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ROKU specifications

Information


Unique identifier OMICS_19658
Name ROKU
Software type Application/Script
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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Maintainers


  • person_outline Koji Kadota <>
  • person_outline Kentaro Shimizu <>
  • person_outline Tohru Terada <>
  • person_outline Yuji Nakai <>
  • person_outline Jiazhen Ye <>

Publication for ROKU

ROKU in publications

 (5)
PMCID: 5954046
PMID: 29780216
DOI: 10.1007/s11627-018-9905-2

[…] of expression outliers, including internal implementation of the shannon’s entropy for information content (hs) and the minimum akaike’s information criterion (maice, aic) as defined in the original roku method and improved on by the roku-spm method https://www.rdocumentation.org/packages/tcc/versions/1.12.1/topics/roku (kadota et al. , , ; guo et al. ) and the resulting matrix loaded into tibco […]

PMCID: 5574374
PMID: 28850115
DOI: 10.1038/sdata.2017.105

[…] lists of genes with prominent expression patterns in a specific tissue relative to those in other tissues. the genes with tissue-specific expression patterns are calculated for all tissues using the roku method. roku was originally developed solely for extracting tissue-specific genes. roku ranks the genes according to their overall tissue specificity using shannon entropy and detects […]

PMCID: 5465533
PMID: 28595592
DOI: 10.1186/s13062-017-0183-4

[…] on shannon entropy, which has been frequently used to measure tissue specificity from expression profile data derived from microarray and rna-seq data [, , , ]. shannon entropy was calculated using roku [], and converted to a tissue-specificity score. in the second method, an outlier analysis was applied to each gene expression profile to detect the tissues exhibiting highly outlying expression […]

PMCID: 3741196
PMID: 23950964
DOI: 10.1371/journal.pone.0070568

[…] by the mas5 algorithm and log2 transformed before further analyses. gds3113 were normalized using the limma method (see for details). lists some additional information regarding the datasets., roku uses shannon entropy to predict whether a gene is specifically or ubiquitously expressed across a set of tissues. if a gene is predicted specific, an outlier detection method is used […]

PMCID: 3478929
PMID: 23027924
DOI: 10.1084/jem.20120127

[…] of samples as significantly separated from the other samples (). memory b cell–specific genes were identified with two distinct statistical methods (fig. s3), tukey’s multiple comparison test and roku, a tissue-specific gene identification method (). if both methods labeled a specific gene as highly expressed in memory b cells, that gene is considered as a memory-specific gene., total rna […]


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ROKU institution(s)
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan

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