[BioC] Bioconductor 2.6 is released

Mon Apr 26 10:07:46 CEST 2010

hi,

if you're just asking about how to use these two versions of R, what i
do in my ubuntu box is to have them living in separate directories
within /opt, i.e., (note that i haven't updated yet to the latest
release of R -shame on me-):

$ ls /opt/R
drwxr-xr-x 13 rcastelo fg 4.0K Feb 25 14:56 R-2.10.1
drwxr-xr-x 13 rcastelo fg 4.0K Feb 26 09:50 R-devel
lrwxrwxrwx  1 rcastelo fg   17 Feb 26 09:50 devel -> ./R-devel/lib64/R
lrwxrwxrwx  1 rcastelo fg   18 Feb 25 14:56 release
-> ./R-2.10.1/lib64/R

so that when i want to execute release i do

$ /opt/R/release/bin/R

and when i want to execute devel i do

$ /opt/R/devel/bin/R

although in fact i have a ~/bin directory with symbolic links R and
Rdevel to these executables, respectively.

hope it helps,

robert.

On Sun, 2010-04-25 at 08:58 -0400, Lax wrote:
> Could any one share instrctions/info on maintaining both the release  
> as well as  development version of R/bioconductor on an Ubuntu box?
> It would certainly help folks like me avoid a lot of experimetation  
> and conflict headache.
> -Best
> -Lax
> Sent from my iPhone
> 
> On Apr 23, 2010, at 5:41 PM, Thomas Girke <thomas.girke at ucr.edu> wrote:
> 
> > Oops, this message was intended for my co-workers only. Sorry for
> > missing to delete the bioc address under CC. - My intention was to
> > remind ourself to install the latest R/BioC release on our shared
> > Linux cluster as soon as possible.
> >
> > I am looking forward using all the new packages.
> >
> > Thanks for the hard work.
> >
> > Thomas
> >
> >
> > On Fri, Apr 23, 2010 at 02:02:02PM -0700, Thomas Girke wrote:
> >> This means that we should now install R-2.11.0 and make it the  
> >> default
> >> if the install goes fine...
> >>
> >> Thomas
> >>
> >> On Fri, Apr 23, 2010 at 12:22:58PM -0700, Patrick Aboyoun wrote:
> >>> Bioconductors:
> >>>
> >>> We are pleased to announce the release of Bioconductor 2.6. This  
> >>> release
> >>> includes 37 new software packages, and many changes to existing
> >>> packages. Bioconductor 2.6 consists of 389 software packages and is
> >>> compatible with the recently released R 2.11.0.
> >>>
> >>> Bioconductor 2.6 is supported on Linux, 32-bit Windows, Mac OS X  
> >>> 10.5
> >>> (Leopard), and Mac OS X 10.6 (Snow Leopard). Bioconductor 2.6 also  
> >>> has
> >>> experimental 64-bit Windows builds for most of its packages.
> >>>
> >>> Please visit http://bioconductor.org for details and downloads.
> >>>
> >>>
> >>> Contents
> >>> ========
> >>>
> >>> o Getting Started with Bioconductor 2.6
> >>> o New Software Packages
> >>> o Additional Software Package Changes
> >>>
> >>>
> >>> Getting Started with Bioconductor 2.6
> >>> =====================================
> >>>
> >>> To install Bioconductor 2.6
> >>>
> >>> 1. Install R 2.11.0.  Bioconductor 2.6 has been designed expressly  
> >>> for
> >>> this version of R.
> >>>
> >>> 2. Follow the instructions here:
> >>>
> >>> http://bioconductor.org/docs/install
> >>>
> >>> Please visit http://bioconductor.org for details and downloads.
> >>>
> >>>
> >>> New Software Packages
> >>> =====================
> >>>
> >>> There are 37 new packages in this release of Bioconductor.
> >>>
> >>> New sequence analysis tools address infrastructure (GenomicRanges,
> >>> Rsamtools, girafe); ChIP-seq (BayesPeak, CSAR, PICS, tigre); digital
> >>> gene expression and RNA-seq (DESeq, goseq, segmentSeq); and motif
> >>> discovery (MotIV, rGADEM).
> >>>
> >>> Microarray analysis includes new packages for pre-process and
> >>> technology-specific assays (affyILM, frma, frmaTools, BeadDataPackR,
> >>> MassArray); analysis of specific experimental protocols (charm,  
> >>> genoCN,
> >>> iChip, methVisual); and novel statistical methods  
> >>> (ConsensusClusterPlus,
> >>> ExpressionView, eisa, GSRI, PROMISE).
> >>>
> >>> Flow cytometry packages include SamSPECTRAL, flowMeans, flowTrans,  
> >>> and
> >>> iFlow.
> >>>
> >>> Annotation and integrative analysis are facilitated by new packages
> >>> interfacing with GEO (GEOsubmission), the Sequence Read Archive  
> >>> (SRAdb),
> >>> and tabulation of genome sequence project data (genomes); the GSRI
> >>> package to estimate differentially expressed genes in a gene set;  
> >>> PCA
> >>> and CCA dependency modeling (pint); and updated access to exon array
> >>> annotations (xmapcore).
> >>>
> >>>
> >>> Packages in detail
> >>> ------------------
> >>>
> >>> 1. affyILM
> >>> Linear Model of background subtraction and the Langmuir isotherm
> >>> http://bioconductor.org/packages/2.6/bioc/html/affyILM.html
> >>>
> >>> 2. BayesPeak
> >>> Bayesian Analysis of ChIP-seq Data
> >>> http://bioconductor.org/packages/2.6/bioc/html/BayesPeak.html
> >>>
> >>> 3. BeadDataPackR
> >>> Compression of Illumina BeadArray data
> >>> http://bioconductor.org/packages/2.6/bioc/html/BeadDataPackR.html
> >>>
> >>> 4. charm
> >>> Analysis of DNA methylation data from CHARM microarrays
> >>> http://bioconductor.org/packages/2.6/bioc/html/charm.html
> >>>
> >>> 5. ConsensusClusterPlus
> >>> Algorithm for determining cluster count and membership by stability
> >>> evidence in unsupervised analysis
> >>> http://bioconductor.org/packages/2.6/bioc/html/ConsensusClusterPlus.html
> >>>
> >>> 6. CSAR
> >>> Statistical tools for the analysis of ChIP-seq data
> >>> http://bioconductor.org/packages/2.6/bioc/html/CSAR.html
> >>>
> >>> 7. DESeq
> >>> Digital gene expresion analysis based on the negative binomial  
> >>> distribution
> >>> http://bioconductor.org/packages/2.6/bioc/html/DESeq.html
> >>>
> >>> 8. eisa
> >>> Expression data analysis via the Iterative Signature Algorithm
> >>> http://bioconductor.org/packages/2.6/bioc/html/eisa.html
> >>>
> >>> 9. ExpressionView
> >>> Visualize biclusters identified in gene expression data
> >>> http://bioconductor.org/packages/2.6/bioc/html/ExpressionView.html
> >>>
> >>> 10. flowMeans
> >>> Non-parametric Flow Cytometry Data Gating
> >>> http://bioconductor.org/packages/2.6/bioc/html/flowMeans.html
> >>>
> >>> 11. flowTrans
> >>> Parameter Optimization for Flow Cytometry Data Transformation
> >>> http://bioconductor.org/packages/2.6/bioc/html/flowTrans.html
> >>>
> >>> 12. frma
> >>> Frozen RMA and Barcode
> >>> http://bioconductor.org/packages/2.6/bioc/html/frma.html
> >>>
> >>> 13. frmaTools
> >>> Frozen RMA Tools
> >>> http://bioconductor.org/packages/2.6/bioc/html/frmaTools.html
> >>>
> >>> 14. genoCN
> >>> genotyping and copy number study tools
> >>> http://bioconductor.org/packages/2.6/bioc/html/genoCN.html
> >>>
> >>> 15. genomes
> >>> Genome sequencing project metadata
> >>> http://bioconductor.org/packages/2.6/bioc/html/genomes.html
> >>>
> >>> 16. GenomicRanges
> >>> Representation and manipulation of genomic intervals
> >>> http://bioconductor.org/packages/2.6/bioc/html/GenomicRanges.html
> >>>
> >>> 17. GEOsubmission
> >>> Prepares microarray data for submission to GEO
> >>> http://bioconductor.org/packages/2.6/bioc/html/GEOsubmission.html
> >>>
> >>> 18. girafe
> >>> Genome Intervals and Read Alignments for Functional Exploration
> >>> http://bioconductor.org/packages/2.6/bioc/html/girafe.html
> >>>
> >>> 19. goseq
> >>> Gene Ontology analyser for RNA-seq and other length biased data
> >>> http://bioconductor.org/packages/2.6/bioc/html/goseq.html
> >>>
> >>> 20. GSRI
> >>> Gene Set Regulation Index
> >>> http://bioconductor.org/packages/2.6/bioc/html/GSRI.html
> >>>
> >>> 21. hyperdraw
> >>> Visualizing Hypergaphs
> >>> http://bioconductor.org/packages/2.6/bioc/html/hyperdraw.html
> >>>
> >>> 22. iChip
> >>> Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
> >>> http://bioconductor.org/packages/2.6/bioc/html/iChip.html
> >>>
> >>> 23. iFlow
> >>> GUI based visualization for flow cytometry
> >>> http://bioconductor.org/packages/2.6/bioc/html/iFlow.html
> >>>
> >>> 24. keggorthology (replaces keggortho)
> >>> graph support for KO, KEGG Orthology
> >>> http://bioconductor.org/packages/2.6/bioc/html/keggorthology.html
> >>>
> >>> 25. MassArray
> >>> Analytical Tools for MassArray Data
> >>> http://bioconductor.org/packages/2.6/bioc/html/MassArray.html
> >>>
> >>> 26. methVisual
> >>> Methods for visualization and statistics on DNA methylation data
> >>> http://bioconductor.org/packages/2.6/bioc/html/methVisual.html
> >>>
> >>> 27. MotIV
> >>> Motif Identification and Validation
> >>> http://bioconductor.org/packages/2.6/bioc/html/MotIV.html
> >>>
> >>> 28. PICS
> >>> Probabilistic inference of ChIP-seq
> >>> http://bioconductor.org/packages/2.6/bioc/html/PICS.html
> >>>
> >>> 29. pint
> >>> Pairwise INTegration of functional genomics data
> >>> http://bioconductor.org/packages/2.6/bioc/html/pint.html
> >>>
> >>> 30. PROMISE
> >>> PRojection Onto the Most Interesting Statistical Evidence
> >>> http://bioconductor.org/packages/2.6/bioc/html/PROMISE.html
> >>>
> >>> 31. rGADEM
> >>> De novo motif discovery
> >>> http://bioconductor.org/packages/2.6/bioc/html/rGADEM.html
> >>>
> >>> 32. Rsamtools
> >>> Import aligned BAM file format sequences into R / Bioconductor
> >>> http://bioconductor.org/packages/2.6/bioc/html/Rsamtools.html
> >>>
> >>> 33. SamSPECTRAL
> >>> Identifies cell population in flow cytometry data
> >>> http://bioconductor.org/packages/2.6/bioc/html/SamSPECTRAL.html
> >>>
> >>> 34. segmentSeq
> >>> Takes high-throughput sequencing data and uses it to define  
> >>> segments of
> >>> the genome to which a high density of reads align
> >>> http://bioconductor.org/packages/2.6/bioc/html/segmentSeq.html
> >>>
> >>> 35. SRAdb
> >>> A compilation of metadata from NCBI SRA and tools
> >>> http://bioconductor.org/packages/2.6/bioc/html/SRAdb.html
> >>>
> >>> 36. tigre
> >>> Transcription factor Inference through Gaussian process  
> >>> Reconstruction
> >>> of Expression
> >>> http://bioconductor.org/packages/2.6/bioc/html/tigre.html
> >>>
> >>> 37. xmapcore
> >>> Core access to the xmap database (installed separately)
> >>> http://bioconductor.org/packages/2.6/bioc/html/xmapcore.html
> >>>
> >>>
> >>> Additional Software Package Changes
> >>> ===================================
> >>>
> >>> keggorth has been renamed keggorthology.
> >>>
> >>> _______________________________________________
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> >>> Bioconductor at stat.math.ethz.ch
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>
> >>
> >> _______________________________________________
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> >>
> >
> > _______________________________________________
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