SimSeq tool statistics

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SimSeq tool specifications


Unique identifier OMICS_07602
Name SimSeq tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A source RNA-seq dataset and a vector of computed normalization factors with one element for each column of the source dataset.
Output data A matrix of RNA-seq read counts.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 1.4.0
Stability Stable
fdrtool, R(≥2.10.0)
Source code URL
Maintained Yes



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  • person_outline Samuel Benidt <>

Publication for SimSeq tool

SimSeq tool in publications

PMCID: 5941160
PMID: 29608719
DOI: 10.1093/gbe/evy044

[…] replacing the irs. this resulted in 234 conservation scores for ir regions and 207 conservation scores for control regions., sequences were simulated along rooted phylogenetic trees using the module simseq of the r package phangorn v2.2.0 (). each ir and each control sequence were simulated according to the phylogenetic tree using the inferred evolutionary model parameters in the region […]

PMCID: 5790136
PMID: 28595363
DOI: 10.1093/sysbio/syx051

[…] for their clocklikeness in a recent transcriptome study in ichneumonid hymenopterans (seraina klopfstein, unpublished data)., we simulated nucleotide sequences on the simulated trees using the simseq function in the “phangorn” package in r (). a range of evolutionary rates was examined from 0.025 to 10 expected substitutions from root to any tip. in the most basic setup, we simulated […]

PMCID: 5368935
PMID: 28351369
DOI: 10.1186/s12864-017-3637-2

[…] ncbi sequence read archive., sequences for chromosomes 1 and 2 of arabidopsis thaliana (tair10) were downloaded from the arabidopsis information resource website []., to simulate the reads we used simseq application that aims to reproduce the biases present in normal illumina data sets []. we ran the application with default parameters to simulate 15 mln 100 bp paired-end reads with the mean […]

PMCID: 5133487
PMID: 28185568
DOI: 10.1186/s12859-016-1290-4

[…] model disease divided in 6 stages, where a small subset of genes have a pattern of up-regulation or down-regulation along the stages. the dataset for this simulation was produced with the r package simseq which includes a data-based algorithm to allow a non-parametric simulation of rna-seq data []. the experimental dataset used as template to generate the simulated data was a rna-seq data […]

PMCID: 4896272
PMID: 26961371
DOI: 10.1186/s12859-016-0910-3

[…] genome and by comparing the predicted methylation values with the simulated ones., datasets simulation to generate the simulated datasets, we used custom scripts [] and [] in conjunction with the simseq reads simulator [] to generate a directional [] bs-seq dataset with simulated snps, indels, sequencing errors, (uniform) bisulfite conversions, and bisulfite conversion failures (usually, […]

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SimSeq tool institution(s)
Department of Statistics, Iowa State University, Ames, IA, USA
SimSeq tool funding source(s)
Supported by the National Science Foundation [grant numbers IOS0922746, IOS1339348 and DMS1313224] and by the National Institute of General Medical Science (NIGMS) of the National Institutes of Health and the joint National Science Foundation/NIGMS Mathematical Biology Program [grant number R01GM109458].

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