Package: SPsimSeq 1.15.0

Joris Meys

SPsimSeq: Semi-parametric simulation tool for bulk and single-cell RNA sequencing data

SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data (single-cell or bulk), and subsequently simulates a new dataset from the estimated marginal distributions using Gaussian-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size.

Authors:Alemu Takele Assefa [aut], Olivier Thas [ths], Joris Meys [cre], Stijn Hawinkel [aut]

SPsimSeq_1.15.0.tar.gz
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SPsimSeq.pdf |SPsimSeq.html✨
SPsimSeq/json (API)
NEWS

# Install 'SPsimSeq' in R:

install.packages('SPsimSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/centerforstatistics-ugent/spsimseq/issues

Datasets:

scNGP.data - Neuroblastoma NGP cells single-cell RNA-seq.
zhang.data.sub - Neuroblastoma bulk RNA-seq data retrieved from Zhang et (2015).

On BioConductor:SPsimSeq-1.15.0(bioc 3.20)SPsimSeq-1.14.0(bioc 3.19)

bioconductor-package

3 exports 1.24 score 134 dependencies 1 dependents 4 mentions

Last updated 2 months agofrom:a578ee94a2

Exports:configExperiment evaluateDensities SPsimSeq

Dependencies:abind ade4 AnnotationDbi ape askpass backports base64enc Biobase BiocGenerics biomformat Biostrings bit bit64 blob bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray digest doParallel dynamicTreeCut edgeR evaluate fansi farver fastcluster fastmap fitdistrplus fontawesome foreach foreign Formula fs GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue GO.db gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr igraph impute IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime multtest munsell mvtnorm nlme nnet openssl permute phyloseq pillar pixmap pkgconfig plogr plyr png preprocessCore R6 rappdirs RColorBrewer Rcpp RcppArmadillo reshape2 rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown rpart RSQLite rstudioapi S4Arrays S4Vectors sass scales SingleCellExperiment sp SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tinytex UCSC.utils utf8 vctrs vegan viridis viridisLite WGCNA withr xfun XVector yaml zlibbioc

Manual for the SPsimSeq package: semi-parametric simulation for bulk and single cell RNA-seq data

Rendered fromSPsimSeq.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2020-05-15
Started: 2020-04-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
SPsimSeq package	SPsimSeq-package
An auxialiary function to quickly construct the polyomial matrix, using Horner's rule	buildXmat
Calculates counts per millions of reads, possibly with log-transform	calculateCPM
Check for data validity	checkInputValidity
Select candidate genes	chooseCandGenes
Configure experiment	configExperiment
Construct the cumulative density	constructDens
Estimate log-normal distribution for the library sizes	estLibSizeDistr
Evaluate the densities in the estimated SPsimSeq object	evaluateDensities
Evaluate the expit function	expit
A function with S4 dispatching to extract the count matrix	extractMat extractMat,data.frame-method extractMat,matrix-method extractMat,phyloseq-method extractMat,SingleCellExperiment-method
Fit log linear model for each gene	fitLLmodel
Fast fit Poisson regression	fitPoisGlm
Extract data and iterate over batches to estimate zero probability models	fracZeroLogitModel
Generate a copula instance	genCopula
Gene level param estimates for density estimation	geneParmEst
Generate library sizes from log-normal	genLibSizes
Match copulas to estimated SP distribution	matchCopula
A function to obtain copulas or uniform random variables	obtCorMatsBatch
Calculates height and mid points of a distribution	obtCount
Density estimation on a single vector	parmEstDensVec
A function to prepare outputs	prepareSPsimOutputs
Return ID for observations to be set to zero	samZeroID
Neuroblastoma NGP cells single-cell RNA-seq.	scNGP.data
Sample genes from candidate genes	selectGenes
A function that generates the simulated data for a single gene	SPsimPerGene
A function to simulate bulk or single cell RNA sequencing data	SPsimSeq
Predict zero probability using logistic rgression	zeroProbModel
Neuroblastoma bulk RNA-seq data retrieved from Zhang et (2015).	zhang.data.sub