Man pages for Galaxeee/TedSim
Temporal Dynamics Simulation of scRNA-seq and CRISR/Cas9 lineage barcodes
| amplify_1cell | This function simulates the amplification, library prep, and... |
| BranchCal | Simulate observed count matrix given technical biases and the... |
| cal_amp_bias | Simulate technical biases |
| CaptureDrop | Simulate capture dropout based on observed counts and barcode... |
| CIF2Truecounts | Simulate true count matrix given simulated CIF values |
| expand2binary | expand transcript counts to a vector of binaries of the same... |
| GeneEffects | Getting GeneEffects matrices |
| generate_dropout | Generate excision dropout |
| generate_mutation | Generate CRISPR induced mutations |
| Generate_profile_multi | Generate joint profile of gene expression and lineage barcode... |
| Get_params | Getting the parameters for simulating gene expression from... |
| Get_params2 | Getting the parameters for simulating gene expression from... |
| Mutated_state_dist | Generate mutated states from a real dataset |
| PlotTsne | Perform tSNE |
| PlotUmap | Perform UMAP |
| rnorm_trunc | sample from truncated normal distribution |
| SampleCIF | Generate Cell Identity Factors recursively via Brownian... |
| SampleDen | sample from smoothed density function |
| SampleEdgeNew | Generate child CIF based on parent CIF |
| Samplelineage | Sample Cell Identity Factors via Brownian motion, based on... |
| SIFGenerate | Simulate State Identity Factor values given a state tree |
| SimulateCellStates | Simulate cell states based on the state tree |
| SimulateCIFs | Simulate Cell Identity Factor Matrix With Lineage Barcodes |
| True2ObservedCounts | Simulate observed count matrix given technical biases and the... |
| WalkTree | Find the child state based on parent state and step size |
