BioC 1.9 Released

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)