Gene Expression
MicroArray Databases
| Database Name |
Description | Tool Name @ crs4 |
|---|---|---|
| BASE | We have installed BASE the BASE - BioArray Software Environment which is a comprehensive free web-based database solution for the
massive amounts of data generated by microarray analysis. It is
released under the GNU General Public License. Interested users should contact us to obtain a login and password to ensure privacy of their data. |
BASE |
| ArrayExpress | ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with MGED
recommendations. The ArrayExpress Data Warehouse stores gene-indexed expression profiles from a curated subset of experiments in the repository. |
|
| SMD | SMD, the Stanford MicroArray Database, stores raw and normalized data from microarray experiments, and provides data retrieval, analysis and visualization tools |
Microarray Tools
We plan to install locally and give access through the web, to the tools needed by our collaborators. If you are interested by such developments, please contact us.| Package name |
description |
Web |
|---|---|---|
| SpliceMiner::arrayPos |
This tool generates an Exon / Variant Coverage Report from a microarray probe sequence file. The report shows the exons that have probes for each gene and also where the probes fall on each splice variant. | arrayPos |
| Expression profiler |
Expression Profiler (http://ep.ebi.ac.uk/) is a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Tools in the Expression Profiler allow to perform cluster analysis, pattern discovery, pattern visualization, study and search Gene Ontology categories, generate sequence logos, extract regulatory sequences, study protein interactions, as well as to link analysis results to external tools and databases. | EP |
| TM4 suite |
The TM4 suite of tools consist of four major applications, Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System (MIDAS), and Multiexperiment Viewer (MeV), as well as a Minimal Information About a Microarray Experiment (MIAME)-compliant MySQL database, all of which are freely available to the scientific research community at TIGR's Software Download Site. | Download |
DataMining
The following tools run locally on the user computer. Please follow the download links to install them locally.| package name | description | FTP download |
|---|---|---|
| R | R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. To download R, please choose your preferred CRAN mirror. | CRAN mirror |
| Bioconductor | Bioconductor is an open source and open development software project for
the analysis and comprehension of genomic data. It has tools and functions for microarray analysis. It has its own web site from which you can download the package. |
bioconductor home |
| Weka |
Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes. |
weka site |