[Bioc-devel] NEWS November 2006

[James MacDonald]

	November 2006

affxparser
	Bugfix for readCdfUnits() with stratifyBy="mm", which
	previously returned pm probes
	
	Bugfix for readCdfGroupNames() which was crashing on Unix

	Added stratifyBy argument to readCdf()
	
affy
	Changed output from exprSet-based objects to ExpressionSet-based
objects

affycoretools	
	Added ability to plot arbitrary principal components in
plotPCA()

	Added hyperGoutput(), a replacement for the hyperG2annaffy()
	function that uses new functions in GOstats/Category package

affyio
	Added gzipped binary cel file support

affyPLM
	Added standard error output to the RMA model

affyQCreport
	Added lattice dependency

AnnBuilder
	egRefseqParser() modified to skip entries with a missing value
	
	Turned off warning message for mis-matched KEGG file names as
	a given organism may not have all the pathways

Biobase
	Changed makeExpressionSetPackage() to makeDataPackage() with
	an ExpressionSet method

	Added Biobase dependency

biomaRt
	Import RCurl, removed RMySQL from suggests

	Enabled query for data coming from more than two tables when
	using biomaRt in MySQL mode

	Added check to see if the server is down when a query returns
	an empty result

	Updated biomaRt to work with new BioMart v0.5 release

Biostrings
	Renamed 'first' and 'last' slots to 'start' and 'end' in
	BStringViews class

BSgenome
	Instead of having all sequences stored in BStringViews
	objects, now single sequences are stored in DNAString objects,
	and multiple sequences are stored in BStrinbViews objects. As
	a consequence, the definition of the BSgenome class has been
	changed and the show() method prints two separated indices

	Fixed bug in buildDataFiles()
	
	Added getSeq() function

	Added the available.genomes() function

BufferedMatrix
	Added ability to use logical vectors to index BufferedMatrix
	objects

	Registered the C-level functionality so it can potentially be
	used in other packages

BufferedMatrixMethods
	New Package: Provides microarray related methods that utilize
	BufferedMatrix objects

	Maintainer: Benjamin Milo Bolstad

Category
	Integrated hyperGTest() to use KEGG and PFAM as well as GO
terms

	Fixed htmlReport() to use the label argument

	Use appand=FALSE in the definition of the generic of
htmlReport()

	Added DBPkg class for SQLite-based annotation packges
	
	Added various functions for SQLite-based annotation packages

cosmo
	New Package: cosmo searches a set of unaligned DNA sequences for
a shared
	motif that may, for example, represent a common transcription
	factor binding site. The algorithm is similar to MEME, but
	also allows the user to specify a set of constraints that the
	
	position weight matrix of the unknown motif must satisfy. 
	Such constraints may include bounds on the information content
	across certain regions of the unknown motif, for example, and
	can often be formulated on the basis of prior knowledge about 
	the structure of the transcription factor in question.
	The unknown motif width, the distribution of motif occurrences
	(OOPS, ZOOPS, or TCM), as well as the appropriate constraint
	set can be selected data-adaptively.

	Maintainer: Oliver Bembom

GOstats
	Code for htmlReport() moved from GOstats to Category

	Bugfix to probeSetSummary() which was failing due to move of
	functions to Category

KEGGSOAP
	Updated to access KEGG API v6. Added functions
	search_compounds_by_name, search_glycans_by_name,
	search_compounds_by_composition,
	search_glycans_by_composition, search_compounds_by_mass,
	search_glycans_by_mass, search_compounds_by_subcomp,
	search_glycans_by_kcam

made4
	Bugfix to bga(), which errored on certain Affy probeset names

occugene
	New Package: Statistical tools for building random mutagenesis
	libraries for prokaryotes. The package has functions for
	handling the occupancy distribution for a multinomial and for
	estimating the number of essential genes in random transposon
	mutagenesis libraries.

	Maintainer: Oliver Will

pdInfoBuilder
	New Package: This package produces SQLite-based cdf/annotation
	databases for SNP chips. It can be extended for handling other
	chip technologies
	
	Maintainer: Seth Falcon

RefPlus
	New Package: The package contains functions for pre-processing
	Affymetrix data using the RMA+ and the RMA++ methods.

	Maintainer: Kai-Ming Chang

SemSim
	New Package: Implementation of semantic similarity measures
	based on information content of Gene Ontology terms.

	Maintainer: Xiang Guo

smoothMiner
	New Package: use smooth regression to investigate families of
	trajectories

	Maintainer: V. Carey





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