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SimSeq tool specifications

Information


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
Requirements
fdrtool, R(≥2.10.0)
Source code URL https://cran.r-project.org/src/contrib/SimSeq_1.4.0.tar.gz
Maintained Yes

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Documentation


Maintainer


  • person_outline Samuel Benidt <>

Publication for SimSeq tool

SimSeq tool citations

 (9)
library_books

The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria

2018
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 […]

library_books

More on the Best Evolutionary Rate for Phylogenetic Analysis

2017
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[…] for their clocklikeness in a recent transcriptome study in ichneumonid hymenopterans (seraina klopfstein, unpublished data)., we simulated nucleotide sequences on the simulated trees using the simseq function in the “phangorn” package in r ().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 […]

library_books

Positional bias in variant calls against draft reference assemblies

2017
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 […]

library_books

Identification of expression patterns in the progression of disease stages by integration of transcriptomic data

2016
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 […]

library_books

Fast, accurate, and lightweight analysis of BS treated reads with ERNE 2

2016
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, […]

library_books

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome

2015
PMCID: 4642669
PMID: 26558718
DOI: 10.1186/s12859-015-0801-z

[…] sequences of arabidopsis thaliana, available at ftp://ftp.arabidopsis.org/home/tair/sequences/whole_chromosomes, served as the template for the generation of the simulated reads for our study. the simseq read simulator (last update 4.12.2011; https://github.com/jstjohn/simseq) was used to generate haploid, error-free paired-end and mate-pair reads (the latter created specifically […]


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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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