Files in lucidif/HiCeekR
GUI for Hi-C data analysis
.Rbuildignore
.gitignore
DESCRIPTION
HiCeekR.Rproj
LICENSE
NAMESPACE
R/BCK_vMod3_ICEnormalization2.R
R/HicDetect.R
R/Mod3_ICEnormalization.R
R/VarianceStabCorrection.R
R/WaveletChangePoint.R
R/buildContactMatrices.R
R/directoryInput.R
R/global.R
R/server.R
R/ui.R
R/vApp_projectManager.R
R/vFun_CaTCH_TADs.R
R/vFun_HCRobserveEv.R
R/vFun_HCRwrite&read.R
R/vFun_HiCsegTADs.R
R/vFun_TopDomTADs.R
R/vFun_asBruteMatrix.R
R/vFun_asSymMatrix.R
R/vFun_bamMatching.R
R/vFun_bamToDataframe.R
R/vFun_bed2track.R
R/vFun_callModuleDescription.R
R/vFun_clickBusy.R
R/vFun_detectChromos.R
R/vFun_extractContact.R
R/vFun_findRegionsInBint.R
R/vFun_folderFrame.R
R/vFun_folderList.R
R/vFun_hcrBck.R
R/vFun_heatmaply_tickNames.R
R/vFun_heatmaply_tickOptions.R
R/vFun_hmmDI.R
R/vFun_importAnnotation.R
R/vFun_importChrFromFragList.R
R/vFun_mainNavBar.R
R/vFun_makeBranch.R
R/vFun_makeInset.R
R/vFun_matrixExport.R
R/vFun_matrixWithNames.R
R/vFun_mergeBed.R
R/vFun_obtainName.R
R/vFun_pointin.R
R/vFun_predictTADs.R
R/vFun_prjManager.R
R/vFun_prova.R
R/vFun_readContactMatrix.R
R/vFun_refGenomeEdit.R
R/vFun_regionsInMatrix.R
R/vFun_restartFrom.R
R/vFun_runApp.R
R/vFun_runModule.R
R/vFun_selectFile.R
R/vFun_shinyFilesPath.R
R/vFun_testInput.R
R/vFun_xPanels_moduleStartPanel.R
R/vFun_xPanels_prjManager.R
R/vFun_zScore.R
R/vFuns_PCA.R
R/vFuns_normalization.R
R/vMod0_moduleTemplate.R
R/vMod1_filtering.R
R/vMod1_projectSettings.R
R/vMod2_Binning.R
R/vMod3_ICEnormalization.R
R/vMod3_wavSisNormalization.R
R/vMod4_EpigeneticFeatures.R
R/vMod4_HMMdownstream.R
R/vMod4_HiCsegTADs.R
R/vMod4_PCAdownstream.R
R/vMod4_TopDomTADs.R
R/vMod4_bed2track.R
R/vMod5_NetworksVisualization.R
R/vMod5_heatmapVisualization.R
R/vMod6_summary.R
R/vScript_prelim.R
R/vScript_runModule.R
R/vfun_heatmaply_searchTick.R
R/vfun_javaNsInput.R
README.md
exec/parse_hic_to_matrix.py
hiceekr_manual.pdf
inst/www/dummy.txt
man/DiffHiC_BinningV2_Server.Rd
man/DiffHiC_BinningV2_UI.Rd
man/EpigeneticFeatures_Server.Rd
man/EpigeneticFeatures_UI.Rd
man/FilmodServer.Rd
man/FilmodUI.Rd
man/HCRobserveEvent.Rd
man/HCRprjManager.Rd
man/HCRread.Rd
man/HCRunlist.Rd
man/HCRwrite.Rd
man/HMM_postProcessing_Server.Rd
man/HMM_postProcessing_UI.Rd
man/HiCeekR.Rd
man/TADsV2_Visualization_Server.Rd
man/TADsV2_Visualization_UI.Rd
man/as.brute.matrix.Rd
man/as.sym.matrix.Rd
man/bamMatching.Rd
man/bamPca.Rd
man/bamToDataFrame.Rd
man/bck_diffHic_Normalization_Server.Rd
man/bck_diffHic_Normalization_UI.Rd
man/busyIndServer.Rd
man/busyIndUI.Rd
man/callModuleDescription.Rd
man/chromoR_Normalization_Server.Rd
man/chromoR_Normalization_UI.Rd
man/detectChromos.Rd
man/detectMatrixCoordinate.Rd
man/diffHic_Normalization_Server.Rd
man/diffHic_Normalization_UI.Rd
man/directoryInput.Rd
man/errorFunc.Rd
man/extractContact.Rd
man/findRegionInBint.Rd
man/folderFrame.Rd
man/folderList.Rd
man/hcrBck.Rd
man/hmmDI.Rd
man/importAnnotation.Rd
man/importChrFromFragList.Rd
man/javaNs.Rd
man/mainNav.Rd
man/makeBranch.Rd
man/makeConfig.Rd
man/makeHCRan.Rd
man/makeHCRprj.Rd
man/makeHCRwd.Rd
man/matrixExport.Rd
man/matrixWithNames.Rd
man/mergeBed.Rd
man/moduleBranchPanel.Rd
man/moduleRestartPanel.Rd
man/moduleStartPanel.Rd
man/moduleStartPanel2.Rd
man/moduleTemplate_Server.Rd
man/moduleTemplate_UI.Rd
man/moduleTest.Rd
man/obtainName.Rd
man/obtainWd.Rd
man/pcaMatrixModel.Rd
man/pca_postProcessing_Server.Rd
man/pca_postProcessing_UI.Rd
man/pointin.Rd
man/predictTADs.Rd
man/prjManPanel_analysisSettings.Rd
man/prjManPanel_anlysisInputType.Rd
man/prjManPanel_inputBAM.Rd
man/prjManPanel_inputMatrix.Rd
man/prjManPanel_inputMulti.Rd
man/prjManPanel_loadProject.Rd
man/prjManPanel_newProject.Rd
man/prjManPanel_prjSelector.Rd
man/prjManPanel_reset.Rd
man/prjManPanel_welcome.Rd
man/prjManagerMainUI.Rd
man/prjSettings_Server.Rd
man/prjSettings_UI.Rd
man/readDirectoryInput.Rd
man/refGenomeEdit.Rd
man/regionsInMatrix.Rd
man/restartFrom.Rd
man/searchTicks.Rd
man/selectFile.Rd
man/setHCRwd.Rd
man/shinyDirPath.Rd
man/shinyFilesPath.Rd
man/sum_Server.Rd
man/sum_UI.Rd
man/test.Rd
man/testInfoTable.Rd
man/tickOptions.Rd
man/ticksNames.Rd
man/updateDirectoryInput.Rd
man/zScore.Rd
vignettes/HCRwd.info
vignettes/HiCeekR.Rmd
www/busy_icon.png
www/js/directory_input_binding.js
www/loaderBar.gif
