Files in xyang2uchicago/NPS

BioTIP: An R package for characterization of Biological Tipping-Point

R/BioTIP-package.R R/BioTIP_update_04202022.R R/data.R README.md examples/BioTIP.wrap_09092022.R examples/code/EB_Zhao2019/1_GSE130146_EB_process.R examples/code/EB_Zhao2019/2_GSE130146_runBioTP.R examples/code/EB_Zhao2019/3_plotHVG_trajectory.R examples/code/EB_Zhao2019/4_plotIc.randomGene.R examples/code/Stability_score.R examples/code/barplot_Jarcard_DNB.Ic.BioTIP.QuanTC_6dbs.R examples/code/gastrulationE8.25_Ibarra-Soria2018/1_E-MTAB-6153_normalized_count.R examples/code/gastrulationE8.25_Ibarra-Soria2018/2_BioTIP_E-MTAB-6153_E8.25.2018.R examples/code/gastrulationE8.25_Ibarra-Soria2018/3_plotHVG_trajectory.R examples/code/gastrulationE8.25_Ibarra-Soria2018/4_plotIc.randomGene.R examples/code/gastrulationE8.25_Pijuan-Sala2019/2.1_E8.25_mesoderm_add.clusterIDs.R examples/code/gastrulationE8.25_Pijuan-Sala2019/2.2_E8.25_mesoderm_runBioTP_different.clustering.R examples/code/gastrulationE8.25_Pijuan-Sala2019/2.3_E8.25_mesoderm_quantify_robustness.R examples/code/gastrulationE8.25_Pijuan-Sala2019/3_E8.25_mesoderm_runBioTIP_stability_1360cell.R examples/code/gastrulationE8.25_Pijuan-Sala2019/4_evaluation.CTS_using2018data.R examples/code/gastrulationE8.25_Pijuan-Sala2019/5_plotIc.randomGene.R examples/code/gastrulationE8.25_Pijuan-Sala2019/BioTIP.tune.parameter.R examples/code/gastrulationE8.25_Pijuan-Sala2019/Stability_score.R examples/code/gastrulationE8.25_Pijuan-Sala2019/myplotIc.R examples/code/hESC_Bargaje2017/1.1_data_matrix_Cluster_CMpath.R examples/code/hESC_Bargaje2017/1.2_data_matrix_timepoint.R examples/code/hESC_Bargaje2017/2.1_hESC_Bargaje2017_add.clusterIDs.R examples/code/hESC_Bargaje2017/2.2_hESC_Bargaje2017_runBioTP_different.clustering.R examples/code/hESC_Bargaje2017/2.3_hESC_Bargaje2017_quantify_robustness.R examples/code/hESC_Bargaje2017/3_hESC_Bargaje2017_runBioTP_stability.R examples/code/hESC_Bargaje2017/4_plotIc.randomGene.R examples/code/lung_Treutlein2014/1_FPKM_preprocess.R examples/code/lung_Treutlein2014/2_Treutlein2014_runBioTP.R examples/code/lung_Treutlein2014/3_BioTIP_GSE52583_feature.selection.plot.R examples/code/lung_Treutlein2014/4_plotIc.randomGene.R examples/code/myplotIc.R examples/code/simulated_EMT/1_QuanTC.data.load_SC3.inputs.R examples/code/simulated_EMT/2_Add.cluster_BioTIP.run.R examples/code/simulated_EMT/3_Plot.R examples/code/simulated_EMT/4_plotIc.randomGene.R examples/result/EB_Zhao2019/2078.variable_RTF.selection.pdf examples/result/EB_Zhao2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/EB_Zhao2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/EB_Zhao2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/EB_Zhao2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/EB_Zhao2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/EB_Zhao2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/EB_Zhao2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/EB_Zhao2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/EB_Zhao2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/EB_Zhao2019/C_SNNGraph_k10/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/EB_Zhao2019/C_SNNGraph_k10/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/EB_Zhao2019/C_SNNGraph_k10/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/EB_Zhao2019/C_Soft/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/EB_Zhao2019/C_Soft/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/EB_Zhao2019/C_Soft/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/EB_Zhao2019/C_Soft_wo.TC/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/EB_Zhao2019/C_Soft_wo.TC/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/EB_Zhao2019/C_Soft_wo.TC/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/EB_Zhao2019/C_Soft_wo.TC/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/EB_Zhao2019/C_consensus_ks17/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/EB_Zhao2019/C_consensus_ks17/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/EB_Zhao2019/C_consensus_ks17/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/EB_Zhao2019/C_consensus_ks19/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/EB_Zhao2019/C_consensus_ks19/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/EB_Zhao2019/C_consensus_ks19/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/EB_Zhao2019/EB_trajectory_libsf_without_endodermPgerm.pdf examples/result/EB_Zhao2019/TSNE_clustering_methods.pdf examples/result/EB_Zhao2019/average.Ic_50randomgene.pdf examples/result/EB_Zhao2019/bar_robustness.pdf examples/result/EB_Zhao2019/cut.meanexpress.logcount.pdf examples/result/Jarcard_CTS.F1_6dbs.pdf examples/result/Venn_CTS_across_3dbs.pdf examples/result/gastrulationE8.25_Ibarra-Soria2018/2294.variable_RTF.selection.pdf examples/result/gastrulationE8.25_Ibarra-Soria2018/average.Ic_50randomgene.pdf examples/result/gastrulationE8.25_Ibarra-Soria2018/bar_robustness_fr.downSizedRuns.pdf examples/result/gastrulationE8.25_Ibarra-Soria2018/cut.meanexpress.logcount.pdf examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/CT.detection_variable.Modulesize_MCIbottom2.pdf examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/CTS.F1_variable.ModuleSize_GS_2CTs.pdf examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_MCIBar_0.1_fdr0.05_minsize30.pdf examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Ibarra-Soria2018/trajectory_UMAP.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph_allcells/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph_allcells/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph_allcells/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4.wo.TC/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4.wo.TC/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4.wo.TC/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k6.wo.TC/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k6.wo.TC/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k6.wo.TC/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k6/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k6/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k6/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks4/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks4/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks4/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks5/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks5/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks5/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks6/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks6/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks6/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks7/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks7/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks7/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks8/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks8/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks8/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/average.Ic_100randomgene.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/bar_robustness.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/CT.detection_variable.MCIbottom2_Modulesize.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/CTS.F1_variable.ModuleSize_GS.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/CTS.F1_variable.ModuleSize_GS_4CTs.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/trajectory_libsf_umap.pdf examples/result/gastrulationE8.25_Pijuan-Sala2019/umap.E8.25_mesoderm_robustness_clustering_methods.pdf examples/result/hESC_Bargaje2017/C_CollectionTime/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_CollectionTime/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_CollectionTime/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_CollectionTime_allcells/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_CollectionTime_allcells/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_CollectionTime_allcells/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_Consensus_929cells/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_Consensus_929cells/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_Consensus_929cells/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_Consensus_allcells/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_Consensus_allcells/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_Consensus_allcells/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_Leiden_0.4/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_Leiden_0.4/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_Leiden_0.4/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_Leiden_1.2/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_Leiden_1.2/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_Leiden_1.2/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_SNNGraph_k10/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_SNNGraph_k10/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_SNNGraph_k10/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_SNNGraph_k20/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_SNNGraph_k20/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_SNNGraph_k20/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_SNNGraph_k20barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_Soft.wo.TC/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_Soft.wo.TC/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_Soft.wo.TC/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_Soft/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_Soft/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_Soft/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_consensus_ks10/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_consensus_ks10/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_consensus_ks10/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_consensus_ks5/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_consensus_ks5/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_consensus_ks5/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_consensus_ks6/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_consensus_ks6/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_consensus_ks6/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_consensus_ks7/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_consensus_ks7/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_consensus_ks7/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_consensus_ks8/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_consensus_ks8/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_consensus_ks8/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/C_consensus_ks9/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/hESC_Bargaje2017/C_consensus_ks9/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf examples/result/hESC_Bargaje2017/C_consensus_ks9/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/hESC_Bargaje2017/QuanTC_run/QuanTC_Bargaje2017_k4_4_time.pdf examples/result/hESC_Bargaje2017/QuanTC_run/k_selection.pdf examples/result/hESC_Bargaje2017/ROC.PS.CTS_clustering.inputs_BioTIP.outputs.pdf examples/result/hESC_Bargaje2017/TSNE.hESC_Bargaje2017_robustness_clustering_methods.pdf examples/result/hESC_Bargaje2017/average.Ic_20randomgene.pdf examples/result/hESC_Bargaje2017/bar_robustness.pdf examples/result/hESC_Bargaje2017/stability/CT.detection_variable.MCIbottom.pdf examples/result/hESC_Bargaje2017/stability/CTS.F1_variable.MCIbottom.pdf examples/result/hESC_Bargaje2017/trajectory_929cells.pdf examples/result/lung_Treutlein2014/C_CollectionTime/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_CollectionTime/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/C_CollectionTime_allcells/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/lung_Treutlein2014/C_CollectionTime_allcells/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_CollectionTime_allcells/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/C_Leiden_0.4/3198.variable_RTF.selection.pdf examples/result/lung_Treutlein2014/C_Leiden_0.4/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/lung_Treutlein2014/C_Leiden_0.4/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_Leiden_0.4/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/C_Leiden_0.8/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_Leiden_1.2/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_Monocle.k4/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/lung_Treutlein2014/C_Monocle.k4/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_Monocle.k4/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/C_SNNGraph_k10/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/lung_Treutlein2014/C_SNNGraph_k10/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_SNNGraph_k10/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/C_SNNGraph_k8/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/lung_Treutlein2014/C_SNNGraph_k8/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_SNNGraph_k8/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/C_Soft.wo.TC/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/lung_Treutlein2014/C_Soft.wo.TC/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_Soft.wo.TC/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/C_Soft/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/lung_Treutlein2014/C_Soft/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_Soft/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/C_by_marker/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/lung_Treutlein2014/C_by_marker/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_by_marker/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/C_by_marker_allcells/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/lung_Treutlein2014/C_by_marker_allcells/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_by_marker_allcells/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/C_consensus_ks3/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/lung_Treutlein2014/C_consensus_ks3/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_consensus_ks3/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/C_consensus_ks5/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/lung_Treutlein2014/C_consensus_ks5/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_consensus_ks5/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/C_consensus_ks7/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf examples/result/lung_Treutlein2014/C_consensus_ks7/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf examples/result/lung_Treutlein2014/C_consensus_ks7/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf examples/result/lung_Treutlein2014/PCA_averageHighgene_standarded_cds_thresholded.pdf examples/result/lung_Treutlein2014/TSNE.AT2.sce.RData_clustering_methods.pdf examples/result/lung_Treutlein2014/average.Ic_50randomgene.pdf examples/result/lung_Treutlein2014/bar_robustness.pdf examples/result/lung_Treutlein2014/pca_averageHighgene_Standardized_trajectory.pdf examples/result/lung_Treutlein2014/stability/CT.detection_variable.MCIbottom2_Modulesize.pdf examples/result/lung_Treutlein2014/stability/CTS.F1_variable.minModuleSize.pdf examples/result/lung_Treutlein2014/trajectory_131cells.pdf examples/result/lung_Treutlein2014/trajectory_196cells.pdf examples/result/lung_Treutlein2014/tsne_131cells_C_Leiden_0.4.pdf examples/result/simulated_EMT/CTS.F1.positive_GS_2CTs.pdf examples/result/simulated_EMT/CTS.F1_GS_2CTs.pdf examples/result/simulated_EMT/C_Leiden_0.4/BioTIP_top1FDR0.05_IC_Delta_SimresultBoth.pdf examples/result/simulated_EMT/C_Leiden_0.4/BioTIP_top1FDR0.05_MCIBar_1_fdr0.05_minsize6.pdf examples/result/simulated_EMT/C_Leiden_0.4/BioTIP_top1FDR0.05_barplot_MCI_Sim_RandomGene.pdf examples/result/simulated_EMT/C_Leiden_0.8/BioTIP_top1FDR0.05_IC_Delta_SimresultBoth.pdf examples/result/simulated_EMT/C_Leiden_0.8/BioTIP_top1FDR0.05_MCIBar_1_fdr0.05_minsize6.pdf examples/result/simulated_EMT/C_Leiden_0.8/BioTIP_top1FDR0.05_barplot_MCI_Sim_RandomGene.pdf examples/result/simulated_EMT/C_Leiden_1.2/BioTIP_top1FDR0.05_IC_Delta_SimresultBoth.pdf examples/result/simulated_EMT/C_Leiden_1.2/BioTIP_top1FDR0.05_MCIBar_1_fdr0.05_minsize6.pdf examples/result/simulated_EMT/C_Leiden_1.2/BioTIP_top1FDR0.05_barplot_MCI_Sim_RandomGene.pdf examples/result/simulated_EMT/C_SNNGraph.k100/BioTIP_top1FDR0.05_IC_Delta_SimresultBoth.pdf examples/result/simulated_EMT/C_SNNGraph.k100/BioTIP_top1FDR0.05_MCIBar_1_fdr0.05_minsize6.pdf examples/result/simulated_EMT/C_SNNGraph.k100/BioTIP_top1FDR0.05_barplot_MCI_Sim_RandomGene.pdf examples/result/simulated_EMT/C_SNNGraph.k20/BioTIP_top1FDR0.05_IC_Delta_SimresultBoth.pdf examples/result/simulated_EMT/C_SNNGraph.k20/BioTIP_top1FDR0.05_MCIBar_1_fdr0.05_minsize6.pdf examples/result/simulated_EMT/C_SNNGraph.k20/BioTIP_top1FDR0.05_barplot_MCI_Sim_RandomGene.pdf examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP_top1FDR0.05_IC_Delta_SimresultBoth.pdf examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP_top1FDR0.05_MCIBar_1_fdr0.05_minsize6.pdf examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP_top1FDR0.05_barplot_MCI_Sim_RandomGene.pdf examples/result/simulated_EMT/average.Ic_10randomgene.pdf examples/result/simulated_EMT/bar_robustness.pdf examples/result/simulated_EMT/boxplot_10genes.pdf examples/result/simulated_EMT/stability/BioTIP_top1FDR0.01_MCIBar_1_fdr0.01_minsize6.pdf examples/result/simulated_EMT/umap.pdf man/BioTIP-package.Rd man/GSE6136_cli.Rd man/GSE6136_matrix.Rd man/ILEF.Rd man/avg.cor.shrink.Rd man/cod.Rd man/cor.shrink.Rd man/gencode.Rd man/getBiotypes.Rd man/getCTS.Rd man/getCluster_methods.Rd man/getIc.Rd man/getIc.new.Rd man/getMCI.Rd man/getMCI_inner.Rd man/getMaxMCImember.Rd man/getMaxStats.Rd man/getNetwork.Rd man/getReadthrough.Rd man/intron.Rd man/optimize.sd_selection.Rd man/plotBar_MCI.Rd man/plotIc.Rd man/plotMaxMCI.Rd man/plot_Ic_Simulation.Rd man/plot_MCI_Simulation.Rd man/plot_SS_Simulation.Rd man/sd_selection.Rd man/simulationMCI.Rd man/simulation_Ic.Rd man/simulation_Ic_sample.Rd results/Jarcard_CTS.F1_6dbs.pdf results/barplot_Jarcard_DNB.Ic.BioTIP.QuanTC_6dbs.R results/robustness.md tutorial/README.md vignettes/BioTIP.Rmd vignettes/subway_map.pdf