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SCODE specifications

Information


Unique identifier OMICS_13693
Name SCODE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A file with G x C matrix of expression data and a file with time point data
Output data A file with G x G matrix; a file with D x D diagonal matrix; a file with G x D matrix and the residual sum of squares of linear regression
Output format TXT
Operating system Unix/Linux
Programming languages R, Ruby, Julia
License MIT License
Computer skills Advanced
Stability Stable
Requirements
MASS
Maintained Yes

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  • person_outline Hirotaka Matsumoto <>

Publication for SCODE

SCODE in publications

 (5)
PMCID: 4795301
PMID: 26537268
DOI: 10.1590/S0102-6720201500S100008

[…] committee of the institution, under reference number 207.630/2013., a longitudinal, exploratory, cross-sectional, descriptive study was performed at the obesity and related diseases surgical center (scode) of a university hospital. a total of 21 women with morbid obesity, evaluated before and after bariatric surgery, participated in this study. data collection was performed from november 2012 […]

PMCID: 3522960
PMID: 23202207
DOI: 10.3390/s121115206

[…] ⋯en″ (where each ei corresponds to an element that can be a string or binary number), a code p=″e1′e2′⋯em′″(m≤n) is called a prefix of c if and only if ei′=ei for (i ≤ m). given a set of codes scode, a range on scode identified by a prefix p represents the subset of scode, each code in which is prefixed with p., generally, exact query (rq14) contains speq and mpeq. range query (rq15) […]

PMCID: 3536661
PMID: 23107417
DOI: 10.1186/1471-2156-13-93

[…] samples were estimated using a bivariate animal model in asreml []:, (1) y ijklmn = μ + b 1 *dim i + b 2 *e − 0 .05*dim i + b 3 *afc j + b 4 *afc j 2 + season k + scode l + herd m + animal n + e ijklmn , , where y was the phenotype; μ was the overall mean; dim was the covariate describing the effect of days in milk; afc was the covariate describing […]

PMCID: 3120725
PMID: 21569316
DOI: 10.1186/1471-2156-12-43

[…] of days in milk; afc was the covariate describing the effect of age at first calving; season was the fixed effect of the class of calving season (june-aug 2004, sept-nov 2004, or dec 2004-jan 2005); scode was the fixed effect accounting for differences in genetic level between groups of proven bull daughters, young bull daughters, and other bull daughters; herd was the random effect of herd, […]

PMCID: 3790987
PMID: 27873956
DOI: 10.3390/s8127753

[…] this is not realistic and it might raise unexpected problems when we deploy the protocol in reality.(5)no gps (global position system) or like is required to provide node's location information. in scode, we have assumed that sensor nodes need to be aware of their locations. however, attaching gps or like increases high cost for sensors, and thus reducing the feasibility of the deployment. […]


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SCODE institution(s)
Bioinformatics Research Unit, Advanced Center for Computing and Communication, Riken, Saitama, Japan; Department of Computational Biology and Medical Sciences, Faculty of Frontier Sciences, The University of Tokyo, Chiba, Japan; Quantitative Biology Center, Riken, Osaka, Japan; Department of Systems Medicine, Keio University School of Medicine, Tokyo, Japan
SCODE funding source(s)
Supported by a Grant-in-Aid for Japan Society for the Promotion of Science (JSPS) Fellows, JSPS KAKENHI (Grant Numbers 16J05079, 15H01465, 25134701, 25870190, and 16H01532) and Core Research for Evolutional Science and Technology (CREST) “Creation of Fundamental Technologies for Understanding and Control of Biosystem Dynamics” from the Japan Science and Technology Agency (JST).

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