ExonMiner – Web Service for GeneChip Exon Array Data Analysis

ExonMiner

:: DESCRIPTION

ExonMiner is the first all-in-one web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells.

::DEVELOPER

ExonMiner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Nov 26;9:494. doi: 10.1186/1471-2105-9-494.
ExonMiner: Web service for analysis of GeneChip Exon array data.
Numata K, Yoshida R, Nagasaki M, Saito A, Imoto S, Miyano S.

AffyGCQC 1.02 – GeneChip Data Quality Control

AffyGCQC 1.02

:: DESCRIPTION

AffyGCQC is the acronym for a bioinformatics tool designed to perform Affymetrix GeneChip Quality Control. This program implements a graphical representation of QC metrics recommended by Affymetrix for GeneChip oligonucleotide array technology. Most importantly, it performs extreme studentized deviate statistical tests for the set of arrays being compared in a given experiment, thus providing an objective measure for outlier detection.

DEVELOPER

Osorio Y Fortéa J, Prina E, Lang T, Milon G, Davory C, Coppée JY, Regnault B.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Apache
R Package
Perl

:: DOWNLOAD

AffyGCQC

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2008 Apr;6(2):317-34.
AffyGCQC: a web-based interface to detect outlying genechips with extreme studentized deviate tests.
Osorio Y Fortéa J, Prina E, Lang T, Milon G, Davory C, Coppée JY, Regnault B.

ProbePlus 1.0 – Analytic Tool for Analyzing Affymetrix GeneChip Gene Expression Array Data

ProbePlus 1.0

:: DESCRIPTION

ProbePlus is an analytical tool for analyzing Affymetrix GeneChip® Gene Expression Array data at probe level. It is able to extract CEL file; integrate Perfect Match (PM) and Mis-match (MM) for a probe pair; generate gene expression index (GEI) from the integrated probe intensities of multiple probe pairs in a probe set; and analyze data directly from probe level data without necessity of generating a GEI for a probe set.

::DEVELOPER

Fred Hutchinson Cancer Research Center

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

ProbePlus

:: MORE INFORMATION

Citation