Question: BioC 2.2 now available
0
gravatar for Martin Morgan
11.6 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
Bioconductors: We are pleased to announce the release of Bioconductor 2.2. This release includes 35 new packages, and many improvements to existing packages. There are now 260 package in Bioconductor 2.2. These packages are compatible with R 2.7.0. IMPORTANT: MAC OS USERS: the 'binary' builds currently available with biocLite are not suitable for Tiger (OS X 10.4). We expect to have Tiger-compatible builds within the next week. If you are using Tiger, please refrain from migrating to R-2.7.0 until these binaries become available, or use the 'type="source"' option to biocLite. As a member of the Bioconductor community, you have contributed greatly to this release. Perhaps you are a perplexed newcomer asking for help on the Bioc mailing list. Perhaps you are an experienced user seeking reproducible and advanced functionality. Or perhaps you are a package developer helping others to make sound sense of their data. Whatever your role, you've made Bioconductor the resource it is today. We are especially grateful to package developers, to members of the Bioconductor team in Seattle, and to those participants on the Bioc mailing list who knowledgeably and patiently answer questions large and small. High-throughput genomic research is a dynamic and exciting field. It is hard to predict what surprising packages are in store for future Bioconductor releases. We anticipate continued integration with diverse data sources, use of R's advanced graphics abilities, and implementation of cutting edge research algorithms for the benefit of all Bioconductor users. Short-read DNA resequencing technologies are one area where growth seems almost certain. We look forward to a vibrant release cycle! Contents ======== * Getting Started With Bioconductor 2.2 * New and Re-introduced Packages * Significant Changes to Annotation Packages Getting Started With Bioconductor 2.2 ===================================== IMPORTANT: MAC USERS: see the important note above. To install Bioconductor 2.2 1. Install R 2.7.0. Bioconductor 2.2 has been designed expressly for this version of R. 2. Follow the instructions here: http://bioconductor.org/download Please visit http://bioconductor.org for details and downloads. New and Re-introduced Packages ============================== The following packages are new in this release of Bioconductor; visit http://bioconductor.org/packages/release/Software.html for links to all package descriptions. AffyCompatible Affymetrix GeneChip software compatibility BAC Bayesian Analysis of Chip-chip experiment BCRANK Predicting binding site consensus from ranked DNA sequences BGmix Bayesian models for differential gene expression BiocCaseStudies Support for the Bioconductor Case Studies Monograph GEOmetadb A compilation of metadata from NCBI GEO GGBase Infrastructure for genetics of gene expression (c) 2008 VJ Carey GSEAlm Linear Model Toolset for Gene Set Enrichment Analysis GeneRfold R for genes and sequences, using viennaRNA package (fold) GeneSelector GeneSelector GenomeGraphs Plotting genomic information from Ensembl GraphAlignment GraphAlignment PCpheno Phenotypes and cellular organizational units RBioinf Support for R for Bioinformatics Monograph Rdisop Decomposition of Isotopic Patterns Rtreemix Mutagenetic trees mixture models. SLGI Synthetic Lethal Genetic Interaction XDE A Bayesian hierarchical model for cross-study analysis of differential gene expression affyPara Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays flowClust Clustering for Flow Cytometry flowQ Qualitiy control for flow cytometry flowUtils Utilities for flow cytometry gaga GaGa hierarchical model for microarray data analysis goProfiles An R package for the statistical analysis of functional profiles mdqc Mahalanobis Distance Quality Control for microarrays occugene Functions for Multinomial Occupancy Distribution plw Probe level Locally moderated Weighted t-tests. rtracklayer R interface to genome browsers and their annotation tracks snpMatrix The snp.matrix and X.snp.matrix classes xps Methods for Processing and Analysis of Affymetrix Oligonucleotide Arrays yaqcaffy Affymetrix expression data quality control and reproducibility analysis Additional packages have been re-introduced to the release branch: GeneticsPed Pedigree and genetic relationship functions Rredland Interface to redland RDF utilities externalVector Vector objects for R with external storage stam Structured Analysis of Microarray Data Packages still present in the 'development' branch, but no longer in the release, include BeadExplorer, GeneRfold, MCRestimate, and SAGElyzer. Packages retired from Bioconductor include arrayMagic, ChromoViz, GeneTS, iSNetwork, iSPlot, and RMAPPER. Significant Changes to Annotation Packages ========================================== Bioconductor 2.2 includes a large number of annotation packages. Descriptions are available here: http://bioconductor.org/packages/release/AnnotationData.html New 'db' annotation packages replace their predecessors, e.g., hgu95av2.db replaces hgu95av2 . Both 'db' and original packages are available in this release, but we anticipate that future releases will only contain 'db' packages. Most db packages now contain Ensembl accessions, New 'organism' packages are available for several model organisms: human, org.Hs.eg.db; mouse, org.Mm.eg.db; rat, org.Rn.eg.db; yeast, org.Sc.sgd.db; fly, org.Dm.eg.db; malaria, org.Pf.plasmo.db. Many of these packages contain additional organism-specific annotations, e.g., flybase (Drosophila) or Jackson Laboratories (mouse) IDs. New 'homology' packages summarize InParanoid homology data. Use these and the organism packages to map between InParanoid and other IDS IDs. Available homology packages include: human, hom.Hs.inp.db; mouse, hom.Mm.inp.db; rat, hom.Rn.inp.db; yeast, hom.Sc.inp.db; fly, hom.Dm.inp.db. The PFAM package is available as PFAM.db Custom CDF packages provided by Manhong Dai are not currently available, but should be shortly. Martin -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
ADD COMMENTlink modified 11.6 years ago by Patrick Aboyoun1.6k • written 11.6 years ago by Martin Morgan ♦♦ 24k
Answer: BioC 2.2 now available
0
gravatar for Patrick Aboyoun
11.6 years ago by
Patrick Aboyoun1.6k
United States
Patrick Aboyoun1.6k wrote:
Last night we replaced the Mac OS X binary packages from Leopard (OS X 10.5) to Tiger (OS X 10.4) at the BioC 2.2 repository. Mac users on Tiger can now migrate to BioC 2.2 using biocLite with the default settings (i.e. type = "mac.binary"). For those users on Mac OS X Leopard, we are still building the Leopard binary packages but are not making them available since the standard CRAN-style repository does not support two types of Mac OS X universal binary packages. If there is a sufficient demand from the Bioconductor user-base, we can create a parallel repository for the Leopard binary packages that will be made available to Leopard users through biocLite. Patrick Martin Morgan wrote: > Bioconductors: > > We are pleased to announce the release of Bioconductor 2.2. This > release includes 35 new packages, and many improvements to existing > packages. There are now 260 package in Bioconductor 2.2. These > packages are compatible with R 2.7.0. > > IMPORTANT: MAC OS USERS: the 'binary' builds currently available with > biocLite are not suitable for Tiger (OS X 10.4). We expect to have > Tiger-compatible builds within the next week. If you are using Tiger, > please refrain from migrating to R-2.7.0 until these binaries become > available, or use the 'type="source"' option to biocLite. > > As a member of the Bioconductor community, you have contributed > greatly to this release. Perhaps you are a perplexed newcomer asking > for help on the Bioc mailing list. Perhaps you are an experienced user > seeking reproducible and advanced functionality. Or perhaps you are a > package developer helping others to make sound sense of their > data. Whatever your role, you've made Bioconductor the resource it is > today. We are especially grateful to package developers, to members of > the Bioconductor team in Seattle, and to those participants on the > Bioc mailing list who knowledgeably and patiently answer questions > large and small. > > High-throughput genomic research is a dynamic and exciting field. It > is hard to predict what surprising packages are in store for future > Bioconductor releases. We anticipate continued integration with > diverse data sources, use of R's advanced graphics abilities, and > implementation of cutting edge research algorithms for the benefit of > all Bioconductor users. Short-read DNA resequencing technologies are > one area where growth seems almost certain. > > We look forward to a vibrant release cycle! > > Contents > ======== > > * Getting Started With Bioconductor 2.2 > > * New and Re-introduced Packages > > * Significant Changes to Annotation Packages > > > > > Getting Started With Bioconductor 2.2 > ===================================== > > IMPORTANT: MAC USERS: see the important note above. > > To install Bioconductor 2.2 > > 1. Install R 2.7.0. Bioconductor 2.2 has been designed expressly for > this version of R. > > 2. Follow the instructions here: > > http://bioconductor.org/download > > Please visit http://bioconductor.org for details and downloads. > > > New and Re-introduced Packages > ============================== > > The following packages are new in this release of Bioconductor; visit > > http://bioconductor.org/packages/release/Software.html > > for links to all package descriptions. > > > AffyCompatible > Affymetrix GeneChip software compatibility > > BAC > Bayesian Analysis of Chip-chip experiment > > BCRANK > Predicting binding site consensus from ranked DNA sequences > > BGmix > Bayesian models for differential gene expression > > BiocCaseStudies > Support for the Bioconductor Case Studies Monograph > > GEOmetadb > A compilation of metadata from NCBI GEO > > GGBase > Infrastructure for genetics of gene expression (c) 2008 VJ Carey > > GSEAlm > Linear Model Toolset for Gene Set Enrichment Analysis > > GeneRfold > R for genes and sequences, using viennaRNA package (fold) > > GeneSelector > GeneSelector > > GenomeGraphs > Plotting genomic information from Ensembl > > GraphAlignment > GraphAlignment > > PCpheno > Phenotypes and cellular organizational units > > RBioinf > Support for R for Bioinformatics Monograph > > Rdisop > Decomposition of Isotopic Patterns > > Rtreemix > Mutagenetic trees mixture models. > > SLGI > Synthetic Lethal Genetic Interaction > > XDE > A Bayesian hierarchical model for cross-study analysis of > differential gene expression > > affyPara > Parallelized preprocessing methods for Affymetrix Oligonucleotide > Arrays > > flowClust > Clustering for Flow Cytometry > > flowQ > Qualitiy control for flow cytometry > > flowUtils > Utilities for flow cytometry > > gaga > GaGa hierarchical model for microarray data analysis > > goProfiles > An R package for the statistical analysis of functional profiles > > mdqc > Mahalanobis Distance Quality Control for microarrays > > occugene > Functions for Multinomial Occupancy Distribution > > plw > Probe level Locally moderated Weighted t-tests. > > rtracklayer > R interface to genome browsers and their annotation tracks > > snpMatrix > The snp.matrix and X.snp.matrix classes > > xps > Methods for Processing and Analysis of Affymetrix Oligonucleotide > Arrays > > yaqcaffy > Affymetrix expression data quality control and reproducibility analysis > > > Additional packages have been re-introduced to the release branch: > > GeneticsPed > Pedigree and genetic relationship functions > > Rredland > Interface to redland RDF utilities > > externalVector > Vector objects for R with external storage > > stam > Structured Analysis of Microarray Data > > > Packages still present in the 'development' branch, but no longer in > the release, include BeadExplorer, GeneRfold, MCRestimate, and > SAGElyzer. Packages retired from Bioconductor include arrayMagic, > ChromoViz, GeneTS, iSNetwork, iSPlot, and RMAPPER. > > > Significant Changes to Annotation Packages > ========================================== > > Bioconductor 2.2 includes a large number of annotation > packages. Descriptions are available here: > > http://bioconductor.org/packages/release/AnnotationData.html > > New 'db' annotation packages replace their predecessors, e.g., > hgu95av2.db replaces hgu95av2 . Both 'db' and original packages are > available in this release, but we anticipate that future releases will > only contain 'db' packages. Most db packages now contain Ensembl > accessions, > > New 'organism' packages are available for several model organisms: human, > org.Hs.eg.db; mouse, org.Mm.eg.db; rat, org.Rn.eg.db; yeast, > org.Sc.sgd.db; fly, org.Dm.eg.db; malaria, org.Pf.plasmo.db. Many of > these packages contain additional organism-specific annotations, e.g., > flybase (Drosophila) or Jackson Laboratories (mouse) IDs. > > New 'homology' packages summarize InParanoid homology data. Use these > and the organism packages to map between InParanoid and other IDS > IDs. Available homology packages include: human, hom.Hs.inp.db; mouse, > hom.Mm.inp.db; rat, hom.Rn.inp.db; yeast, hom.Sc.inp.db; fly, > hom.Dm.inp.db. > > The PFAM package is available as PFAM.db > > Custom CDF packages provided by Manhong Dai are not currently > available, but should be shortly. > > > Martin >
ADD COMMENTlink written 11.6 years ago by Patrick Aboyoun1.6k
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