I-Biostat Software Bioinformatics

Software - Bioinformatics

This section contains models in the area of Bioinformatics.
For software in other areas, go to the general overview of software.

For Bioinformatics, the following software is available:

LMM NORMALIZATION OF MICROARRAYS
Program:	Version:	Software:	Version:	Last updated:
Prepared by:
Description:	as described in "Using Linear Mixed Model for Normalization of cDNA
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LMMNORM: GRAPHICAL USER INTERFACE FOR LINEAR MIXED MODEL NORMALIZATION
Program:	Version:	Software:	Version:	Last updated:
Prepared by:
Description:
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TESTING FOR MONOTONIC RELATIONSHIP BETWEEN GENE EXPRESSION AND DOSES IN A MICROARRAY EXPERIMENT
Program: IsoGene	Version: 1.0-1.3	Software: R	Version: 2.7.2	Last updated: 09/09/2008
Prepared by:	Dan Lin
Description:	Library IsoGene aims to identify for genes with a monotonic trend in the expression levels with respect to the increasing doses in the microarray setting using several test statistics. They include the global likelihood ratio test (E^2, Bartholomew 1961, Barlow et al. 1972 and Robertson et al. 1988), Williams (1971, 1972), Marcus (1976), the M (Hu et al. 2005) and the modified M (Lin et al. 2007). The p-values of the five test statistics are obtained using permutation and they are adjusted using BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutilie 2004) procedures which control for the FDR
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DOSE-RESPONSE IN MICROARRAY, IN FUNCTIONAL GENOMICS AREA
Program: IsoGeneGUI	Version: 1.2.1	Software: R	Version: 2.12	Last updated: 31/05/2011
Prepared by:	Setia Pramana
Description:	The IsoGene Graphical User Interface (IsoGeneGUI) is a user friendly interface of the IsoGene package which is aimed to perform analysis of dose-response studies in microarray experiments. The IsoGeneGUI is developed for the user with no or limited knowledge about R programming so he/she can perform the analysis of dose-response in microarray setting easily.
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BICLUSTGUI PACKAGE: A USER FRIENDLY SOFTWARE FOR BICLUSTERING ANALYSIS
Program: BiclustGUI	Version: 1.1.1	Software: R	Version: 2.12	Last updated: 15/07/2011
Prepared by:	Setia Pramana
Description:	BiclustGUI is an extension for Rcmdr (Rcmdr Plug-in) for biclustering analysis. The BiclustGUI was developed by using the R-Tcl/Tk interface implemented in the tcltk package. The BiclustGUI package is the interface of several R packages for biclustering analysis: biclust (Kaiser and Leisch, 2008), fabia (Hochreiter et al., 2010), and isa2 (Csardi et al., 2010). In this current version, the BiclustGUI package has implemented biclustering methods the Plaid, Bimax, delta biclustering (CC), Spectral, Xmotif and Quest from the biclust package, the Factor Analysis for Bicluster Acquisition (FABIA) algorithm from the Fabia package and the Iterative Signature Algorithm (ISA) from the isa2 package.
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