oneChannelGUI

This package extends the capabilities of affylmGUI graphical interface. Affymetrix 3' IVT, gene an exon arrays are actually implemented togheter with Illumina, GEO matrix series files and tab delimited files. Next Generation Sequencing secondary analysis for ncRNA quantification is also available.

Bioconductor version: 2.7

This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface for microarray gene and exon level analysis as well as basic secondary analysis of NGS data for ncRNA quantification.

Author: Raffale A Calogero, Bioinformatics and Genomics Unit, Dept. of Clinical and Biological Sciences Torino (Italy)

Maintainer: Raffaele A Calogero <raffaele.calogero at unito.it>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("oneChannelGUI")

To cite this package in a publication, start R and enter:

    citation("oneChannelGUI")

Documentation

PDF		fignew42.pdf
PDF	R Script	oneChannelGUI Installation
PDF	R Script	oneChannelGUI Next generation Sequencing
PDF	R Script	oneChannelGUI Overview
PDF	R Script	oneChannelGUI Stand Alone Functions
PDF	R Script	oneChannelGUI What is New
PDF		Reference Manual

Details

biocViews	HighThroughputSequencing, RNAseq, Microarray, OneChannel, DataImport, QualityControl, Preprocessing, Statistics, DifferentialExpression, MultipleComparisons
Depends	Biobase, limma, affylmGUI, tkWidgets, GOstats, AnnotationDbi, preprocessCore, IRanges, edgeR, baySeq, girafe
Imports
Suggests	annotate, genefilter, maSigPro, pamr, pdmclass, ChIPpeakAnno, chipseq, BSgenome, Rgraphviz, affy, annaffy, affyPLM, multtest, ssize, sizepower, siggenes, RankProd, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, metaArray, MergeMaid, biomaRt, GenomeGraphs, AffyCompatible, Biostrings, IRanges, rtracklayer, Genominator, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, ragene10sttranscriptcluster.db, HuExExonProbesetLocationHg19, MoExExonProbesetLocation, RaExExonProbesetLocation, snow, RmiR, RmiR.Hs.miRNA
System Requirements
License	The Artistic License, Version 2.0
URL	http://www.bioinformatica.unito.it/oneChannelGUI/
Depends On Me
Imports Me
Suggests Me
Version	1.16.5
Since	Bioconductor 2.0 (R-2.5)

Package Downloads

Package Source	oneChannelGUI_1.16.5.tar.gz
Windows Binary	oneChannelGUI_1.16.5.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	oneChannelGUI_1.16.5.tgz
Package Downloads Report	Download Stats

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