August Changes in BioC Devel

   August 2005

affxparser
    Added support for parsing just the headers of cdf and celfiles
    Added man files for parsing celfiles

affy
    Changed rma2.c to avoid segfault in extremely high memory usage situations.
   
AnnBuilder   
    Fixed UniGene URL
    Modified getPubDataArabidopsis in order to create local mirror for Arabidopsis
    Fixed bug that caused errors when thee are more than two otherSrc in the ABPkgBuilder
    Fixed parseKEGGGenome to accept KEGG entries that don't have 'Definition' slots.
    Modified egGoParser to handle the '\s' character at end of line
   
Biobase
    Removed dependency on hu6800 and golubMerge
    Changes to eSet class:
        reporterInfo slot in annotatedDataset
        data.frameORNULL union to support legacy annotated Dataset objects
    Added eset.Rnw for discussion of eSet class

biomaRt
    Use mget instead of get
    Added comments to examples
    Added first version of BioMart API functions
    New vignette
    Fixed bug in getFeature

DNAcopy
    Added code for hybrid p-value computation and made it the default
   
gcrma
    Version updated to 2.0 details in vignette

GlobalAncova
    Vignette added

goCluster
    Fixed bug discovered by Mark W. Kimpel
    goCluster now accepts specifying something other than rownames in the configuration dialog
   
GOstats
    Fixed example for shortestPath
graph
    Major reorganization of code
    Vectorized edgeProps, isAdjacent and edgeAttributes methods
    Added check for symmetric incidence matrix for undirected case of graphIM
    Can now specify how to interpret values in incidence matrix,
    for example to use values as weights or color values
    Added removeEdge method to graphIM
    Added ability to set weights based on inciMat in initialize
    Default is to set an edgeSet attribute weight with default value of 1
    Added simple clearNode and removeNode implementations
    Added a test for difected graphs
    Added a test for clearNode
    Use lists instead of environments for internal data structures
    Added edgemode to graphIM constructor   
    Added addNotes and Edge methods to graphIM
    Refactor edgeSet methods for use within a graphIM instance
    Added isAdjacent method to test for existence of an edge in a graph
    Added tests to define edge attribute API
    Added isDirected generic
    Added numNodes and numEdges for graphIM
    Added beginnings of edgeSet class, a generic container for edges
    Added ability to track arbitrary node objects in a graphIM instance
    Added nodes method for graphIM

iSNetwork
    Created functions to create children models
    Fixed bug in callback functions
    Made changes so graph models and views can be updated through messages

limma   
    Version 2.0.7

maanova
    New package:
        Analysis of N-dye Micro Array experiment using mixed model effect.
        Containing anlysis of variance, permutation and bootstrap, cluster and consensus tree.
    Maintainer:
        Hao Wu

makePlatformDesign
    Changed order of probes

matchprobes
    Patch from Paul Roebuck - getProbeDataAffy can now use connections
   
MVCClass
    Created functions to create children models
    Fixed bug in callback functions


oligo
    Changed rma2.c to avoid segfault in extremely high memory usage situations.
    Minor changes to accomodate eSet structure
    Added quantile normalization for oligoBatch
    Depends on Biobase 1.6.6
   
pdmclass
    New vignette

prada
    Default coloring for plotNorm2 is now according to density (uses densCols)
   
RBGL
    Fixed brandes.betweenness.centrality
    Fixed configure script for Solaris
    Implement highlyConnSG function
reb
    New package:
        A set of functions to dentify regional expression biases
    Maintainer:
        Karl J. Dykema
    Added buildChromLocation.2 function
    Added ideogram v1.2.2 requirement
   
Resourcerer
    Code modified to allow users to access data for more species
   
tilingArray
    Updated plot.segmentation to handle large segmentation objects
    Fixed plotAlongChrom
    plotAlongChrom2 is now obsolete
    Added confidence interval computations
    Extended plotAlongChrom to show ALL features

timecourse
    New package:
        Functions for data analysis and graphical displays for developmental microarray
        time course data.
    Maintainer:
        Yu Chuan Tai
xcms
    findPeaks now returns full precision mass values regardless of step size
    Added check for invalid retention times and possibly corrupt index
    Added rounding to EIC plot titles
    Added mzXML raw data import
    Added linear alignment method to retcor
    Added check for too small span in retcor
    Ported RAMP to Linux x86_64, Windows MinGW, and Mac OS X
    Added base peak and total ion current header parsing
    Added preprocessing vignette   
    Added xcmsEIC class