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SimSeq  

Nonparametric Simulation of RNA-Seq Data
View on CRAN: Click here


Download and install SimSeq package within the R console
Install from CRAN:
install.packages("SimSeq")

Install from Github:
library("remotes")
install_github("cran/SimSeq")

Install by package version:
library("remotes")
install_version("SimSeq", "1.4.0")



Attach the package and use:
library("SimSeq")
Maintained by
Samuel Benidt
[Scholar Profile | Author Map]
First Published: 2014-02-18
Latest Update: 2015-11-23
Description:
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.
How to cite:
Samuel Benidt (2014). SimSeq: Nonparametric Simulation of RNA-Seq Data. R package version 1.4.0, https://cran.r-project.org/web/packages/SimSeq. Accessed 30 Apr. 2025.
Previous versions and publish date:
1.0.0 (2014-02-18 07:27), 1.2.0 (2014-12-10 08:06), 1.3.0 (2015-03-07 07:50)
Other packages that cited SimSeq R package
View SimSeq citation profile
Other R packages that SimSeq depends, imports, suggests or enhances
Complete documentation for SimSeq
Functions, R codes and Examples using the SimSeq R package
Some associated functions: CalcPvalWilcox . SimData . SimSeq-package . SortData . kidney . 
Some associated R codes: CalcPvalWilcox.R . SimData.R . SortData.R .  Full SimSeq package functions and examples
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