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/CustomCD F/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 D?ez <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)