[BioC] BioC 1.9 is released!

[Seth Falcon]

Hello all,

It is my pleasure to announce the release of Bioconductor 1.9.  This
release includes 26 new packages and many improvements and bug fixes
to existing packages.  Bioconductor 1.9 is compatible with R 2.4.0
released on 3 October.

Please visit http://bioconductor.org for details and downloads.  More
details on the release are below.

Best Wishes,

+ seth (along with the Biocore Team)


Contents
========

Release Highlights
Getting Started With Bioconductor 1.9
Known Issues
25 New Packages
Packages in 1.8 that have been renamed in 1.9
Packages in 1.8 that didn't make it to 1.9


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

Try our package search web application (alpha) and let us know what
you think about it:

   http://mamba41.fhcrc.org/apptest/biocPackageSearch/

The BiocViews are still available in the usual place:

http://www.bioconductor.org/packages/1.9/BiocViews.html

OS X universal binary packages are available.  Special thanks to Simon
Urbanek for his efforts in building these packages.


Getting Started With Bioconductor 1.9
=====================================

To get started:

1. Install R 2.4.0.  Bioconductor 1.9 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:

       arrayQCplot    RdbiPgSQL
       EBImage        RMAGEML
       GGtools        Rredland
       iSNetwork      SAGElyzer
       iSPlot         widgetInvoke
       pgUtils 


25 New Packages
===============

ABarray
  Microarray QA and statistical data analysis for Applied Biosystems

aroma.light
  Light-weight methods for normalization and visualization of
  microarray data using only basic R data types

arrayQCplot
  Explore microarray data and check quality and reproducibility.

beadarraySNP
  Normalization and reporting of Illumina SNP bead arrays

BeadExplorer
  QC, normalisation, annotation and exploration of Illumina BeadChip
  data

BioMVCClass
  Model-View-Controller (MVC) Classes That Use Biobase

gaggle
  Broadcast data between R and Java bioinformatics programs

GGtools
  software and data for genetical genomics (c) 2006 VJ Carey

Harshlight
  A "corrective make-up" program for microarray chips

iSNetwork
  Interactive Network Plots

lapmix
  Laplace Mixture Model in Microarray Experiments

nem
  Nested Effects Models to reconstruct phenotypic hierarchies

pcaMethods
  A collection of PCA methods.

pcot2
  Principle Coordinates and Hotelling's T-Square method

pkgDepTools
  Package Dependency Tools

ppiStats
  Protein-Protein Interaction Statistical Package

quantsmooth
  Quantile smoothing and genomic visualization of array data

RbcBook1
  Support for Springer monograph on Bioconductor

Rredland
  interface to redland RDF utilities

SAGx
  Statistical Analysis of the GeneChip

sigPathway
  Pathway Analysis

spikeLI
  Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool

splots
  Visualization routines for high throughput screens

TypeInfo
  Optional Type Specification Prototype

weaver
  Tools and extensions for processing Sweave documents


Packages in 1.8 that have been renamed in 1.9
=============================================

GenomeBase has been renamed BSgenome
  Infrastructure for Biostrings-based genome data packages


Packages in 1.8 that didn't make it to 1.9
==========================================

1. exprExternal (depends on externalVector)
2. externalVector (unable to pass check)
3. goCluster (removed at maintainer request)
4. MiPP (unable to pass check)
5. reposTools (defunct)
6. rfcdmin (moved to experiment data repository)
7. RLMM (version < 0.99.0)
8. SNAData (moved to experiment data repository)
9. y2hStat (defunct, replaced by more general ppiStats)