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Question: Bioconductor 2.6 is released
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gravatar for Patrick Aboyoun
7.6 years ago by
Patrick Aboyoun1.6k
United States
Patrick Aboyoun1.6k 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.ht ml 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.
ADD COMMENTlink modified 14 months ago by wangyizhusss0 • written 7.6 years ago by Patrick Aboyoun1.6k
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gravatar for Thomas Girke
7.6 years ago by
Thomas Girke1.6k
United States
Thomas Girke1.6k 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 7.6 years ago by Thomas Girke1.6k
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/ConsensusClusterPlu s.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. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 7.6 years ago by Thomas Girke1.6k
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/ConsensusClusterPlu s.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. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.6 years ago by Lakshmanan Iyer250
It depends on what you mean by maintain. Certainly if you know how to keep R 2.11 and R 2.12 (devel) running and accessible to the users (perhaps with suitable aliases or instructions on how to start the interpreter of choice) you can run biocLite or update.packages (with suitable repos setting) periodically within each R version and packages from both release and devel branches will be accessible. Users will need to attend to the versions with which serialized objects and workspaces were created, and should use sessionInfo() in their Sweave documents to avoid confusion. If you want to have access to both release and devel source archives, svn can be used to populate different folders with the desired sources. A recent posting to the list from Patrick gives details of the relevant URLs. On Sun, Apr 25, 2010 at 8:58 AM, Lax <laxvid@gmail.com> 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@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/ConsensusClusterPl us.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. >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 7.6 years ago by Vincent J. Carey, Jr.6.2k
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/ConsensusClusterP lus.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. > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at stat.math.ethz.ch > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 7.6 years ago by Robert Castelo2.0k
On Fri, 23 Apr 2010 14:41:33 -0700 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 > --- Hello Thomas, Speaking (OT) of Linux, are there any pointers on how to coax a Debian distribution into upgrading R past a certain point? I seem to be stuck with R 2.7.1 Regards, Edwin --- > sessionInfo() R version 2.7.1 (2008-06-23) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.7.1 --- > 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 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor --- Dr. Edwin Groot, postdoctoral associate AG Laux Institut fuer Biologie III Schaenzlestr. 1 79104 Freiburg, Deutschland +49 761-2032945
ADD REPLYlink written 7.6 years ago by Edwin Groot230
0
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14 months ago by
wangyizhusss0 wrote:

Thanks for sharing all the content you've sorted. I am coming for the detailed information about the sequenom massarray. I would be more grateful if you could sort out more of the information in this area.

ADD COMMENTlink written 14 months ago by wangyizhusss0
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