Package: RTools4TB
Type: Package
Title: Data mining of public microarray data through connections to the
        TranscriptomeBrowser database.
Version: 1.2.0
Date: 2009-10-08
Author: Aurelie Bergon, Fabrice Lopez, Julien Textoris, Samuel
        Granjeaud and Denis Puthier
Maintainer: Aurelie Bergon <bergon@tagc.univ-mrs.fr>
Depends: R (>= 2.5.1), Biobase, limma, methods
Collate: script_RTools4TB.R zzz.R
Description: TranscriptomeBrowser (TBrowser) hosts a large collection
        of transcriptional signatures (TS) automatically extracted from
        the Gene Expression Omnibus (GEO) database. Each GEO experiment
        (GSE) was processed so that a subset of the original expression
        matrix containing the most relevant/informative genes was kept
        and organized into a set of homogeneous signatures. Each
        signature was tested for functional enrichment using
        annotations terms obtained from numerous ontologies or curated
        databases (Gene Ontology, KEGG, BioCarta, Swiss-Prot, BBID,
        SMART, NIH Genetic Association DB, COG/KOG...) using the DAVID
        knowledgebase. The RTools4TB package can be used to perform
        complexe queries to the database. Thereby, RTools4TB can be
        helpful (i) to define the biological contexts (i.e,
        experiments) in which a set of genes are co-expressed and (ii)
        to define their most frequent neighbors. In addition, RTools4TB
        comes with a new algoritm, "Density Based Filtering And Markov
        Clustering" (DBF-MCL), whose goal is to partition large and
        noisy datasets. DBF-MCL is a tree-step adaptative algorithm
        that (i) find elements located in dense areas (ie. clusters)
        (ii) uses selected items to construct a graph and (iii)
        performs graph partitioning using MCL. This algorithm is
        implemented in the RTools4TB package although it requires a
        UNIX-like systems.
biocViews: Microarray, OneChannel, TwoChannel, Clustering,
        Classification, DataImport, Annotation, GeneExpression
License: LGPL
Suggests: RColorBrewer, biocGraph, ALL
LazyLoad: yes
URL: http://tagc.univ-mrs.fr/tbrowser/
Packaged: 2009-10-28 10:51:48 UTC; biocbuild
Built: R 2.10.0; i386-pc-mingw32; 2009-10-28 14:44:02 UTC; windows
