| amplify_1cell | This function simulates the amplification, library prep, and... |
| basek2decimal | convert a k based number to decimal number |
| BestMatchParams | Get the best matched parameter |
| cal_amp_bias | Simulate technical biases |
| cal_ARI | calculate adjusted rand index between labels from a... |
| cal_AUC | calculate area under curve |
| cal_KNNP | calculate knn purity of a data space with given labels |
| ClusterQuality | cluster-ability of a dataset |
| ContinuousEVF | Generating EVFs for cells sampled along the trajectory of... |
| cor_pseudotime | calculate pseudotime correlation between our true pseudotime... |
| cv | Calculate the coefficient of variation of a vector x |
| Dec2k_based | convert a decimal number to k based number |
| DiscreteEVF | Generating EVFs for cells sampled from tip populations from a... |
| dist2diag | how well do dots fit to the diagonal (for evaluating our... |
| DivideBatches | Divide the observed counts into multiple batches by adding... |
| evalImpulse | Compute value of impulse function given parameters. Enforces... |
| expand2binary | expand transcript counts to a vector of binaries of the same... |
| fano | Calculate the fano factor of a vector x |
| GeneEffects | Getting GeneEffects matrices |
| gene_len_pool | a pool of gene lengths to sample from |
| getDEgenes | retrieve genes' differential expression information it... |
| Get_params | Getting the parameters for simulating gene expression from... |
| Get_params2 | Getting the parameters for simulating gene expression from... |
| getTrajectoryGenes | retrieve the information of cells on continuous trajectories... |
| len2nfrag | from transcript length to number of fragments (for the nonUMI... |
| LogDist | Getting logged expression distribution |
| match_params | distribution of kinetic parameters learned from the Zeisel... |
| multiplot | arrange multiple plots from ggplot2 to one figure. From... |
| percent_nonzero | Calculate the percentage of non-zero values in a vector x |
| Phyla3 | Creating an example tree with 3 tips |
| Phyla5 | Creating an example tree with 5 tips |
| PlotCountHeatmap | Plotting logged expression distribution |
| plot_nreads_UMI | plot the histogram of number of reads per UMI |
| PlotPCA | Perform PCA |
| plotPCAbasic | Plotting PCA results (PC1 and PC2) |
| PlotTsne | Perform tSNE |
| QQplot2RealData | function QQplot2RealData; plot both with ggplot2 and with... |
| rand.index | rand index |
| rescale2range | rescale2range |
| rnorm_trunc | sample from truncated normal distribution |
| SampleDen | sample from smoothed density function |
| sens_and_spec | calculate sensitivity and specificity |
| SimulateTrueCounts | Generate both evf and gene effect and simulate true... |
| True2ObservedCounts | Simulate observed count matrix given technical biases and the... |
