Man pages for CenterForStatistics-UGent/SPsimSeq
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data

buildXmatAn auxialiary function to quickly construct the polyomial...
calculateCPMCalculates counts per millions of reads, possibly with...
checkInputValidityCheck for data validity
chooseCandGenesSelect candidate genes
configExperimentConfigure experiment
constructDensConstruct the cumulative density
estLibSizeDistrEstimate log-normal distribution for the library sizes
evaluateDensitiesEvaluate the densities in the estimated SPsimSeq object
expitEvaluate the expit function
extractMatA function with S4 dispatching to extract the count matrix
fitLLmodelFit log linear model for each gene
fitPoisGlmFast fit Poisson regression
fracZeroLogitModelExtract data and iterate over batches to estimate zero...
genCopulaGenerate a copula instance
geneParmEstGene level param estimates for density estimation
genLibSizesGenerate library sizes from log-normal
matchCopulaMatch copulas to estimated SP distribution
obtCorMatsBatchA function to obtain copulas or uniform random variables
obtCountCalculates height and mid points of a distribution
parmEstDensVecDensity estimation on a single vector
prepareSPsimOutputsA function to prepare outputs
samZeroIDReturn ID for observations to be set to zero
scNGP.dataNeuroblastoma NGP cells single-cell RNA-seq.
selectGenesSample genes from candidate genes
SPsimPerGeneA function that generates the simulated data for a single...
SPsimSeqA function to simulate bulk or single cell RNA sequencing...
SPsimSeq-packageSPsimSeq package
zeroProbModelPredict zero probability using logistic rgression bulk RNA-seq data retrieved from Zhang et...
CenterForStatistics-UGent/SPsimSeq documentation built on May 23, 2020, 2:38 p.m.