├── DESCRIPTION ├── NAMESPACE ├── R ├── GE_LB_sim.R ├── GeneExpression_sim.R ├── LineageBarcode_sim.R ├── SimulateCIFs.R ├── Utilities.R └── sysdata.rda ├── README.md ├── TedSim.Rproj ├── data ├── gene_len_pool.RData ├── larvae4_sub.rda ├── len2nfrag.RData ├── match_params.rda └── param_realdata.zeisel.imputed.RData ├── man ├── BranchCal.Rd ├── CIF2Truecounts.Rd ├── CaptureDrop.Rd ├── GeneEffects.Rd ├── Generate_profile_multi.Rd ├── Get_params.Rd ├── Get_params2.Rd ├── Mutated_state_dist.Rd ├── PlotTsne.Rd ├── PlotUmap.Rd ├── SIFGenerate.Rd ├── SampleCIF.Rd ├── SampleDen.Rd ├── SampleEdgeNew.Rd ├── Samplelineage.Rd ├── SimulateCIFs.Rd ├── SimulateCellStates.Rd ├── True2ObservedCounts.Rd ├── WalkTree.Rd ├── amplify_1cell.Rd ├── cal_amp_bias.Rd ├── expand2binary.Rd ├── generate_dropout.Rd ├── generate_mutation.Rd └── rnorm_trunc.Rd ├── output ├── cell_meta_larvae4_20.txt ├── cell_meta_tedsim_pa0.75_step0.25.csv ├── character_matrix_pd0.txt ├── counts_larvae4_20.txt ├── counts_tedsim_pa0.75_step0.25.csv ├── observed_counts_larvae4_20.txt ├── profile_c_tedsim.txt ├── top_genes_tedsim.txt └── tree_gt_bin_tedsim_pd0.newick ├── tmp_junktree.tree └── vignettes ├── FitObservedCounts.Rmd ├── Simulate-data-multi.Rmd ├── TrajectoryInferTest.Rmd ├── cell_meta_larvae4_20.txt ├── counts_larvae4_20.txt ├── observed_counts_larvae4_20.txt └── responses_NAR.Rmd /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Galaxeee/TedSim/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Galaxeee/TedSim/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/GE_LB_sim.R: -------------------------------------------------------------------------------- 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