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: 2.8

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, GUI, 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, HuExExonProbesetLocation, 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 1.18.7
Since Bioconductor 2.0 (R-2.5)

Package Downloads

Package Source oneChannelGUI_1.18.7.tar.gz
Windows Binary oneChannelGUI_1.18.7.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary oneChannelGUI_1.18.7.tgz
Package Downloads Report Download Stats

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