[BioC] Bioconductor 1.8 for R 2.3.0 is released!

[Seth Falcon]

We are pleased to announce the release of Bioconductor 1.8.  This
release includes 35 new packages and many improvements and bug fixes
to existing packages.

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

Thanks to all of the package maintainers for their hard work.

Best Wishes,

+ seth

Contents
========

- Release Highlights
- Getting Started With Bioconductor 1.8
- Known Issues
- 35 New Packages
- Packages in 1.7 that didn't make it to 1.8

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

- BiocViews, a new way to browse the Bioconductor package
  repositories.  Have a look:
  http://bioconductor.org/packages/1.8/BiocViews.html

- New cdf and probe packages produced by the Molecular and Behavioral
  Neuroscience Institute (MBNI) at the University of Michigan. These
  packages re-map the individual probes using the most current
  annotation sources (UniGene, RefSeq, ENSEMBL, Entrez Gene, Tigr,
  DoTS, and dbSNP). For more information, please see the MBNI web
  page__

  The naming convention for these packages is more complex than for
  the normal probe and cdf packages, especially since some are mapped
  against related species.  The name is derived as follows:
  SPECIES_CHIP_MAPPED-SPECIES_VERSION_TYPE.  For example, a cdf for
  the HG-U133A chip, mapped to the human genome, and based on Entrez
  Gene would be named hs133ahsentrezg7cdf (based on
  Hs_133A_Hs_version-7_CDF).  The same chip mapped to chimpanzee (Pan
  troglodytes) would be hs133aptentrezg7cdf.

  __ http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp


Getting Started With Bioconductor 1.8
=====================================

To get started with Bioconductor 1.8, please:

- Install R 2.3.0.  Bioconductor 1.8 has been designed expressly for
  this version of R.

- Follow the instructions here:
  http://www.bioconductor.org/docs/install-howto.html


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

- The following packages are not currently available for Windows:

     EBImage      GeneR        iSPlot       maDB
     MVCClass     pgUtils      RdbiPgSQL    RMAGEML      widgetInvoke

- Due to a hardware failure, OS X binaries for Bioconductor 1.8 are
  not currently available.  We expect to have OS X binaries available
  within the next three weeks.

- The YEAST annotation package contains two GO ids (GO:0043625 and
  GO:0043626) that are not present in the GO annotation package.  The
  yeast data used a slightly newer GO build.  We aim to synchronize
  these data resources in the next release.

35 New Packages
===============

affyio
Title: Tools for parsing Affymetrix data files
Maintainer: Benjamin Milo Bolstad <bmb at bmbolstad.com>

gtkWidgets
Title: Widgets built using RGtk
Maintainer: Jianhua Zhang<jzhang at jimmy.harvard.edu>

exprExternal
Title: Implementation of exprSet using externalVectors
Maintainer: Biocore Team <biocpkgs at lists.fhcrc.org>

MVCClass
Title: Model-View-Controller (MVC) Classes
Maintainer: Elizabeth Whalen <ewhalen at hsph.harvard.edu>

LMGene
Title: LMGene Software for Date Transformation and Identification 
Maintainer: Geun Cheol Lee <gcxlee at ucdavis.edu>

biocViews
Title: Categorized views of R package repositories
Maintainer: Seth Falcon <sfalcon at fhcrc.org>

RLMM 
Title: A Genotype Calling Algorithm for Affymetrix SNP Arrays 
Maintainer: Nusrat Rabbee <nrabbee at post.harvard.edu>

affycoretools
Title: Functions useful for those doing repetitive analyses
Maintainer: James W. MacDonald <jmacdon at med.umich.edu>

applera
Title: applera
Maintainer: Francesca Cordero <fcordero at di.unito.it>

MantelCorr
Title: Compute Mantel Cluster Correlations
Maintainer: Brian Steinmeyer <steinmeb at ilya.wustl.edu>

panp
Title: Presence-Absence Calls from Negative Strand Matching Probesets
Maintainer: Peter Warren <peter.warren at verizon.net>

pathRender
Title: Render molecular pathways
Maintainer: Li Long <lilong at isb-sib.ch>

GEOquery
Title: Get data from NCBI Gene Expression Omnibus (GEO)
Maintainer: Sean Davis <sdavis2 at mail.nih.gov>

codelink
Title: Manipulation of Codelink Bioarrays data.
Maintainer: Diego Díez <ddiez at iib.uam.es>

metaArray
Title: Integration of Microarray Data for Meta-analysis
Maintainer: Hyungwon Choi <hwchoi at umich.edu>

snapCGH
Title: Segmentation, normalisation and processing of aCGH data.
Maintainer: Mike Smith <mls40 at cam.ac.uk>

sscore
Title: S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
Maintainer: Richard Kennedy <rkennedy at vcu.edu>

ScISI
Title: In Silico Interactome
Maintainer: Tony Chiang <tchiang at fhcrc.org>

beadarray
Title: Quality control and low-level analysis of BeadArrays
Maintainer: Mark Dunning <md392 at cam.ac.uk>

Mfuzz
Title:  Soft clustering of time series gene expression data 
Maintainer:  Matthias Futschik <m.futschik at biologie.hu-berlin.de>

adSplit
Title: Annotation-Driven Clustering
Maintainer: Claudio Lottaz <claudio.lottaz at molgen.mpg.de>

copa
Title: Functions to perform cancer outlier profile analysis.
Maintainer: James W. MacDonald <jmacdon at med.umich.edu>

sizepower
Title: Sample Size and Power Calculation in Micorarray Studies
Maintainer: Weiliang Qiu <weiliang.qiu at gmail.com>

cellHTS
Title: Analysis of cell-based screens
Maintainer: Wolfgang Huber <huber at ebi.ac.uk>

EBImage
Title: EBImage: R image processing toolkit
Maintainer: Oleg Sklyar <osklyar at ebi.ac.uk>

OCplus
Title: Operating characteristics plus sample size and local fdr for microarray experiments
Maintainer: Alexander Ploner <Alexander.Ploner at ki.se>

Heatplus
Title: A heat map displaying covariates and coloring clusters  
Maintainer: Alexander Ploner <Alexander.Ploner at ki.se>

maCorrPlot
Title: Visualize artificial correlation in microarray data
Maintainer: Alexander Ploner <Alexander.Ploner at ki.se>

nudge
Title: Normal Uniform Differential Gene Expression detection
Maintainer: N. Dean <nemad at stat.washington.edu>

cghMCR
Title: Find chromosome regions showing common gains/losses
Maintainer: J. Zhang <jzhang at jimmy.harvard.edu>

RMAPPER
Title: interface to mapper.chip.org
Maintainer: VJ Carey <stvjc at channing.harvard.edu>

OrderedList
Title: Similarities of Ordered Gene Lists
Maintainer: Claudio Lottaz <Claudio.Lottaz at molgen.mpg.de>

logicFS
Title: Identification of SNP Interactions
Maintainer: Holger Schwender <holger.schwender at udo.edu>

GenomeBase
Title: Base functions for genome data package manipulation
Maintainer: H. Pages <hpages at fhcrc.org>

y2hStat
Title: Y2H Statistical Package
Maintainer: Tony Chiang <tchiang at fhcrc.org>


Packages in 1.7 that didn't make it to 1.8
==========================================

- rhdf5
- msbase
- ideogram (was renamed to idiogram)