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COSIE specifications

Information


Unique identifier OMICS_11618
Name COSIE
Alternative name Corrected Splicing Indices for Exon Arrays
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Michael B. Stadler <>

Publication for Corrected Splicing Indices for Exon Arrays

COSIE in publications

 (6)
PMCID: 4298068
PMID: 25297679
DOI: 10.1186/1471-2164-15-879

[…] covering less than 60% of the gene locus (as described in figureĀ  )., the performance of the three approaches, eslima, eslimc and eslimt, was compared with three other methods: firma [], arh [] and cosie []. all the methods were run in r and applied to the same sample datasets. as indicated above, we used the set of 270 human genes known to undergo splicing as a reference []. the differences […]

PMCID: 3935942
PMID: 24587092
DOI: 10.1371/journal.pone.0089877

[…] siberian historical period from the beginning of its colonization., administrative and research work were permitted through the program of the france-russia associated international laboratory (lia cosie number 1029), associating the north-eastern federal university (yakutsk, sakha republic), the state medical university of krasnoyask, the russia foundation for fundamental research (moscow, […]

PMCID: 3202805
PMID: 21952137
DOI: 10.1038/msb.2011.69

[…] this can minimize interference from antisense transcripts., exon array data were normalized by the robust multichip average (rma) method and were corrected for hybridization bias using the cosie program (). expressed genes were selected by the detection above background (dabg) method. gene expression level was calculated using probesets in constitutive exons, based on ncbi cdnas/ests […]

PMCID: 3142162
PMID: 21799842
DOI: 10.1371/journal.pone.0022391

[…] probe intensity changes using our exon array data for 1 w and 4 w tac and sham samples. using the splicing index method, which examines exon usage by normalization to gene expression, and the cosie method for correction of probe hybridization bias (see for detail), we identified 2,086 and 1,942 exons with significant change of usage (>3*standard deviation) in 1 w and 4 w tac samples, […]

PMCID: 3051901
PMID: 21324185
DOI: 10.1186/1471-2105-12-55

[…] practice a technical bias of exon array platforms leads to a dramatic overestimation of as in the presence of differential gene expression. to correct for this bias, the authors developed the method cosie, which adjusts splicing indices using a non-linear model that incorporates probeset-specific response characteristics and saturation effects []. all of these computational methods […]


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COSIE institution(s)
Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland
COSIE funding source(s)
Novartis Research Foundation

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