[BioC] Recent changes to Bioconductor packages
madman at jimmy.harvard.edu
madman at jimmy.harvard.edu
Sat Mar 15 05:00:02 MET 2003
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.
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March 13, 2003: annotate - locuslinkByID and locuslinkQuery now have
a parameter "browse=TRUE". If TRUE (default), the behaviour is as
it was before. If FALSE, the user's browser does not open up on
the URL constructed, but rather will return the URL
acquired. JG
March 13, 2003: AnnBuilder - AnnBuilder has been modified to take advantage
of the functions provided by pubRepo. A PostgreSQL database is no longer
required. Examples of making annotation data packages are given in the
vigenette. - JZ
March 12, 2003: pubRepo - a new package for gettting/processing data from
various public data libraries were added. Class pubRepo has functions to
read data from a source url (using readLines), download data from a source
url, and parse data from source url using a predefined parser and base
file. Subclasses of pubRepo include LL(LocusLink), UG(UniGene), KEGG,
GO(Gene Ontology), GEO(Gene Expression Omnibus), YG(Yease Genome),
GP(GoldenPath) that may have methods for processing data for each
repositoy. Documentation is not complete yet but will be ready soon. -JZ
March 11, 2003: reposTools - winConvertSourceRepos now generates windows
binary packages w/ the name structure of <pkg>.zip instead of
<pkg>_<version>.zip. -JG
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