Man pages for JINJINT/ESCO
Simple Simulation of Single-cell RNA Sequencing Data
| amplify_cell | Simulate amplification, library prep, and the sequencing... |
| cal_amp_bias | Simulate technical biases. (This function is borrowed from... |
| escoEstBCV | Estimate esco Biological Coefficient of Variation parameters |
| escoEstDE | Estimate esco expression DE parameters for discrete cell... |
| escoEstDropout | Estimate esco dropout parameters |
| escoEstGroupLib | Estimate esco library size parameters for discrete cell... |
| escoEstGroupMean | Estimate esco mean parameters for discrete cell groups |
| escoEstGroupOutlier | Estimate esco Group expression outlier parameters for... |
| escoEstimate | Estimate esco simulation parameters |
| escoEstLib | Estimate esco library size parameters |
| escoEstMean | Estimate esco group mean parameters |
| escoEstOutlier | Estimate esco expression outlier parameters for a single cell... |
| escogcn | Compute the gene co-expression network |
| escogcnerr | Compute the estiamtion error of gene co-expression networks |
| escoheatdata | Visualize a set of gene expression matrix |
| escoheatgcn | Visualize a set of gene correlation matrix |
| escoParams | The escoParams class |
| escoSimDownSample | Simulate observed count matrix though downsampling. (This... |
| escoSimGeneMean | Simulate gene means |
| escoSimGroupCellMeans | Simulate group cell means |
| escoSimGroupDE | Simulate differential expression (DE) factors for discrete... |
| escoSimLib | Simulate library sizes |
| escoSimSingleCellMeans | Simulate cell means |
| escoSimTrajDE | Simulate differential expression (DE) factors for trajectory |
| escoSimTrajMeans | Simulate esco trajetory cell means |
| escoSimTreeCellMeans | Simulate tree cell means |
| escoSimTreeDE | Simulate differential expression (DE) factors for tree... |
| escoSimTrueCounts | Simulate true counts |
| escoSimulate | ESCO simulation |
| escoSimZeroInflate | Simulate noisy observed count matirx via adding more zeros... |
| expandParams | Expand values of parameters |
| gene_len_pool | a pool of gene lengths to sample from |
| getBetaStepProbs | Get Beta step probabilities |
| getLNormFactors | Get log-normal factors |
| getParam | Get a parameter |
| getParams | Get parameters |
| logistic | Logistic function |
| makespd | Make positive definite Make a matrix positive definite... |
| newParams | Initiate a new escoParam object |
| Params | The Params virtual class |
| puri_data | a purified gene expression data set to sample correlation... |
| randcop | Sample from a gaussian copula |
| randcor | Random sampeled correlation from the reallife gene... |
| rbindMatched | Bind rows (matched) |
| rnorm_truc | Sample from truncated normal distribution |
| sampleDensity | Sample density |
| setParam | Set a parameter |
| setParams | Set mutiple parameters |
| setParamsUnchecked | Set parameters UNCHECKED |
| setParamUnchecked | Set a parameter UNCHECKED |
| winsorize | Winsorize vector |
