[BioC] Release 1.7 - Oligo package?

Mikko Arvas Mikko.Arvas at vtt.fi
Mon Oct 17 10:48:53 CEST 2005


I thought the Oligo package would be coming with this release. I'll be 
getting set of xys format files from Nimblegen this week and would have 
liked to give it a go. Can I get it from somewhere else?

All the best,

At 16:56 14.10.2005 -0700, Seth Falcon wrote:
>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.
>- 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
>Title: Affymetrix File Parsing SDK
>Author: James Bullard, Kasper Daniel Hansen
>Title: QC Report Generation for affyBatch objects
>Author: Craig Parman, Conrad Halling
>Title: Compute cluster stability scores for microarray data
>Author: James W. MacDonald, Debashis Ghosh, Mark Smolkin
>Title: Performs differential gene expression Analysis
>Author: Choudary Jagarlamudi
>Title: Vector objects for R with external storage
>Author: Saikat DebRoy
>Title: FDR adjustments of Microarray Experiments (FDR-AME)
>Author: Yoav Benjamini, Effi Kenigsberg, Anat Reiner, Daniel Yekutieli
>Title: Calculates a global test for differential gene expression
>Author: U. Mansmann, R. Meister
>Title: Heterogeneous error model for identification of differentially 
>expressed genes under multiple conditions
>Author: HyungJun Cho
>Title: Significant Gene Expression Profile Differeneces in Time Course 
>Microarray Data
>Author: Ana Conesa, Maria José Nueda
>Title: Tools for analyzing Micro Array experiments
>Author: Hao Wu <hao at jax.org>, with ideas from Gary Churchill, Katie Kerr 
>and Xiangqin Cui
>Title: Micro-Array NORmalization
>Author: Pierre Neuvial, Philippe Hupé
>Title: multi-chip modified gamma Model of Oligonucleotide Signal
>Author: Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence
>Title: Classification of Microarray Samples using Penalized Discriminant 
>Author: James W. MacDonald, Debashis Ghosh, based in part on
>Title: Regional Expression Biases
>Author: Kyle A. Furge and Karl Dykema
>Title: Computationally simulates the AP-MS technology.
>Author: Tony Chiang <tchiang at fhcrc.org>
>Title: SBML-R Interface and Analysis Tools
>Author: Tomas Radivoyevitch
>Title: Statistical Analysis for Developmental Microarray Time Course Data
>Author: Yu Chuan Tai
>Best Wishes,
>+ seth
>For the Bioconductor Core Team
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Mikko Arvas
VTT Biotechnology

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