesspSparseMstringistringrsuperbiclustsurveysurvivalsystcltk2tibbletidyrtidyselecttinytextzdbUCSC.utilsutf8V8vctrsviridisviridisLitevroomwithrxfunXMLxtableXVectoryamlzlibbioczoo

BiclustGUI Full Guide

Rendered fromGuideBiclustGUI.Rnwusingknitr::knitron Oct 18 2024.

Last update: 2020-07-13
Started: 2016-06-28

Readme and manuals

Help Manual

Help pageTopics
The BiclustGUI packageRcmdrPlugin.BiclustGUI-package RcmdrPlugin.BiclustGUI
GUI Functionsbcdiaghighlight_WINDOW bibit3_BC_GUI BiBitDendrogram.GUI BiBitWorkflow.GUI bicare.genesetenrichment bicare.GUI bicare.makereport bicare.pdata bicare.residuplot bicare.samplesenrichment biclust.bimax.GUI biclust.quest.GUI biclust.robust.fuse biclust.robust.fuse.GUI biclustguiwebsitelink biclustGUI_help chooseresultsGUI ClusterRowCoverage.GUI ColNoiseBC.GUI export.Biclust export.fabia export.fabia.threshL ExtractBiclustersGUI ExtractBiclustersGUI_general fabia.biplot FindBiclusters HeatmapBC.GUI isa.extract isa.GUI isa.scoreplots isa.summary isadefault_WIN_TEMPORARY openGUIScripts openGUIVignette parallelCoordinates2 parallelCoordinates3 plotSuper.GUI repeatanalysis.GUI resetworkflow.GUI robust.reset rqubic.GUI saveworkflow.GUI shinylinkstandalone shinylinkwebsite spfabia.GUI summaryBICARE summaryworkflow.GUI superbiclust.GUI superbiclust.robust.GUI Update.GUI writeBic.GUI
List of Internal Functions.AssignEnvBiclustGUI .bicare2biclust .binary.activematrix.check .build.button.function .build.command.argument .checkplotgridpref .correctdataforresults .eval.command .fabia2biclust .find.frame .GetEnvBiclustGUI .give.doublequote .is.binary.matrix .isa2biclust .isbiclustGUIresult .isBiclustresult .isISA .isListofBiclustGUIresults .make.correct.frame .makeResultList .makesearchdata .makeSuperbiclustResultList .order.button.frames .output.sparse.txt .putbefore .rcmdr.warning .tobiclust .tobiclust_transf .transform.vector2text .update.biclustering.object as.ExprSet BCDIAG_isa2biclust greenred indexedBic redgreen robust.fuse.support SearchMethodData Setwd viridis
Template Script Functions.add.frame .combine.rows .grid.matrix .initialize.grid.config .initialize.grid.rows .initialize.new.frames cluster_template newtool_template
Window Functionsbcdiagwrite_WINDOW bcdiag_WINDOW bibit3_WIN bibitworkflow_WIN bibit_WIN bicarebiclust_WINDOW bicare_WINDOW biclustbimax_WIN biclustCC_WIN biclustextraplots_WINDOW biclustplaid_WIN biclustquest_WIN biclustspectral_WIN biclustXMotif_WIN clearresults_WINDOW exportFURBY_WINDOW exportTXT_WINDOW extractbicluster_WINDOW fabiabiclust_WINDOW fabialaplace_WIN fabiapostprojection_WIN fabiasparsenessprojection_WIN fabiaSPARSE_WIN findbiclusters_WINDOW heatmapJI_WINDOW iBBiG_WIN image_WINDOW isadefault_WIN isaextraplots_WINDOW jaccard_WINDOW MaxBC_WINDOW newmethod_WINDOW newtool_WINDOW plotgridpref_WINDOW rqubic_WINDOW s4vd_WIN saveload_WINDOW search_WINDOW ssvd_WIN superbiclust_WINDOW