IsoGeneGUI

DOI: 10.18129/B9.bioc.IsoGeneGUI  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see IsoGeneGUI.

A graphical user interface to conduct a dose-response analysis of microarray data

Bioconductor version: 3.16

The IsoGene Graphical User Interface (IsoGene-GUI) is a user friendly interface of the IsoGene package which is aimed to identify for genes with a monotonic trend in the expression levels with respect to the increasing doses. Additionally, GUI extension of original package contains various tools to perform clustering of dose-response profiles. Testing is addressed through several test statistics: global likelihood ratio test (E2), 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 global likelihood ratio test (E2) are obtained using the exact distribution and permutations. The other four test statistics are obtained using permutations. Several p-values adjustment are provided: Bonferroni, Holm (1979), Hochberg (1988), and Sidak procedures for controlling the family-wise Type I error rate (FWER), and BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2001) procedures are used for controlling the FDR. The inference is based on resampling methods, which control the False Discovery Rate (FDR), for both permutations (Ge et al., 2003) and the Significance Analysis of Microarrays (SAM, Tusher et al., 2001). Clustering methods are outsourced from CRAN packages ORCME, ORIClust. The package ORCME is based on delta-clustering method (Cheng and Church, 2000) and ORIClust on Order Restricted Information Criterion (Liu et al., 2009), both perform same task but from different perspective and their outputs are clusters of genes. Additionally, profile selection for given gene based on Generalized ORIC (Kuiper et al., 2014) from package goric and permutation test for E2 based on package orQA are included in IsoGene-GUI. None of these four packages has GUI.

Author: Setia Pramana, Dan Lin, Philippe Haldermans, Tobias Verbeke, Martin Otava

Maintainer: Setia Pramana <setia.pramana at ki.se>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("IsoGeneGUI")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	DifferentialExpression, GUI, Microarray, Software
Version	2.34.0
In Bioconductor since	BioC 2.7 (R-2.12) (12.5 years)
License	GPL-2
Depends	tcltk, xlsx
Imports	Rcpp, tkrplot, multtest, relimp, geneplotter, RColorBrewer, Iso, IsoGene, ORCME, ORIClust, orQA, goric, ff, Biobase, jpeg
LinkingTo
Suggests	RUnit
SystemRequirements
Enhances
URL	http://ibiostat.be/online-resources/online-resources/isogenegui/isogenegui-package
Depends On Me
Imports Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/IsoGeneGUI
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IsoGeneGUI
Package Short Url	https://bioconductor.org/packages/IsoGeneGUI/
Package Downloads Report	Download Stats