Man pages for SPsimSeq
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
| buildXmat | An auxialiary function to quickly construct the polyomial... |
| calculateCPM | Calculates counts per millions of reads, possibly with... |
| checkInputValidity | Check for data validity |
| chooseCandGenes | Select candidate genes |
| configExperiment | Configure experiment |
| constructDens | Construct the cumulative density |
| estLibSizeDistr | Estimate log-normal distribution for the library sizes |
| evaluateDensities | Evaluate the densities in the estimated SPsimSeq object |
| expit | Evaluate the expit function |
| extractMat | A function with S4 dispatching to extract the count matrix |
| fitLLmodel | Fit log linear model for each gene |
| fitPoisGlm | Fast fit Poisson regression |
| fracZeroLogitModel | Extract data and iterate over batches to estimate zero... |
| genCopula | Generate a copula instance |
| geneParmEst | Gene level param estimates for density estimation |
| genLibSizes | Generate library sizes from log-normal |
| matchCopula | Match copulas to estimated SP distribution |
| obtCorMatsBatch | A function to obtain copulas or uniform random variables |
| obtCount | Calculates height and mid points of a distribution |
| parmEstDensVec | Density estimation on a single vector |
| prepareSPsimOutputs | A function to prepare outputs |
| samZeroID | Return ID for observations to be set to zero |
| scNGP.data | Neuroblastoma NGP cells single-cell RNA-seq. |
| selectGenes | Sample genes from candidate genes |
| SPsimPerGene | A function that generates the simulated data for a single... |
| SPsimSeq | A function to simulate bulk or single cell RNA sequencing... |
| SPsimSeq-package | SPsimSeq package |
| zeroProbModel | Predict zero probability using logistic rgression |
| zhang.data.sub | Neuroblastoma bulk RNA-seq data retrieved from Zhang et... |
