Files in CL-CHEN-Lab/User_interface_for_Kronos_scRT

R-package and Shiny App interface for the analysis of single cell replication timing data

R/10XtoKronos.R R/BinRepProbPlot.R R/CNV_functions.R R/Clustering.R R/Diagnostic.R R/Imports.R R/KCorr_plot.R R/Load_multiple_df.R R/Plot_functions.R R/RT_changes_plot.R R/String_to_Range.R R/TSNE.R R/Variability_functions.R R/binning.R R/data.R R/fromFastqToBam.R R/launch.R R/right_format.R R/scRT_processing.R R/split_subpop.R README.md inst/Kronos_RT_tools/R/Correlation.R inst/Kronos_RT_tools/R/RTChanges.R inst/Kronos_RT_tools/R/RTclustering.R inst/Kronos_RT_tools/R/Utilities.R inst/Kronos_RT_tools/app.R inst/Kronos_pre_processing/app.R inst/Kronos_processing/R/Diagnostic.R inst/Kronos_processing/app.R inst/Kronos_scRT/Kronos.R inst/Kronos_scRT/modules/10XtoKronos.R inst/Kronos_scRT/modules/Kronos_BinRepProb.R inst/Kronos_scRT/modules/Kronos_Corr.R inst/Kronos_scRT/modules/Kronos_DRed.R inst/Kronos_scRT/modules/Kronos_RT.R inst/Kronos_scRT/modules/Kronos_RefRT.R inst/Kronos_scRT/modules/Kronos_binning.R inst/Kronos_scRT/modules/Kronos_cluster_RT.R inst/Kronos_scRT/modules/Kronos_cnv.R inst/Kronos_scRT/modules/Kronos_compare_RT.R inst/Kronos_scRT/modules/Kronos_compare_TW.R inst/Kronos_scRT/modules/Kronos_diagnostic.R inst/Kronos_scRT/modules/Kronos_fastqtoBAM.R inst/Kronos_scRT/modules/Kronos_scPlots.R inst/Kronos_scRT/modules/Kronos_whoSwho.R inst/Kronos_scRT_tools/R/BinRepProb.R inst/Kronos_scRT_tools/R/Dim_red_sub_pop.R inst/Kronos_scRT_tools/R/Twidth.R inst/Kronos_scRT_tools/R/Utilities.R inst/Kronos_scRT_tools/R/scCN.R inst/Kronos_scRT_tools/R/scPLots.R inst/Kronos_scRT_tools/app.R man/AdjustCN.Rd man/AdjustPerCell.Rd man/Assign_subpop.Rd man/AverageVariability.Rd man/BackGround.Rd man/BamMetrics.Rd man/BinRepProbPlot.Rd man/CallCNV.Rd man/Cluster_enrichment.Rd man/Decompress_if_needed.Rd man/FastqToBam.Rd man/FilterCells.Rd man/GM12878_Reference.Rd man/GenomeBinning.Rd man/HeLa_Reference.Rd man/HeLa_rep1.Rd man/HeLa_rep2.Rd man/IdAdapters.Rd man/Jeff_rep1.Rd man/Jeff_rep2.Rd man/KCorr_plot.Rd man/MCF7.Rd man/MCF7_Reference.Rd man/MCF7_subpop1.Rd man/MCF7_subpop2.Rd man/Plot_bulkRT.Rd man/Pre_processing.Rd man/Prepare_G1G2_phase_cells_forBinRepProb.Rd man/Prepare_S_phase_cells_forBinRepProb.Rd man/Processing.Rd man/RT_changes_plot.Rd man/RT_clustering.Rd man/RT_tools.Rd man/Rebin.Rd man/RebinRT.Rd man/Replication_state.Rd man/String_to_Range.Rd man/T25_75.Rd man/TSNE.Rd man/TW_GenomeAnnotation.Rd man/TW_RTAnnotation.Rd man/TenXtoKronos.Rd man/Twidth.Rd man/Twidth_barplot.Rd man/Twidth_extended_plot.Rd man/Twidth_fit_data.Rd man/Twidth_pval.Rd man/Variability.Rd man/WhoIsWho.Rd man/binning.Rd man/cat_levels.Rd man/diagnostic.Rd man/extractSubpop.Rd man/find_known_sequences.Rd man/load_multiple_df.Rd man/mergefastq.Rd man/mutate_sequence.Rd man/pseudoBulkRT.Rd man/recover_and_mutate.Rd man/rejoinSubpop.Rd man/reshape_and_save.Rd man/rev_com.Rd man/right_format.Rd man/scCNplot.Rd man/scRT_tools.Rd man/scRTplot.Rd man/sequential_trimming.Rd man/shell_interface.Rd man/split_into_categoreis.Rd man/split_subpop.Rd