[BioC] Bioconductor 2.6 is released

Sun Apr 25 14:58:02 CEST 2010

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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>>>
>>
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>
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