[BioC] Release 1.7 - Oligo package?

[Benilton Carvalho]

Hi Mikko,

you'll be able to get oligo from the devel branch soon.

if you get your files before, please let me know, so i can provide you the 
packages.

b.

On Mon, 17 Oct 2005, Mikko Arvas wrote:

>
> Hi,
>
> 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,
> Mikko
>
> 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.
>>
>> 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 José 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 Hupé
>>
>> 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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
> Mikko Arvas
> VTT Biotechnology
>
> Please note new tel/fax number
> from start of year 2005.
>
> e-mail:            mikko.arvas at vtt.fi
> tel:                 +358-(0)20-722 5827
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>
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>
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