compcodeR statistics

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compcodeR specifications

Information


Unique identifier OMICS_04050
Name compcodeR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Charlotte Soneson <>

Publication for compcodeR

compcodeR in publications

 (3)
PMCID: 5860609
PMID: 29028961
DOI: 10.1093/bioinformatics/btx631

[…] that the synthetic data mimic real data, since this is not always easy to assess from a text description of a simulation model. we note that it is not the first effort in this direction; the compcoder package () as well as powsim () contain functions for summarizing the characteristics of a single dataset, and the splatter package () also provides the opportunity to generate figures […]

PMCID: 5649605
PMID: 29062598
DOI: 10.7717/peerj.3859

[…] \begin{document} }{}\begin{eqnarray*}& & {\text{fp}}_{k}={|}\{i:{\hat {l}}_{i}=\text{de}\wedge {l}_{i}=\text{nde}\}{|}.\end{eqnarray*}\end{document}fpk=|i:l ˆi=de∧li=nde|. , the tool compcoder () was used to generate all simulated data. the tool generates count data based on a negative binomial distribution model with parameters estimated from real transcriptome data (; ). […]

PMCID: 4634584
PMID: 26538400
DOI: 10.1186/s12859-015-0794-7

[…] advanced versions for edger and deseq, respectively, and are robust against count outliers such as abnormally high counts (for details, see [, ]). to the best of our knowledge, only one r package, compcoder [], can generate simulation count data with outliers, but it has been restricted to only two-group comparisons so far. extending the simulation framework of compcoder to multi-group data […]


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compcodeR institution(s)
Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, Switzerland

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