ITALICS 2.28.0 – Normalize of Affymetrix GeneChip Human Mapping 100K and 500K set

ITALICS 2.28.0

:: DESCRIPTION

ITALICS (ITerative and Alternative normaLIzation and Copy number calling for affymetrix Snp arrays) is a normalization method that estimates both biological and non-relevant effects in an alternate, iterative manner, accurately eliminating irrelevant effects.

::DEVELOPER

U900 Institut Curie – INSERM/Mines ParisTech “Bioinformatics and Computational Systems Biology of Cancer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

ITALICS

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Mar 15;24(6):768-74. doi: 10.1093/bioinformatics/btn048.
ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays.
Rigaill G, Hupé P, Almeida A, La Rosa P, Meyniel JP, Decraene C, Barillot E.

BGX 1.34.0 – Bayesian integrated analysis of Affymetrix GeneChips

BGX 1.34.0

:: DESCRIPTION

BGX is a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.

::DEVELOPER

Dr Ernest Turro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BGX

:: MORE INFORMATION

Citation

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.
Turro E, Bochkina N, Hein AM, Richardson S.
BMC Bioinformatics. 2007 Nov 12;8:439.

VIZARD 1.2 – Affymetrix GeneChip® Data Analysis & Visualization

VIZARD 1.2

:: DESCRIPTION

VIZARD is a Java program for analysis and visualization of Affymetrix GeneChip® data.VIZARD includes several integrated tools for filtering, sorting, clustering and visualization of gene expression data as well as tools for discovery of regulatory motifs in upstream sequences. It also includes annotation and upstream sequence databases for the majority of genes represented on the Affymetrix Arabidopsis 8K GeneChip® array.

When VIZARD was created its name originated from VIsualiZe microARray Data. Now it does much more than visualization of gene expression data, however, we have decided to keep the name.

::DEVELOPER

Nick Moseyko

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

VIZARD

:: MORE INFORMATION

It is available free of charge for educational, research, and not-for-profit purposes. To read full text of the terms under which the program is distributed, click here.