SimSeq: Nonparametric Simulation of RNA-Seq Data
Version 1.4.0

RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method. We develop a data-based simulation algorithm for RNA-seq data. The vector of read counts simulated for a given experimental unit has a joint distribution that closely matches the distribution of a source RNA-seq dataset provided by the user. Users control the proportion of genes simulated to be differentially expressed (DE) and can provide a vector of weights to control the distribution of effect sizes. The algorithm requires a matrix of RNA-seq read counts with large sample sizes in at least two treatment groups. Many datasets are available that fit this standard.

AuthorSamuel Benidt
Date of publication2015-11-23 12:33:58
MaintainerSamuel Benidt <sgbenidt@gmail.com>
LicenseGPL (>= 2)
Version1.4.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SimSeq")

Getting started

Package overview

Popular man pages

CalcPvalWilcox: Calculate P-values of Differential Expression
kidney: Kidney Renal Clear Cell Carcinoma [KIRC] RNA-Seq data
SimData: SimData
SimSeq-package: Nonparametric Simulation of RNA-Seq Data
SortData: SortData
See all...

All man pages Function index File listing

Man pages

CalcPvalWilcox: Calculate P-values of Differential Expression
kidney: Kidney Renal Clear Cell Carcinoma [KIRC] RNA-Seq data
SimData: SimData
SimSeq-package: Nonparametric Simulation of RNA-Seq Data
SortData: SortData

Functions

CalcPvalWilcox Man page Source code
SimData Man page Source code
SimSeq Man page
SimSeq-package Man page
SortData Man page Source code
kidney Man page

Files

inst
inst/CITATION
NAMESPACE
demo
demo/SimSeq.R
demo/00Index
NEWS
data
data/datalist
data/kidney.rda
R
R/CalcPvalWilcox.R
R/SortData.R
R/SimData.R
MD5
DESCRIPTION
man
man/SimData.Rd
man/SimSeq-package.Rd
man/SortData.Rd
man/CalcPvalWilcox.Rd
man/kidney.Rd
SimSeq documentation built on May 19, 2017, 4:04 p.m.

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