Man pages for beyondpie/mssc
Multiple-sample differential analysis for single-cell RNA sequencing data
| calColAUC | Calculate AUCs for stats in colume-wise. |
| compileStanModel | Compile stan model with cmdstanr |
| evalDeltaMean | Evaluate delta mean between two conditions. |
| evalTstat | Evaluate t statistics and p-value between two conditions. |
| extractDraws | Extract draws/samples from the MSSC2 model |
| extractDrawsAll | Extract all parameters' samples from MSSC2 Model. |
| extractGLMDraws | Extract draws/samples from the generalized linear model. |
| extractGLMDrawsAll | Extract all parameters' samples from generalised linear... |
| fitDispersionParams | Get parameters for the prior of dispersion. We assume the... |
| fitGeneGlobalMeanPriorParams | NOTE previous name: est_varofmu |
| fitGenewiseBatchPriorParams | NOTE previous name: est_varofind |
| fitGenewiseCondPriorParams | Estimate parameters of inv-gamma dist as the prior for... |
| fitGenewiseNBModel | A summary fit function for Genewise Negative Binomial Model... |
| getNameOfMatrixFromCmdstanr | Get names of matrix in cmdstanr. |
| getNameOfVectorFromCmdstanr | Get names of vector in cmdstanr. |
| initMSSC2GenewiseParams | Initialize MSSC2 Genewise parameters, which is further used... |
| initNBParam | Get the mu (log-level mean) and r (dispersion) in Negative... |
| initNBParamWithCondBatch | Fit mu, mucond, muind for Negative Binomial with scaling. No... |
| new_MSSC2 | Create MSSC2 model object |
| normLogMean | Estimate the normalized mean of a numeric vector on... |
| PSIS | Get Pareto Smoothed Importance Sampling weights. Weights are... |
| repVecColwise | Replicate a vector in column-wise for n times. |
| repVecRowise | Replicate a vector in row-wise for n times. |
| runGLMAP | Run MAP optimization for generalized lineaer model. |
| runMAP | Run MAP optimization for mssc2. |
| runVI | Run variational inference for mssc2. |
| setGLMInitialParams | Set initial values for the generalized linear model. TODO:... |
| setStanHyperparams | Set hyper parameters for the stan model of mssc2. |
| setStanInitialParams | Set initial values for the parameters in the stan model of... |
| split_matrix_col | Split matrix columns into a matrix, which is row-major order |
| toStanInput | Convert input data to the format of Stan Input. |
