Software

INCLUSive

INCLUSive is suite of web-based tools and is aimed at the automatic multistep analysis of microarray data. The goal is to provide an integrated platform where several sources of information can be linked together to facilitate the analysis of microarray data. Currently, preprocessing of microarray data, adaptive quality-based clustering, information retrieval of genes in clusters, retrieval of upstream sequences and motif finding algorithms are accessible from this website or from the results pages of the different analysis steps.

To facilitate intergration we also provide a set of SOAP web services for the different tools in INCLUSive. Check them out at the web portal.

Name	Description
Maran	Microarray Analysis using ANOVA
AQBC	Adaptive quality-based clustering of gene expression profiles.
Intergenic Select	Select intergenic regions based on the accession number and the name of the gene of interest.
MotifSampler	Detection of over-represented motifs in the upstream region of coregulated genes.
MotifScanner	Detection of pre-defined motif models in DNA sequences.
ModuleSearcher	ModuleSearcher localizes modules of cooperating transcription factors.
Go4G	Find statistical significant GO terms in set of genes.

Mailing List If you like to be informed on updates and new versions of our programs, you should join the INCLUSive mailing list.

Gibbs BiClustering

Gibbs BiClustering is a web-service that allows to search for specific patterns of subsets of genes and conditions witin a microarray data matrix.

TOUCAN

TOUCAN is a workbench for regulatory sequence analysis on metazoan genomes, especially for detecting significant transcription factor binding sites. It is a platform independent, standalone Java application and was built using the BioJava package.

Mailing List If you like to be informed on TOUCAN, you should join the TOUCAN mailing list.

Endeavour

Endeavour is a software application for the computational prioritisation of test genes, based on a set of training genes. The ranking of a test gene is based on its similarity with the training genes, using many different information sources.

TXTGate

TXTGate is a web-service that combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes. By means of tailored vocabularies, selected textual fields and MEDLINE abstracts of LocusLink and SGD are indexed. Subclustering and links to external resources allow for an in-depth analysis of the resulting term profiles.
The accompanying article "TXTGate: profiling gene groups with text-based information", was published in Genome Biology.

GeneTimer

GeneTimer fetches temporal profiles for HUGO Gene Names from PUBMED abstracts. When you enter a gene name, a graph will pop up and show how this gene has emerged in biomedical literature throughout time. The application looks as far back as 1970, and includes PUBMED abstracts up until mid 2004.

M@CBETH

M@CBETH is an online benchmarking tool to build an optimal two-class classifier with your microarray data.

Downloads

Here are the links to the pages where you can download software or specific data sets.

INCLUSive Motif finding tools	Download stand alone executable and auxiliary programs for our suite of motif finding tools.
Background Models	Select and retrieve pre-compiled background models.
Motif Models	Matrix files of Transfac, SCPD, PlantCARE and Jaspar that can be used with TOUCAN, MotifScanner, MotifLocator, ...
Expected Frequency	Files with expected frequencies that can be used with TOUCAN
ModuleSearcher	jar file to run ModuleSearcher in a standalone fashion.
RMAGEML	RMAGEML provides a link between cDNA microarray data stored in MAGE-ML format and the Bioconductor framework for preprocessing, visualization and analysis of microarray experiments.
biomaRt	biomaRt is a new Bioconductor package that integrates BioMart data resources such as Ensembl, with data analysis in Bioconductor.