AACK 1.0 – Add Annotation

AACK 1.0

:: DESCRIPTION

AACK adds annotation from a file to a PCL (pre-clustering) data file. AACK is written in perl.

The annotation file requires an ID and Name column. The ID’s are read from the first column of the PCL file, and the annotations are added to the second column. Does not affect the data. Intended for situations in which a different annotation is desired, such as when an annotation is published for a microarray constructed pre-annotation.

::DEVELOPER

Falkow Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac Os / Linux
Perl
TK

:: DOWNLOAD

AACK for Win ; Source Code

:: MORE INFORMATION

The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.

CAGED 1.1 – Cluster Analysis of Gene Expression Dynamics

CAGED 1.1

:: DESCRIPTION

CAGED (Cluster Analysis of Gene Expression Dynamics) is a model based,Bayesian clustering procedure developed by Ramoni et al. to cluster gene expression profiles measured with microarrays in temporal experiments. Contrary to popular clustering methods, CAGED takes into account explicitly the fact that expression profiles in temporal experiments may be serially correlated and uses a model-based, Bayesian procedure to identify the best grouping of the gene expression data in an automated way.

CAGED implements a Bayesian clustering method designed to handle temporal experiments and subsuming standard independent experiments as a special case.

::DEVELOPER

Marco Ramoni & Paola Sebastiani

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

CAGED

:: MORE INFORMATION

You will need a password to use this program. Please email sebas@bu.edu for a password.

AMIADA 2.0.7 – Analysis of Microarray Data

AMIADA 2.0.7

:: DESCRIPTION

AMIADA is an integrated computer program for organizing, exploring, visualizing, and analyzing microarray data. It features an EXCEL-like user interface and performs data transformation, principal component analysis, a variety of cluster analysis and extensive graphic functions for visualizing expression profiles.

::DEVELOPER

Dr. Xuhua Xia

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

AMIADA

:: MORE INFORMATION

Citation : Xia, X., and Xie. Z., 2001 AMADA: Analysis of microarray data. Bioinformatics 17:569-570.

MAExplorer 0.96.34.01 – MicroArray Explorer Tool

MAExplorer 0.96.34.01

:: DESCRIPTION

The MAExplorer is a Java-based bioinformatics exploratory data-analysis and data-mining program for analyzing sets of quantitative spotted cDNA or oligonucleotide microarray data . It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user written MAEPlugins, documentation, tutorials, demo data. The exploratory data analysis environment provides tools for the data-mining of quantitative expression profiles across multiple microarrays.

With MAExplorer, it is possible to: 1) analyze the expression of individual genes; 2) analyze the expression of gene families and clusters; 3) compare expression patterns and outliers; 4) directly access other genomic databases for genes of interest. Previously quantified array data is copied to your local computer where it is read by MAExplorer and intermediate results as well as the data mining session state may be saved between data mining sessions.

::DEVELOPER

Dr. Peter Lemkin (LECB/NCI-Frederick) with help from Gregory Thornwall (SAIC) and Jai Evans (DECA/CIT, NIH)

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Linux
MacOsX
Java

:: DOWNLOAD

MAExplorer 0.96.34.01 , Manual

:: MORE INFORMATION

MAExplorer is available as Open Source at the SourceForge at http://maexplorer.sourceforge.net/ under the Mozilla Public License 1.1 (MPL 1.1) with an acompanying LEGAL document required by the U.S. Government.