[BioC] BioC 2.0 is available

[Seth Falcon]

It is my pleasure to announce the release of Bioconductor 2.0.  This
release includes 36 new packages and many improvements and bug fixes
to existing packages.  The 214 package in Bioconductor 2.0 are
compatible with R 2.5.0 released on 24 April.

Please visit http://bioconductor.org for details and downloads.


Contents
========

Release Highlights
Getting Started With Bioconductor 2.0
Known Issues
36 New Packages
Packages in 1.9 that didn't make it to 2.0


Release Highlights
==================

This release, I'd like to make special mention of four people who have
contributed annotation data packages.  These individuals worked
closely with us to keep the data sources used in sync.  Their efforts
in adding to the available collection of annotation data packages is
appreciated.

Diego Diez: annotation packages for GE CodeLink chips
	adme16cod  h10kcod  h20kcod  hi16cod  hwgcod  m10kcod  m20kcod
        mi16cod  mwgcod  r10kcod  ri16cod  rwgcod

Simon de Bemard: annotation packages for RNG_MRC chips
	hs25kresogen  mm24kresogen

Pan Du: annotation packages for Illumina chips
	lumiHumanV1  lumiHumanV2  lumiMouseV1  lumiRatV1

Lynn Amon: annotation packages for Illumina chips
	illuminaHumanv1  illuminaHumanv2  illuminaMousev1  	
	illuminaMousev1p1


Getting Started With Bioconductor 2.0
=====================================

To get started:

1. Install R 2.5.0.  Bioconductor 2.0 has been designed expressly for
   this version of R.

2. Follow the instructions here:

       http://bioconductor.org/docs/install-howto.html


Known Issues
============

1. The following packages are not currently available for Windows:

        bgx            pgUtils         widgetInvoke
        exonmap        RdbiPgSQL
        GGtools        RMAGEML
        iSNetwork      Rredland
        iSPlot         RWebServices

2. OS X binary packages are not currently available, but we expect
   these packages to be posted on Monday.  A big thanks to Simon
   Urbanek for his efforts that have made the OS X binary packages
   possible.


36 New Packages
===============

ACME
    Algorithms for Calculating Microarray Enrichment (ACME)
annotationTools
    Annotate microarrays and find orthologs using flat file databases
bgx
    Bayesian Gene eXpression
BufferedMatrix
    A matrix data storage object held in temporary files
BufferedMatrixMethods
    Microarray Data related methods that utlize BufferedMatrix objects
CALIB
    Calibration model for estimating absolute expression
CORREP
    Multivariate Correlation Estimator and Statistical Inference Procedures.
cosmo
    Supervised detection of conserved motifs in DNA sequences
cosmoGUI
    GUI for constructing constraint sets used by the cosmo package 
exonmap
    High level analysis of Affymetrix exon array data
fbat
    Family Based Association Tests for genetic data.
flowCore
    flowCore: Basic structures for flow cytometry data
flowViz
    Visualization for flow cytometry
GeneticsBase
    Classes and functions for handling genetic data
GeneticsDesign
    Functions for designing genetics studies
GeneticsPed
    Pedigree and genetic relationship functions
LBE
    Estimation of the false discovery rate.
lumi
    BeadArray Specific Methods for Illumina Microarrays
makePlatformDesign
    Platform Design Package
MassSpecWavelet
    Mass spectrum processing by wavelet-based algorithms
MiPP
    Misclassification Penalized Posterior Classification
oligo
    Oligonucleotide Arrays
oneChannelGUI
    Set of functions extending the capability of affylmGUI package.
pdInfoBuilder
    Platform Design Information Package Builder
PGSEA
    Parametric Gene Set Enrichment Analysis
puma
    Propagating Uncertainty in Microarray Analysis
rbsurv
    Robust likelihood-based survival modeling with microarray data
RefPlus
    A function set for the RMA+ and the RMA++ methods.
rHVDM
    Hidden Variable Dynamic Modeling
Ringo
    R Investigation of NimbleGen Oligoarrays
RWebServices
    Expose R functions as web services through Java/Axis/Apache
SemSim
    Gene Ontology-based Semantic Similarity Measures
seqLogo
    Sequence logos for DNA sequence alignments
SLqPCR
    Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
SNPchip
    Classes and Methods for high throughput SNP chip data 
topGO
    topGO: Enrichment analysis for Gene Ontology


Packages in 1.9 that didn't make it to 2.0
==========================================

1. applera
2. gff3Plotter
3. MCRestimate
4. mmgmos
5. nudge
6. pairseqsim
7. sagenhaft
8. stam
9. timecourse

For the Biocore Team,

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org