[BioC] Recent changes to Bioconductor packages

madman at jimmy.harvard.edu madman at jimmy.harvard.edu
Sat May 22 11:00:02 CEST 2004

This is an automated message sent out weekly to report recent changes
to Bioconductor packages.  Please see the URL 
http://www.bioconductor.org/changelog.html for a complete history of 
changes.  Unless otherwise noted, these changes apply to the developmental
packages only.
May 19, 2004. MetaData - Developmental annotation data packages
     (1.6.0) are available. New features include:
     a. Environments pkgNameNM and pkgNameNP (e. g. hgu95av2NM) no
        longer exist in the platform specific packages
        (e. g. hgu95av2) but are replaced by a new environment
        pkgNameREFSEQ that contains the annotation data for all the
        RefSeq accession records. The environment HGID has been
        droped. Mappings between probe ids to HGID can be obtained
        through the mappings to LocusLink ids to HGIDs in the homology data
     b. GO package contains new environments ANCESTOR and OFFSPRING
        that maps GO ids to all the ancestor and offspring along the
        GO tree. GOTERM no longer exists and is replaced by GOTERMS
        that maps GO ids to GOTerms objects with a GOId, Ontology
        (originally in GOTERM), Synonym, Secondary, Definition, and 
        Category slots.
     c. homology package now maps internal HomoloGeneIds to homoData
        objects that has slots for organism name, LocusLink ids, 
        internal HomoloGeneIds, GenBack Accession numbers, type of
        similarities, percent of identity, and urls for homologous 
        genes in other organism. Environment LL2HGID maps LocusLink
        ids to internal HomoloGeneIds.
     d. New annotation data packages for non-Affymetrix chips have
        been added. New packages include hguMWG30kA, hguMWG30kB,
        mguAtlas5k mguG4104A, mguG4120A, mguG4121A, mguMWG30kA,
        mguMWG30kB, rguAtlas5k, rguG4105A, rguG4130A, rguMWG10k,
        rguMWG5k. Pakckages with Atlas as part of the names are for BD
        Biosciences microarrays, MWG are for MWGAG BIOTECH microarrays, and G
        for Agilent microarrays.

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