├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── .Rhistory ├── ContinuousTree.R ├── benchmark_functions.R ├── data.R ├── simulation_functions.R └── summary_functions.R ├── README.md ├── data ├── gene_len_pool.RData ├── len2nfrag.RData └── param_realdata.zeisel.imputed.RData ├── inst └── extdata │ ├── Newick_ABCDE.txt │ ├── Newick_animals.txt │ ├── Th17_data.RData │ ├── cortex_counts.txt │ └── grid_summary │ ├── mean_bins_UMI.txt │ ├── mean_bins_nonUMI.txt │ ├── nonzero_bins_UMI.txt │ ├── nonzero_bins_nonUMI.txt │ ├── sd_bins_UMI.txt │ ├── sd_bins_nonUMI.txt │ ├── sim_params_UMI.RData │ └── sim_params_nonUMI.RData ├── man ├── .Rapp.history ├── BestMatchParams.Rd ├── ClusterQuality.Rd ├── ContinuousEVF.Rd ├── Dec2k_based.Rd ├── DiscreteEVF.Rd ├── DivideBatches.Rd ├── GeneEffects.Rd ├── Get_params.Rd ├── Get_params2.Rd ├── LogDist.Rd ├── Phyla3.Rd ├── Phyla5.Rd ├── PlotCountHeatmap.Rd ├── PlotPCA.Rd ├── PlotTsne.Rd ├── QQplot2RealData.Rd ├── SampleDen.Rd ├── SimulateTrueCounts.Rd ├── True2ObservedCounts.Rd ├── amplify_1cell.Rd ├── basek2decimal.Rd ├── cal_ARI.Rd ├── cal_AUC.Rd ├── cal_KNNP.Rd ├── cal_amp_bias.Rd ├── cor_pseudotime.Rd ├── cv.Rd ├── dist2diag.Rd ├── evalImpulse.Rd ├── expand2binary.Rd ├── fano.Rd ├── gene_len_pool.Rd ├── getDEgenes.Rd ├── getTrajectoryGenes.Rd ├── len2nfrag.Rd ├── match_params.Rd ├── multiplot.Rd ├── percent_nonzero.Rd ├── plotPCAbasic.Rd ├── plot_nreads_UMI.Rd ├── rand.index.Rd ├── rescale2range.Rd ├── rnorm_trunc.Rd └── sens_and_spec.Rd └── vignettes ├── SymSimTutorial.Rmd ├── SymSimTutorial.html └── SymSimTutorial_files └── figure-html ├── unnamed-chunk-10-1.png ├── unnamed-chunk-11-1.png ├── unnamed-chunk-12-1.png ├── unnamed-chunk-2-1.png ├── unnamed-chunk-3-1.png ├── unnamed-chunk-4-1.png ├── unnamed-chunk-4-2.png ├── unnamed-chunk-4-3.png ├── unnamed-chunk-4-4.png ├── unnamed-chunk-5-1.png ├── unnamed-chunk-5-2.png ├── unnamed-chunk-6-1.png ├── unnamed-chunk-7-1.png ├── unnamed-chunk-7-2.png ├── unnamed-chunk-8-1.png ├── 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