Question: ANN: Bioconductor Release 1.7 is available
0
gravatar for Seth Falcon
14.0 years ago by
Seth Falcon7.4k
Seth Falcon7.4k 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 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
ADD COMMENTlink modified 14.0 years ago by Norman Pavelka190 • written 14.0 years ago by Seth Falcon7.4k
Answer: ANN: Bioconductor Release 1.7 is available
0
gravatar for Wolfgang Huber
14.0 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Hi Seth + Team, great job! Thank you very much for getting this release out - You did a tremendous amount of work for this. Best wishes Wolfgang 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. ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber
ADD COMMENTlink written 14.0 years ago by Wolfgang Huber13k
Answer: ANN: Bioconductor Release 1.7 is available
0
gravatar for Mikko Arvas
14.0 years ago by
Mikko Arvas90
European Union
Mikko Arvas90 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 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 > >_______________________________________________ >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 mobile: +358-(0)44-381 0502 fax: +358-(0)20-722 7071 mail: Tietotie 2, Espoo P.O. Box 1500 FIN-02044 VTT, Finland Protein production group's website: http://www.vtt.fi/bel/bpro/proteinprod/indexe.htm
ADD COMMENTlink written 14.0 years ago by Mikko Arvas90
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 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 >> >> _______________________________________________ >> 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 > mobile: +358-(0)44-381 0502 > fax: +358-(0)20-722 7071 > mail: Tietotie 2, Espoo > P.O. Box 1500 > FIN-02044 VTT, Finland > > Protein production group's website: > http://www.vtt.fi/bel/bpro/proteinprod/indexe.htm > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
ADD REPLYlink written 14.0 years ago by Benilton Carvalho4.3k
Answer: ANN: Bioconductor Release 1.7 is available
0
gravatar for Norman Pavelka
14.0 years ago by
Norman Pavelka190 wrote:
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ADD COMMENTlink written 14.0 years ago by Norman Pavelka190
Hi Norman this is going to happen this week as Simon Urbanek is traveling and Fritz L. is setting up the new mirroring. I can assure that everything is already in place, tested and working. Just wait a couple of days more. stefano On 17/ott/05, at 12:38, Norman Pavelka wrote: > First of all, congratulations to the whole BioC team for the new > release! > > Secondly, since BioC 1.7 relies on R 2.2, are there any news > regarding when the R 2.2 installer is scheduled to be released for > Mac OS X (in the form of the usual disk image)? I still couldn't > find it on CRAN... Maybe Stefano has any clues? I'd like to avoid > installing it from source... > > Thanks in advance! > > Best, > Norman > > Norman Pavelka > Department of Biotechnology and Bioscience > University of Milano-Bicocca > Piazza della Scienza, 2 > 20126 Milan, Italy > > Phone: +39 02 6448 3556 > Fax: +39 02 6448 3552 > > On 15 Oct 2005, at 12:00, bioconductor-request at stat.math.ethz.ch > wrote: > > >> From: Seth Falcon <sfalcon at="" fhcrc.org=""> >> Date: 15 October 2005 01:56:16 GMT+02:00 >> To: bioconductor at stat.math.ethz.ch, bioc-devel at stat.math.ethz.ch >> Subject: [BioC] ANN: Bioconductor Release 1.7 is available >> >> >> 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. >> >> >
ADD REPLYlink written 14.0 years ago by stefano iacus430
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