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YuGene specifications

Information


Unique identifier OMICS_04030
Name YuGene
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.1.6
Stability Stable
Requirements
R(≥2.10), mixOmics
Maintained Yes

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Publication for YuGene

YuGene in publications

 (6)
PMCID: 5790494
PMID: 29423077
DOI: 10.18632/oncotarget.23364

[…] the gene expression levels of all samples in each dataset were transformed and rescaled to cumulative proportion values from 0 (lowest expression) to 1 (highest expression) with an r package “yugene” (version 1.1.5) before integration. the degs were discovered using linear model computed with empirical bayes analysis by the functions “lmfit” and “ebayes” provided by the r package “limna” […]

PMCID: 5731943
PMID: 29254233
DOI: 10.18632/oncotarget.22240

[…] a perl program (). the second challenge was to identify a proper method for removing the batch effect, and to perform proper cross-platform normalization of these array data from various origins. yugene [] uses a cumulative proportion transform. let pi denote the expression of a gene, and p(i) denote the expression of the same gene, but in descending order. the yugene transformed value […]

PMCID: 5576330
PMID: 28851360
DOI: 10.1186/s12943-017-0717-5

[…] based on affymetrix u133 plus2.0 microarray were downloaded from arrayexpress (http://www.ebi.ac.uk/arrayexpress/). integrated analysis of all data collected from tcga and arrayexpress using the yugene program is summarized in additional file : table s6 [], including 340 normal lung tissues and 2032 lung cancer tissues. the integrative expression profile of lung cancer was named […]

PMCID: 5000670
PMID: 27527159
DOI: 10.3390/ijms17081272

[…] the gene expression levels of all samples in each dataset were transformed and rescaled to cumulative proportion values from 0 (lowest expression) to 1 (highest expression) with an r package “yugene” (version 1.1.5) before integration. the degs were discovered using linear model computed with empirical bayes analysis by the functions “lmfit” and “ebayes” provided by the r package “limna” […]

PMCID: 4926420
PMID: 27275818
DOI: 10.3390/ijms17060886

[…] and carried out integrative analysis. the gene expression levels were transformed and rescaled to cumulative proportion values from 0 (lowest expression) to 1 (highest expression) with an r package “yugene” (version 1.1.5) for all samples in each dataset before integration. the degs were discovered using linear model computed with empirical bayes analysis by the functions “lmfit” and “ebayes” […]


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YuGene institution(s)
Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia

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