Man pages for YosefLab/LineagePulse
Differential expression analysis and model fitting for single-cell RNA-seq data
| accessors | LineagePulseObject accession methods |
| calcNormConst | Compute size factors for a LineagePulse-object |
| calcPostDrop_Matrix | Calculate posterior of drop-out |
| calcPostDrop_Vector | Calculate posterior of drop-out |
| cash-LineagePulseObject-method | List-like accessor methods for LineagePulseObject: $ |
| decompressDispByGene | Compute dispersion parameter estimates from mean parameter... |
| decompressDispByGeneMM | Compute mean parameter estimate matrix from mean parameter... |
| decompressDropoutRateByCell | Compute dropout rate parameter estimates from dropout rate... |
| decompressDropoutRateByGene | Compute dropout rate parameter estimates from dropout rate... |
| decompressMeansByGene | Compute mean parameter estimates from mean parameter model... |
| decompressMuByGeneMM | Compute mean parameter estimate matrix from mean parameter... |
| evalDropoutModel | Compute value of logistic dropout function given with scale... |
| evalDropoutModel_comp | Compiled function: evalDropoutModel |
| evalImpulseModel | Compute value of impulse function given parameters. |
| evalImpulseModel_comp | Compiled function: evalImpulseModel |
| evalLogLikGene | Wrapper for log likelihood of (zero-inflated) negative... |
| evalLogLikGeneMM | Wrapper for log likelihood of zero-inflated negative binomial... |
| evalLogLikMatrix | Wrapper for log likelihood of (zero-inflated) negative... |
| evalLogLikMuDispGeneFit | Cost function (zero-inflated) negative binomial model for... |
| evalLogLikMuDispGeneFit_comp | Compiled function: evalLogLikMuDispGeneFit |
| evalLogLikNB | Compute loglikelihood of negative binomial model for a vector... |
| evalLogLikNB_comp | Compiled function: evalLogLikNB |
| evalLogLikPiZINB_ManyCells | Cost function zero-inflated negative binomial model for... |
| evalLogLikPiZINB_ManyCells_comp | Cost function zero-inflated negative binomial model for... |
| evalLogLikPiZINB_SingleCell | Cost function zero-inflated negative binomial model for... |
| evalLogLikPiZINB_SingleCell_comp | Cost function zero-inflated negative binomial model for... |
| evalLogLikZINB | Compute loglikelihood of zero-inflated negative binomial... |
| evalLogLikZINB_comp | Compiled function: evalLogLikZINB |
| fitLPModels | Fit all models necessary for LineagePulse |
| fitModel | Fit (zero-inflated) negative binomial model to data |
| fitMuDisp | Coordinate mean and dispersion parameter co-estimation step |
| fitMuDispGene | Optim wrapper for gene-wise models other than mixture model. |
| fitMuDispGeneImpulse | Multiple initilalisation wrapper for impulse mean model |
| fitMuDispGeneMM | Optim wrapper for gene-wise models other than mixture model. |
| fitPi | Global wrapper for fitting of all drop-out models |
| fitPi_ManyCells | Optim wrapper for drop-out model fitting on many cells |
| fitPi_SingleCell | Optim wrapper for drop-out model fitting on single cell |
| getFitsDispersion | Get dispersion model fits |
| getFitsDropout | Get drop-out model fits |
| getFitsMean | Get mean model fits |
| getNormData | Return depth and batch corrected data |
| getPostDrop | Get posteriors of drop-out |
| initDispModel | Initialise dispersion model container object |
| initDropModel | Initialise drop-out model container object |
| initialiseImpulseParameters | Estimate impulse model parameter initialisations |
| initMuModel | Initialise mean model container object |
| LineagePulseObject-class | Container class for LineagePulse output |
| LPsetters | LineagePulseObject setters |
| names-LineagePulseObject-method | List-like accessor methods for LineagePulseObject: names() |
| plotCellDensity | Plot density of cells in continuous covariate |
| plotGene | Plot counts and model for one gene |
| processSCData | Prepare single cell data for analysis |
| runDEAnalysis | Differential expression analysis |
| runLineagePulse | LineagePulse wrapper: Differential expression analysis on... |
| simulateContinuousDataSet | Simulate a data set for LinagePulse Simulates a data set with... |
| sortGeneTrajectories | Cluster expression mean trajectories |
| sub-sub-LineagePulseObject-character-missing-method | List-like accessor methods for LineagePulseObject: names() |
| testDropout | Test for existance of drop-out with log-likelihood ratio test |
| writeReport | Print LineagePulse report |
