Files in xyang2uchicago/NPS
BioTIP: An R package for characterization of Biological Tipping-Point
.DS_Store
DESCRIPTION
NAMESPACE
R/.DS_Store
R/.Rhistory
R/BioTIP-package.R
R/BioTIP_update_04202022.R
R/data.R
README.md
data/GSE6136_cli.RData
data/GSE6136_matrix.RData
data/ILEF.RData
data/cod.RData
data/gencode.RData
data/intron.RData
data/membersL.RData
data/subcounts.optimize_80per.RData
examples/.DS_Store
examples/code/.DS_Store
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/EB_Zhao2019/readme.txt
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_Ibarra-Soria2018/readme.txt
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/readme.txt
examples/code/hESC_Bargaje2017/.Rhistory
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/hESC_Bargaje2017/readme.txt
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/lung_Treutlein2014/readme.txt
examples/code/myplotIc.R
examples/code/simulated_EMT/0_export_data.m
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/code/simulated_EMT/readme.txt
examples/data/.DS_Store
examples/data/EB_Zhao2019/.DS_Store
examples/data/gastrulationE8.25_Ibarra-Soria2018/sce_16subtype.RData
examples/data/gastrulationE8.25_Pijuan-Sala2019/sce_E8.25_HEP.RData
examples/data/hESC_Bargaje2017/sce_hESC.RData
examples/data/lung_Treutlein2014/AT2.sce.RData
examples/data/lung_Treutlein2014/sce.RData
examples/data/sce.GSE130146_noenderdormPgerm.RData
examples/data/simulated_EMT/sce.RData
examples/result/.DS_Store
examples/result/EB_Zhao2019/2078.variable_RTF.selection.pdf
examples/result/EB_Zhao2019/C_Leiden_0.4/BioTIP.res.RData
examples/result/EB_Zhao2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_CTS.candidate.RData
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_IC_sim.Permutation.RData
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_SimuMCI_100_0.1_fdr0.2_minsize30.RData
examples/result/EB_Zhao2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
examples/result/EB_Zhao2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
examples/result/EB_Zhao2019/C_Leiden_0.8/BioTIP.res.RData
examples/result/EB_Zhao2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_CTS.candidate.RData
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_IC_sim.Permutation.RData
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_SimuMCI_100_0.1_fdr0.2_minsize30.RData
examples/result/EB_Zhao2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
examples/result/EB_Zhao2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
examples/result/EB_Zhao2019/C_Leiden_1.2/BioTIP.res.RData
examples/result/EB_Zhao2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_CTS.candidate.RData
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_IC_sim.Permutation.RData
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_SimuMCI_100_0.1_fdr0.2_minsize30.RData
examples/result/EB_Zhao2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
examples/result/EB_Zhao2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
examples/result/EB_Zhao2019/C_SNNGraph_k10/BioTIP.res.RData
examples/result/EB_Zhao2019/C_SNNGraph_k10/BioTIP_top0.1FDR0.2_CTS.candidate.RData
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_IC_sim.Permutation.RData
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_SimuMCI_100_0.1_fdr0.2_minsize30.RData
examples/result/EB_Zhao2019/C_SNNGraph_k10/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
examples/result/EB_Zhao2019/C_SNNGraph_k10/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
examples/result/EB_Zhao2019/C_Soft/BioTIP.res.RData
examples/result/EB_Zhao2019/C_Soft/BioTIP_top0.1FDR0.2_CTS.candidate.RData
examples/result/EB_Zhao2019/C_Soft/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
examples/result/EB_Zhao2019/C_Soft/BioTIP_top0.1FDR0.2_IC_sim.Permutation.RData
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_SimuMCI_100_0.1_fdr0.2_minsize30.RData
examples/result/EB_Zhao2019/C_Soft/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
examples/result/EB_Zhao2019/C_Soft/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
examples/result/EB_Zhao2019/C_Soft_wo.TC/BioTIP.res.RData
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.res.RData
examples/result/EB_Zhao2019/C_consensus_ks17/BioTIP_top0.1FDR0.2_CTS.candidate.RData
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_IC_sim.Permutation.RData
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_SimuMCI_100_0.1_fdr0.2_minsize30.RData
examples/result/EB_Zhao2019/C_consensus_ks17/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
examples/result/EB_Zhao2019/C_consensus_ks17/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
examples/result/EB_Zhao2019/C_consensus_ks19/BioTIP.res.RData
examples/result/EB_Zhao2019/C_consensus_ks19/BioTIP_top0.1FDR0.2_CTS.candidate.RData
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_IC_sim.Permutation.RData
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_SimuMCI_100_0.1_fdr0.2_minsize30.RData
examples/result/EB_Zhao2019/C_consensus_ks19/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
examples/result/EB_Zhao2019/C_consensus_ks19/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
examples/result/EB_Zhao2019/EB_trajectory_libsf_without_endodermPgerm.pdf
examples/result/EB_Zhao2019/GS.CTS.CMP_at.least.3identificaitons_fr.6predicitons.txt
examples/result/EB_Zhao2019/GS.CTS.MEP_at.least.3identificaitons_fr.5predicitons.txt
examples/result/EB_Zhao2019/GS.CTS.MP_at.least.4identificaitons_fr.9predicitons.txt
examples/result/EB_Zhao2019/QuanTC_run/CTS.RData
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/best.matched.clusterID.RData
examples/result/EB_Zhao2019/cut.meanexpress.logcount.pdf
examples/result/EB_Zhao2019/existing.Ic_50gene.RData
examples/result/EB_Zhao2019/jaccard.CT_F1.CTS.txt
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/existing.Ic_50gene.RData
examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/BioTIP_res_10runs_MCIbottom2_Modulesize20.RData
examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/BioTIP_res_10runs_MCIbottom2_Modulesize30.RData
examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/BioTIP_res_10runs_MCIbottom2_Modulesize40.RData
examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/CT.detection_variable.Modulesize.Rdata
examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/CT.detection_variable.Modulesize_MCIbottom2.pdf
examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/CT.list_Modulesize20.Rdata
examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/CT.list_Modulesize30.Rdata
examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/CT.list_Modulesize40.Rdata
examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/CTS.F1_variable.ModuleSize_GS_2CTs.pdf
examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/F1.CTS.eCardiac.a_MCIbottom2.RData
examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/F1.CTS.endothelial.b_MCIbottom2.RData
examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/jaccard.CT_F1.CTS.txt
examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP.res.RData
examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_CTS.candidate.RData
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_IC_sim.Permutation.RData
examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_MCIBar_0.1_fdr0.05_minsize30.pdf
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examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_barplot_MCI_Sim_RandomGene.pdf
examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_optimized_local.HVG_selection.RData
examples/result/gastrulationE8.25_Ibarra-Soria2018/trajectory_UMAP.pdf
examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.4/BioTIP.res.RData
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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.res.RData
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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.res.RData
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examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph_allcells/BioTIP_top0.1FDR0.2_SimuMCI_100_0.1_fdr0.2_minsize30.RData
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examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4.wo.TC/BioTIP.res.RData
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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.res.RData
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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.res.RData
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.res.RData
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.res.RData
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
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examples/result/hESC_Bargaje2017/TSNE.hESC_Bargaje2017_robustness_clustering_methods.pdf
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examples/result/lung_Treutlein2014/existing.Ic_50gene.RData
examples/result/lung_Treutlein2014/jaccard.CT_F1.CTS.txt
examples/result/lung_Treutlein2014/pca_averageHighgene_Standardized_trajectory.pdf
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examples/result/lung_Treutlein2014/trajectory_196cells.pdf
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examples/result/simulated_EMT/C_SNNGraph.k100/BioTIP_top1FDR0.05_IC_Delta_SimresultBoth.pdf
examples/result/simulated_EMT/C_SNNGraph.k100/BioTIP_top1FDR0.05_IC_sim.PermutateBoth.RData
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_SimuMCI_100_1_fdr0.05_minsize6.RData
examples/result/simulated_EMT/C_SNNGraph.k100/BioTIP_top1FDR0.05_barplot_MCI_Sim_RandomGene.pdf
examples/result/simulated_EMT/C_SNNGraph.k100/BioTIP_top1FDR0.05_optimized_local.HVG_selection.RData
examples/result/simulated_EMT/C_SNNGraph.k20/BioTIP.res.RData
examples/result/simulated_EMT/C_SNNGraph.k20/BioTIP_top1FDR0.05_CTS.candidate.RData
examples/result/simulated_EMT/C_SNNGraph.k20/BioTIP_top1FDR0.05_IC_Delta_SimresultBoth.pdf
examples/result/simulated_EMT/C_SNNGraph.k20/BioTIP_top1FDR0.05_IC_sim.PermutateBoth.RData
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_SimuMCI_100_1_fdr0.05_minsize6.RData
examples/result/simulated_EMT/C_SNNGraph.k20/BioTIP_top1FDR0.05_barplot_MCI_Sim_RandomGene.pdf
examples/result/simulated_EMT/C_SNNGraph.k20/BioTIP_top1FDR0.05_optimized_local.HVG_selection.RData
examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP.res.RData
examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP_top1FDR0.05_CTS.candidate.RData
examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP_top1FDR0.05_IC_Delta_SimresultBoth.pdf
examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP_top1FDR0.05_IC_sim.PermutateBoth.RData
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_SimuMCI_100_1_fdr0.05_minsize6.RData
examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP_top1FDR0.05_barplot_MCI_Sim_RandomGene.pdf
examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP_top1FDR0.05_optimized_local.HVG_selection.RData
examples/result/simulated_EMT/GS.CTS_at.least.4identificaitons_fr.4predicitons.txt
examples/result/simulated_EMT/QuanTC_run/CTS.RData
examples/result/simulated_EMT/QuanTC_run/Fig2a_genes.txt
examples/result/simulated_EMT/QuanTC_run/transition_gene_I1.I2.txt
examples/result/simulated_EMT/average.Ic_10randomgene.pdf
examples/result/simulated_EMT/bar_robustness.pdf
examples/result/simulated_EMT/best.matched.clusterID.RData
examples/result/simulated_EMT/boxplot_10genes.pdf
examples/result/simulated_EMT/existing.Ic_10gene.RData
examples/result/simulated_EMT/jaccard.CT_F1.CTS.txt
examples/result/simulated_EMT/stability/BioTIP_top1FDR0.01_CTS.candidate.RData
examples/result/simulated_EMT/stability/BioTIP_top1FDR0.01_MCIBar_1_fdr0.01_minsize6.pdf
examples/result/simulated_EMT/umap.pdf
imgs/Fig1_scRNARNAseq_pipeline_2021_xy.jpg
imgs/FigS1_BioTIP_pipeline_detailed_v7.jpg
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/.DS_Store
results/6db_for_git.jpg
results/Fig1_BioTIP_github.jpg
results/FigS1_robustness_xy_v3.jpg
results/Jarcard_CTS.F1_6dbs.pdf
results/barplot_Jarcard_DNB.Ic.BioTIP.QuanTC_6dbs.R
results/robustness.md
tutorial/.DS_Store
tutorial/Gastrulation.html
tutorial/README.md
vignettes/.DS_Store
vignettes/.Rhistory
vignettes/BioTIP.Rmd
vignettes/CTS_Id.jpg
vignettes/DNB_Sim_M.jpg
vignettes/Fig1_scRNARNAseq_pipeline_2021_xy.jpg
vignettes/Fig2.jpg
vignettes/FigS1_BioTIP_pipeline_detailed_v7.jpg
vignettes/Fig_Table1_xy.jpg
vignettes/cell_info.tsv
vignettes/chr21.JPG
vignettes/delta.jpg
vignettes/subway_map.jpg
vignettes/subway_map.pdf
