├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── HiCeekR.Rproj ├── LICENSE ├── NAMESPACE ├── R ├── BCK_vMod3_ICEnormalization2.R ├── HicDetect.R ├── Mod3_ICEnormalization.R ├── VarianceStabCorrection.R ├── WaveletChangePoint.R ├── buildContactMatrices.R ├── directoryInput.R ├── global.R ├── server.R ├── ui.R ├── vApp_projectManager.R ├── vFun_CaTCH_TADs.R ├── vFun_HCRobserveEv.R ├── vFun_HCRwrite&read.R ├── vFun_HiCsegTADs.R ├── vFun_TopDomTADs.R ├── vFun_asBruteMatrix.R ├── vFun_asSymMatrix.R ├── vFun_bamMatching.R ├── vFun_bamToDataframe.R ├── vFun_bed2track.R ├── vFun_callModuleDescription.R ├── vFun_clickBusy.R ├── vFun_detectChromos.R ├── vFun_extractContact.R ├── vFun_findRegionsInBint.R ├── vFun_folderFrame.R ├── vFun_folderList.R ├── vFun_hcrBck.R ├── vFun_heatmaply_tickNames.R ├── vFun_heatmaply_tickOptions.R ├── vFun_hmmDI.R ├── vFun_importAnnotation.R ├── vFun_importChrFromFragList.R ├── vFun_mainNavBar.R ├── vFun_makeBranch.R ├── vFun_makeInset.R ├── vFun_matrixExport.R ├── vFun_matrixWithNames.R ├── vFun_mergeBed.R ├── vFun_obtainName.R ├── vFun_pointin.R ├── vFun_predictTADs.R ├── vFun_prjManager.R ├── vFun_prova.R ├── vFun_readContactMatrix.R ├── vFun_refGenomeEdit.R ├── vFun_regionsInMatrix.R ├── vFun_restartFrom.R ├── vFun_runApp.R ├── vFun_runModule.R ├── vFun_selectFile.R ├── vFun_shinyFilesPath.R ├── vFun_testInput.R ├── vFun_xPanels_moduleStartPanel.R ├── vFun_xPanels_prjManager.R ├── vFun_zScore.R ├── vFuns_PCA.R ├── vFuns_normalization.R ├── vMod0_moduleTemplate.R ├── vMod1_filtering.R ├── vMod1_projectSettings.R ├── vMod2_Binning.R ├── vMod3_ICEnormalization.R ├── vMod3_wavSisNormalization.R ├── vMod4_EpigeneticFeatures.R ├── vMod4_HMMdownstream.R ├── vMod4_HiCsegTADs.R ├── vMod4_PCAdownstream.R ├── vMod4_TopDomTADs.R ├── vMod4_bed2track.R ├── vMod5_NetworksVisualization.R ├── vMod5_heatmapVisualization.R ├── vMod6_summary.R ├── vScript_prelim.R ├── vScript_runModule.R ├── vfun_heatmaply_searchTick.R └── vfun_javaNsInput.R ├── README.md ├── exec └── parse_hic_to_matrix.py ├── hiceekr_manual.pdf ├── inst └── www │ └── dummy.txt ├── man ├── DiffHiC_BinningV2_Server.Rd ├── DiffHiC_BinningV2_UI.Rd ├── EpigeneticFeatures_Server.Rd ├── EpigeneticFeatures_UI.Rd ├── FilmodServer.Rd ├── FilmodUI.Rd ├── HCRobserveEvent.Rd ├── HCRprjManager.Rd ├── HCRread.Rd ├── HCRunlist.Rd ├── HCRwrite.Rd ├── HMM_postProcessing_Server.Rd ├── HMM_postProcessing_UI.Rd ├── HiCeekR.Rd ├── TADsV2_Visualization_Server.Rd ├── TADsV2_Visualization_UI.Rd ├── as.brute.matrix.Rd ├── as.sym.matrix.Rd ├── bamMatching.Rd ├── bamPca.Rd ├── bamToDataFrame.Rd ├── bck_diffHic_Normalization_Server.Rd ├── bck_diffHic_Normalization_UI.Rd ├── busyIndServer.Rd ├── busyIndUI.Rd ├── callModuleDescription.Rd ├── chromoR_Normalization_Server.Rd ├── chromoR_Normalization_UI.Rd ├── detectChromos.Rd ├── detectMatrixCoordinate.Rd ├── diffHic_Normalization_Server.Rd ├── diffHic_Normalization_UI.Rd ├── directoryInput.Rd ├── errorFunc.Rd ├── extractContact.Rd ├── findRegionInBint.Rd ├── folderFrame.Rd ├── folderList.Rd ├── hcrBck.Rd ├── hmmDI.Rd ├── importAnnotation.Rd ├── importChrFromFragList.Rd ├── javaNs.Rd ├── mainNav.Rd ├── makeBranch.Rd ├── makeConfig.Rd ├── makeHCRan.Rd ├── makeHCRprj.Rd ├── makeHCRwd.Rd ├── matrixExport.Rd ├── matrixWithNames.Rd ├── mergeBed.Rd ├── moduleBranchPanel.Rd ├── moduleRestartPanel.Rd ├── moduleStartPanel.Rd ├── moduleStartPanel2.Rd ├── moduleTemplate_Server.Rd ├── moduleTemplate_UI.Rd ├── moduleTest.Rd ├── obtainName.Rd ├── obtainWd.Rd ├── pcaMatrixModel.Rd ├── pca_postProcessing_Server.Rd ├── pca_postProcessing_UI.Rd ├── pointin.Rd ├── predictTADs.Rd ├── prjManPanel_analysisSettings.Rd ├── prjManPanel_anlysisInputType.Rd ├── prjManPanel_inputBAM.Rd ├── prjManPanel_inputMatrix.Rd ├── prjManPanel_inputMulti.Rd ├── prjManPanel_loadProject.Rd ├── prjManPanel_newProject.Rd ├── prjManPanel_prjSelector.Rd ├── prjManPanel_reset.Rd ├── prjManPanel_welcome.Rd ├── prjManagerMainUI.Rd ├── prjSettings_Server.Rd ├── prjSettings_UI.Rd ├── readDirectoryInput.Rd ├── refGenomeEdit.Rd ├── regionsInMatrix.Rd ├── restartFrom.Rd ├── searchTicks.Rd ├── selectFile.Rd ├── setHCRwd.Rd ├── shinyDirPath.Rd ├── shinyFilesPath.Rd ├── sum_Server.Rd ├── sum_UI.Rd ├── test.Rd ├── testInfoTable.Rd ├── tickOptions.Rd ├── ticksNames.Rd ├── updateDirectoryInput.Rd └── zScore.Rd ├── vignettes ├── HCRwd.info └── HiCeekR.Rmd └── www ├── busy_icon.png ├── js └── directory_input_binding.js └── loaderBar.gif /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /HiCeekR.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/HiCeekR.Rproj -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/LICENSE -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | # Generated by roxygen2: do not edit by hand 2 | 3 | export(HiCeekR) 4 | -------------------------------------------------------------------------------- /R/BCK_vMod3_ICEnormalization2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/BCK_vMod3_ICEnormalization2.R -------------------------------------------------------------------------------- /R/HicDetect.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/HicDetect.R -------------------------------------------------------------------------------- /R/Mod3_ICEnormalization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/Mod3_ICEnormalization.R -------------------------------------------------------------------------------- /R/VarianceStabCorrection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/VarianceStabCorrection.R -------------------------------------------------------------------------------- /R/WaveletChangePoint.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/WaveletChangePoint.R -------------------------------------------------------------------------------- /R/buildContactMatrices.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/buildContactMatrices.R -------------------------------------------------------------------------------- /R/directoryInput.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/directoryInput.R -------------------------------------------------------------------------------- /R/global.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/global.R -------------------------------------------------------------------------------- /R/server.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/server.R -------------------------------------------------------------------------------- /R/ui.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/ui.R -------------------------------------------------------------------------------- /R/vApp_projectManager.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vApp_projectManager.R -------------------------------------------------------------------------------- /R/vFun_CaTCH_TADs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_CaTCH_TADs.R -------------------------------------------------------------------------------- /R/vFun_HCRobserveEv.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_HCRobserveEv.R -------------------------------------------------------------------------------- /R/vFun_HCRwrite&read.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_HCRwrite&read.R -------------------------------------------------------------------------------- /R/vFun_HiCsegTADs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_HiCsegTADs.R -------------------------------------------------------------------------------- /R/vFun_TopDomTADs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_TopDomTADs.R -------------------------------------------------------------------------------- /R/vFun_asBruteMatrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_asBruteMatrix.R -------------------------------------------------------------------------------- /R/vFun_asSymMatrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_asSymMatrix.R -------------------------------------------------------------------------------- /R/vFun_bamMatching.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_bamMatching.R -------------------------------------------------------------------------------- /R/vFun_bamToDataframe.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_bamToDataframe.R -------------------------------------------------------------------------------- /R/vFun_bed2track.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_bed2track.R -------------------------------------------------------------------------------- /R/vFun_callModuleDescription.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_callModuleDescription.R -------------------------------------------------------------------------------- /R/vFun_clickBusy.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_clickBusy.R -------------------------------------------------------------------------------- /R/vFun_detectChromos.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_detectChromos.R -------------------------------------------------------------------------------- /R/vFun_extractContact.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_extractContact.R -------------------------------------------------------------------------------- /R/vFun_findRegionsInBint.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_findRegionsInBint.R -------------------------------------------------------------------------------- /R/vFun_folderFrame.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_folderFrame.R -------------------------------------------------------------------------------- /R/vFun_folderList.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_folderList.R -------------------------------------------------------------------------------- /R/vFun_hcrBck.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_hcrBck.R -------------------------------------------------------------------------------- /R/vFun_heatmaply_tickNames.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_heatmaply_tickNames.R -------------------------------------------------------------------------------- /R/vFun_heatmaply_tickOptions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_heatmaply_tickOptions.R -------------------------------------------------------------------------------- /R/vFun_hmmDI.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_hmmDI.R -------------------------------------------------------------------------------- /R/vFun_importAnnotation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_importAnnotation.R -------------------------------------------------------------------------------- /R/vFun_importChrFromFragList.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_importChrFromFragList.R -------------------------------------------------------------------------------- /R/vFun_mainNavBar.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_mainNavBar.R -------------------------------------------------------------------------------- /R/vFun_makeBranch.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_makeBranch.R -------------------------------------------------------------------------------- /R/vFun_makeInset.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_makeInset.R -------------------------------------------------------------------------------- /R/vFun_matrixExport.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_matrixExport.R -------------------------------------------------------------------------------- /R/vFun_matrixWithNames.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_matrixWithNames.R -------------------------------------------------------------------------------- /R/vFun_mergeBed.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_mergeBed.R -------------------------------------------------------------------------------- /R/vFun_obtainName.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_obtainName.R -------------------------------------------------------------------------------- /R/vFun_pointin.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_pointin.R -------------------------------------------------------------------------------- /R/vFun_predictTADs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_predictTADs.R -------------------------------------------------------------------------------- /R/vFun_prjManager.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_prjManager.R -------------------------------------------------------------------------------- /R/vFun_prova.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_prova.R -------------------------------------------------------------------------------- /R/vFun_readContactMatrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_readContactMatrix.R -------------------------------------------------------------------------------- /R/vFun_refGenomeEdit.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_refGenomeEdit.R -------------------------------------------------------------------------------- /R/vFun_regionsInMatrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_regionsInMatrix.R -------------------------------------------------------------------------------- /R/vFun_restartFrom.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_restartFrom.R -------------------------------------------------------------------------------- /R/vFun_runApp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_runApp.R -------------------------------------------------------------------------------- /R/vFun_runModule.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_runModule.R -------------------------------------------------------------------------------- /R/vFun_selectFile.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_selectFile.R -------------------------------------------------------------------------------- /R/vFun_shinyFilesPath.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_shinyFilesPath.R -------------------------------------------------------------------------------- /R/vFun_testInput.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_testInput.R -------------------------------------------------------------------------------- /R/vFun_xPanels_moduleStartPanel.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_xPanels_moduleStartPanel.R -------------------------------------------------------------------------------- /R/vFun_xPanels_prjManager.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_xPanels_prjManager.R -------------------------------------------------------------------------------- /R/vFun_zScore.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFun_zScore.R -------------------------------------------------------------------------------- /R/vFuns_PCA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFuns_PCA.R -------------------------------------------------------------------------------- /R/vFuns_normalization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vFuns_normalization.R -------------------------------------------------------------------------------- /R/vMod0_moduleTemplate.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod0_moduleTemplate.R -------------------------------------------------------------------------------- /R/vMod1_filtering.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod1_filtering.R -------------------------------------------------------------------------------- /R/vMod1_projectSettings.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod1_projectSettings.R -------------------------------------------------------------------------------- /R/vMod2_Binning.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod2_Binning.R -------------------------------------------------------------------------------- /R/vMod3_ICEnormalization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod3_ICEnormalization.R -------------------------------------------------------------------------------- /R/vMod3_wavSisNormalization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod3_wavSisNormalization.R -------------------------------------------------------------------------------- /R/vMod4_EpigeneticFeatures.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod4_EpigeneticFeatures.R -------------------------------------------------------------------------------- /R/vMod4_HMMdownstream.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod4_HMMdownstream.R -------------------------------------------------------------------------------- /R/vMod4_HiCsegTADs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod4_HiCsegTADs.R -------------------------------------------------------------------------------- /R/vMod4_PCAdownstream.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod4_PCAdownstream.R -------------------------------------------------------------------------------- /R/vMod4_TopDomTADs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod4_TopDomTADs.R -------------------------------------------------------------------------------- /R/vMod4_bed2track.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod4_bed2track.R -------------------------------------------------------------------------------- /R/vMod5_NetworksVisualization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod5_NetworksVisualization.R -------------------------------------------------------------------------------- /R/vMod5_heatmapVisualization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod5_heatmapVisualization.R -------------------------------------------------------------------------------- /R/vMod6_summary.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vMod6_summary.R -------------------------------------------------------------------------------- /R/vScript_prelim.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vScript_prelim.R -------------------------------------------------------------------------------- /R/vScript_runModule.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vScript_runModule.R -------------------------------------------------------------------------------- /R/vfun_heatmaply_searchTick.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vfun_heatmaply_searchTick.R -------------------------------------------------------------------------------- /R/vfun_javaNsInput.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/R/vfun_javaNsInput.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/README.md -------------------------------------------------------------------------------- /exec/parse_hic_to_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/exec/parse_hic_to_matrix.py -------------------------------------------------------------------------------- /hiceekr_manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/hiceekr_manual.pdf -------------------------------------------------------------------------------- /inst/www/dummy.txt: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /man/DiffHiC_BinningV2_Server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/DiffHiC_BinningV2_Server.Rd -------------------------------------------------------------------------------- /man/DiffHiC_BinningV2_UI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/DiffHiC_BinningV2_UI.Rd -------------------------------------------------------------------------------- /man/EpigeneticFeatures_Server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/EpigeneticFeatures_Server.Rd -------------------------------------------------------------------------------- /man/EpigeneticFeatures_UI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/EpigeneticFeatures_UI.Rd -------------------------------------------------------------------------------- /man/FilmodServer.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/FilmodServer.Rd -------------------------------------------------------------------------------- /man/FilmodUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/FilmodUI.Rd -------------------------------------------------------------------------------- /man/HCRobserveEvent.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/HCRobserveEvent.Rd -------------------------------------------------------------------------------- /man/HCRprjManager.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/HCRprjManager.Rd -------------------------------------------------------------------------------- /man/HCRread.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/HCRread.Rd -------------------------------------------------------------------------------- /man/HCRunlist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/HCRunlist.Rd -------------------------------------------------------------------------------- /man/HCRwrite.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/HCRwrite.Rd -------------------------------------------------------------------------------- /man/HMM_postProcessing_Server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/HMM_postProcessing_Server.Rd -------------------------------------------------------------------------------- /man/HMM_postProcessing_UI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/HMM_postProcessing_UI.Rd -------------------------------------------------------------------------------- /man/HiCeekR.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/HiCeekR.Rd -------------------------------------------------------------------------------- /man/TADsV2_Visualization_Server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/TADsV2_Visualization_Server.Rd -------------------------------------------------------------------------------- /man/TADsV2_Visualization_UI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/TADsV2_Visualization_UI.Rd -------------------------------------------------------------------------------- /man/as.brute.matrix.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/as.brute.matrix.Rd -------------------------------------------------------------------------------- /man/as.sym.matrix.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/as.sym.matrix.Rd -------------------------------------------------------------------------------- /man/bamMatching.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/bamMatching.Rd -------------------------------------------------------------------------------- /man/bamPca.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/bamPca.Rd -------------------------------------------------------------------------------- /man/bamToDataFrame.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/bamToDataFrame.Rd -------------------------------------------------------------------------------- /man/bck_diffHic_Normalization_Server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/bck_diffHic_Normalization_Server.Rd -------------------------------------------------------------------------------- /man/bck_diffHic_Normalization_UI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/bck_diffHic_Normalization_UI.Rd -------------------------------------------------------------------------------- /man/busyIndServer.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/busyIndServer.Rd -------------------------------------------------------------------------------- /man/busyIndUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/busyIndUI.Rd -------------------------------------------------------------------------------- /man/callModuleDescription.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/callModuleDescription.Rd -------------------------------------------------------------------------------- /man/chromoR_Normalization_Server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/chromoR_Normalization_Server.Rd -------------------------------------------------------------------------------- /man/chromoR_Normalization_UI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/chromoR_Normalization_UI.Rd -------------------------------------------------------------------------------- /man/detectChromos.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/detectChromos.Rd -------------------------------------------------------------------------------- /man/detectMatrixCoordinate.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/detectMatrixCoordinate.Rd -------------------------------------------------------------------------------- /man/diffHic_Normalization_Server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/diffHic_Normalization_Server.Rd -------------------------------------------------------------------------------- /man/diffHic_Normalization_UI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/diffHic_Normalization_UI.Rd -------------------------------------------------------------------------------- /man/directoryInput.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/directoryInput.Rd -------------------------------------------------------------------------------- /man/errorFunc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/errorFunc.Rd -------------------------------------------------------------------------------- /man/extractContact.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/extractContact.Rd -------------------------------------------------------------------------------- /man/findRegionInBint.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/findRegionInBint.Rd -------------------------------------------------------------------------------- /man/folderFrame.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/folderFrame.Rd -------------------------------------------------------------------------------- /man/folderList.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/folderList.Rd -------------------------------------------------------------------------------- /man/hcrBck.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/hcrBck.Rd -------------------------------------------------------------------------------- /man/hmmDI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/hmmDI.Rd -------------------------------------------------------------------------------- /man/importAnnotation.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/importAnnotation.Rd -------------------------------------------------------------------------------- /man/importChrFromFragList.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/importChrFromFragList.Rd -------------------------------------------------------------------------------- /man/javaNs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/javaNs.Rd -------------------------------------------------------------------------------- /man/mainNav.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/mainNav.Rd -------------------------------------------------------------------------------- /man/makeBranch.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/makeBranch.Rd -------------------------------------------------------------------------------- /man/makeConfig.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/makeConfig.Rd -------------------------------------------------------------------------------- /man/makeHCRan.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/makeHCRan.Rd -------------------------------------------------------------------------------- /man/makeHCRprj.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/makeHCRprj.Rd -------------------------------------------------------------------------------- /man/makeHCRwd.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/makeHCRwd.Rd -------------------------------------------------------------------------------- /man/matrixExport.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/matrixExport.Rd -------------------------------------------------------------------------------- /man/matrixWithNames.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/matrixWithNames.Rd -------------------------------------------------------------------------------- /man/mergeBed.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/mergeBed.Rd -------------------------------------------------------------------------------- /man/moduleBranchPanel.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/moduleBranchPanel.Rd -------------------------------------------------------------------------------- /man/moduleRestartPanel.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/moduleRestartPanel.Rd -------------------------------------------------------------------------------- /man/moduleStartPanel.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/moduleStartPanel.Rd -------------------------------------------------------------------------------- /man/moduleStartPanel2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/moduleStartPanel2.Rd -------------------------------------------------------------------------------- /man/moduleTemplate_Server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/moduleTemplate_Server.Rd -------------------------------------------------------------------------------- /man/moduleTemplate_UI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/moduleTemplate_UI.Rd -------------------------------------------------------------------------------- /man/moduleTest.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/moduleTest.Rd -------------------------------------------------------------------------------- /man/obtainName.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/obtainName.Rd -------------------------------------------------------------------------------- /man/obtainWd.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/obtainWd.Rd -------------------------------------------------------------------------------- /man/pcaMatrixModel.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/pcaMatrixModel.Rd -------------------------------------------------------------------------------- /man/pca_postProcessing_Server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/pca_postProcessing_Server.Rd -------------------------------------------------------------------------------- /man/pca_postProcessing_UI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/pca_postProcessing_UI.Rd -------------------------------------------------------------------------------- /man/pointin.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/pointin.Rd -------------------------------------------------------------------------------- /man/predictTADs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/predictTADs.Rd -------------------------------------------------------------------------------- /man/prjManPanel_analysisSettings.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjManPanel_analysisSettings.Rd -------------------------------------------------------------------------------- /man/prjManPanel_anlysisInputType.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjManPanel_anlysisInputType.Rd -------------------------------------------------------------------------------- /man/prjManPanel_inputBAM.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjManPanel_inputBAM.Rd -------------------------------------------------------------------------------- /man/prjManPanel_inputMatrix.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjManPanel_inputMatrix.Rd -------------------------------------------------------------------------------- /man/prjManPanel_inputMulti.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjManPanel_inputMulti.Rd -------------------------------------------------------------------------------- /man/prjManPanel_loadProject.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjManPanel_loadProject.Rd -------------------------------------------------------------------------------- /man/prjManPanel_newProject.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjManPanel_newProject.Rd -------------------------------------------------------------------------------- /man/prjManPanel_prjSelector.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjManPanel_prjSelector.Rd -------------------------------------------------------------------------------- /man/prjManPanel_reset.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjManPanel_reset.Rd -------------------------------------------------------------------------------- /man/prjManPanel_welcome.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjManPanel_welcome.Rd -------------------------------------------------------------------------------- /man/prjManagerMainUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjManagerMainUI.Rd -------------------------------------------------------------------------------- /man/prjSettings_Server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjSettings_Server.Rd -------------------------------------------------------------------------------- /man/prjSettings_UI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/prjSettings_UI.Rd -------------------------------------------------------------------------------- /man/readDirectoryInput.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/readDirectoryInput.Rd -------------------------------------------------------------------------------- /man/refGenomeEdit.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/refGenomeEdit.Rd -------------------------------------------------------------------------------- /man/regionsInMatrix.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/regionsInMatrix.Rd -------------------------------------------------------------------------------- /man/restartFrom.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/restartFrom.Rd -------------------------------------------------------------------------------- /man/searchTicks.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/searchTicks.Rd -------------------------------------------------------------------------------- /man/selectFile.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/selectFile.Rd -------------------------------------------------------------------------------- /man/setHCRwd.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/setHCRwd.Rd -------------------------------------------------------------------------------- /man/shinyDirPath.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/shinyDirPath.Rd -------------------------------------------------------------------------------- /man/shinyFilesPath.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/shinyFilesPath.Rd -------------------------------------------------------------------------------- /man/sum_Server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/sum_Server.Rd -------------------------------------------------------------------------------- /man/sum_UI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/sum_UI.Rd -------------------------------------------------------------------------------- /man/test.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/test.Rd -------------------------------------------------------------------------------- /man/testInfoTable.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/testInfoTable.Rd -------------------------------------------------------------------------------- /man/tickOptions.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/tickOptions.Rd -------------------------------------------------------------------------------- /man/ticksNames.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/ticksNames.Rd -------------------------------------------------------------------------------- /man/updateDirectoryInput.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/updateDirectoryInput.Rd -------------------------------------------------------------------------------- /man/zScore.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/man/zScore.Rd -------------------------------------------------------------------------------- /vignettes/HCRwd.info: -------------------------------------------------------------------------------- 1 | /test/ 2 | -------------------------------------------------------------------------------- /vignettes/HiCeekR.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/vignettes/HiCeekR.Rmd -------------------------------------------------------------------------------- /www/busy_icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/www/busy_icon.png -------------------------------------------------------------------------------- /www/js/directory_input_binding.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/www/js/directory_input_binding.js -------------------------------------------------------------------------------- /www/loaderBar.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lucidif/HiCeekR/HEAD/www/loaderBar.gif --------------------------------------------------------------------------------