genArise statistics

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genArise specifications

Information


Unique identifier OMICS_01993
Name genArise
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
Version 1.56.0
Stability Stable
Requirements
methods, stats, graphics, utils, grDevices, locfit, xtable, tcltk, R(>=1.7.1), tkrplot
Maintained Yes

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Documentation


genArise in publications

 (16)
PMCID: 5367803
PMID: 28373998
DOI: 10.1016/j.dib.2017.03.010

[…] scanarray 4000 (packard biochips). all images were captured using 65% pmt gain, 70–75% laser power and 10 µm resolution at 50% scan rate., microarray data analysis was performed with free software genarise, developed in the computing unit of cellular physiology institute of unam (http://www.ifc.unam.mx/genarise/). genarise carry out a number of transformations: background correction, […]

PMCID: 4524895
PMID: 26300899
DOI: 10.3389/fpls.2015.00602

[…] and the cy3 and cy5 background mean value were calculated with an arraypro analyzer software (media cybernetics, rockville, md, usa). microarray data analysis was performed with the free software genarise, developed in the computing unit of the cellular physiology institute at unam (http://www.ifc.unam.mx/genarise/). genarise performs a number of transformations: background correction, lowess […]

PMCID: 4583671
PMID: 26484261
DOI: 10.1016/j.gdata.2015.06.013

[…] using a custom designed microarray with the complete genome from n. fischeri nrrl 181 in order to identify genes related to the transformation of asphaltenes . data analysis was performed using the genarise software. results showed that 287 genes were up-regulated and 118 were down-regulated., here we describe experimental procedures and methods about our dataset (ncbi geo accession number […]

PMCID: 3888727
PMID: 24453416
DOI: 10.1155/2013/381815

[…] seven to ten times more intensive than the background signal, and the background evaluation was always evaluated immediately beside the labeled spot., microarray data analysis was performed using genarise free software. the goal of genarise is to identify genes that are good candidates for differential expression by calculating an intensity-dependent z-score, successfully used and recently […]

PMCID: 3967154
PMID: 24287597
DOI: 10.3390/v5122931

[…] the corresponding software (packard biochips). to perform the analysis of microarray data and select genes that are significantly differentially expressed between classes of samples, we used the genarise package developed by the computer unit of the institute of cellular physiology (unam). data were normalized and the mean and standard deviation of the distribution of log2 (ratio) values […]


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