We are pleased to announce the release of Bioconductor 1.7. This release includes 17 new packages and many improvements and bug fixes to existing packages. Please visit http://www.bioconductor.org for details and downloads. Contents ======== - Release Highlights - Getting Started With Bioconductor 1.7 - Known Issues - 17 New Packages Release Highlights ================== - Rgraphviz is now available as a binary package for Windows - Annotation data packages now include protein information from IPI (see the PFAM and PROSITE environments in the data packages). Getting Started With Bioconductor 1.7 ===================================== To get started with Bioconductor 1.7, please: - Install R 2.2.0. Bioconductor 1.7 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: affxparser biomaRt GeneR GeneTraffic iSPlot KEGGSOAP maDB MANOR msbase pgUtils RdbiPgSQL rhdf5 RMAGEML SAGElyzer SBMLR stam widgetInvoke - The following packages are not currently available for OS X: aCGH edd RdbiPgSQL rhdf5 RMAGEML xcms - The genbank() function in package annotate is broken. The CGI script it was accessing at NCBI appears not to be functioning. You will see a message like:: parser error : Start tag expected, '<' not found Content-Type: text/html; charset=UTF-8 - The hexbin package is unable to execute its vignette on Windows. A plot method fails giving an error message about -Inf, Inf xlim. - The golubEsets dataset is temporarily unavailable, it will be fixed next week. 17 New Packages =============== affxparser Title: Affymetrix File Parsing SDK Author: James Bullard, Kasper Daniel Hansen affyQCReport Title: QC Report Generation for affyBatch objects Author: Craig Parman, Conrad Halling clusterStab Title: Compute cluster stability scores for microarray data Author: James W. MacDonald, Debashis Ghosh, Mark Smolkin diffGeneAnalysis Title: Performs differential gene expression Analysis Author: Choudary Jagarlamudi externalVector Title: Vector objects for R with external storage Author: Saikat DebRoy fdrame Title: FDR adjustments of Microarray Experiments (FDR-AME) Author: Yoav Benjamini, Effi Kenigsberg, Anat Reiner, Daniel Yekutieli GlobalAncova Title: Calculates a global test for differential gene expression Author: U. Mansmann, R. Meister HEM Title: Heterogeneous error model for identification of differentially expressed genes under multiple conditions Author: HyungJun Cho maSigPro Title: Significant Gene Expression Profile Differeneces in Time Course Microarray Data Author: Ana Conesa, Maria Jos? Nueda maanova Title: Tools for analyzing Micro Array experiments Author: Hao Wu <hao at jax.org>, with ideas from Gary Churchill, Katie Kerr and Xiangqin Cui MANOR Title: Micro-Array NORmalization Author: Pierre Neuvial, Philippe Hup? mmgmos Title: multi-chip modified gamma Model of Oligonucleotide Signal Author: Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence pdmclass Title: Classification of Microarray Samples using Penalized Discriminant Methods Author: James W. MacDonald, Debashis Ghosh, based in part on reb Title: Regional Expression Biases Author: Kyle A. Furge and Karl Dykema simulatorAPMS Title: Computationally simulates the AP-MS technology. Author: Tony Chiang <tchiang at fhcrc.org> SBMLR Title: SBML-R Interface and Analysis Tools Author: Tomas Radivoyevitch timecourse Title: Statistical Analysis for Developmental Microarray Time Course Data Author: Yu Chuan Tai Best Wishes, + seth For the Bioconductor Core Team
[Bioc-devel] ANN: Bioconductor Release 1.7 is available
1 message · Seth Falcon