[Bioc-sig-seq] Bioconductor 2.8 is released
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.1 years ago
United States
On Fri, Apr 15, 2011 at 8:10 AM, Ivan Gregoretti <ivangreg at="" gmail.com=""> wrote: > Hello Dan, > > Updating Bioconductor devel packages as instructed in > > http://bioconductor.org/install/ > > usually leads to stalled downloads when it retrieves large packages. > The BSgenome packages are notorious for this. > > Can you or anybody recommend a solution that does not involve manually > downloading the tar balls one by one? (Perhaps the is a mirror for > devel.) Hi Ivan, There are mirrors for release and devel here: http://bioconductor.org/about/mirrors/ Dan > > Thank you, > > Ivan > > > > On Thu, Apr 14, 2011 at 5:33 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> Bioconductors: >> >> We are pleased to announce Bioconductor 2.8, consisting of 466 >> software packages and more than 500 up-to-date annotation packages. >> There are 48 new software packages, and many updates and improvements >> to existing packages. Two software packages that were in the previous >> version have been removed. Bioconductor 2.8 is compatible with >> R 2.13.0, and is supported on Linux, 32- and 64-bit Windows, and Mac >> OS. ?Visit >> >> http://bioconductor.org >> >> for details and downloads. >> >> Contents >> ======== >> >> * Getting Started with Bioconductor 2.8 >> * New Software Packages >> * Using Bioconductor in the cloud >> >> Getting Started with Bioconductor 2.8 >> ===================================== >> >> To install Bioconductor 2.8: >> >> 1. Install R 2.13.0. ?Bioconductor 2.8 has been designed expressly for >> this version of R. >> >> 2. Follow the instructions here: >> >> http://bioconductor.org/install/ >> >> Please visit http://bioconductor.org for details and downloads. >> >> New Software Packages >> ===================== >> >> There are 48 new packages in this release of Bioconductor. >> >> a4 >> >> ?Automated Affymetrix Array Analysis Umbrella Package >> >> a4Base >> >> ?Automated Affymetrix Array Analysis Base Package >> >> a4Classif >> >> ?Automated Affymetrix Array Analysis Classification Package >> >> a4Core >> >> ?Automated Affymetrix Array Analysis Core Package >> >> a4Preproc >> >> ?Automated Affymetrix Array Analysis Preprocessing Package >> >> a4Reporting >> >> ?Automated Affymetrix Array Analysis Reporting Package >> >> AnnotationFuncs >> >> ?Annotation translation functions >> >> anota >> >> ?ANalysis Of Translational Activity >> >> chopsticks >> >> ?The snp.matrix and X.snp.matrix classes >> >> Clonality >> >> ?Clonality testing >> >> clst >> >> ?Classification by local similarity threshold >> >> clstutils >> >> ?Tools for performing taxonomic assignment >> >> clusterProfiler >> >> ?statistical analysis and visulization of >> ?functional profiles for genes and gene clusters >> >> cn.farms >> >> ?Factor Analysis for copy number estimation >> >> ENVISIONQuery >> >> ?Retrieval from the ENVISION bioinformatics data portal into R >> >> ExiMiR >> >> ?R functions for the normalization of Exiqon miRNA array data >> >> flowPhyto >> >> ?Methods for Continuous Flow Cytometry >> >> flowPlots >> >> ?analysis plots and data class for gated flow cytometry data >> >> gaia >> >> ?An R package for genomic analysis of significant >> ?chromosomal aberrations >> >> genefu >> >> ?Relevant Functions for Gene Expression Analysis, >> ?Especially in Breast Cancer >> >> genoset >> >> ?Provides classes similar to ExpressionSet for copy number analysis >> >> GSVA >> >> ?Gene Set Variation Analysis >> >> ibh >> >> ?Interaction Based Homogeneity for Evaluating Gene Lists >> >> inveRsion >> >> ?Inversions in genotype data >> >> IPPD >> >> ?Isotopic peak pattern deconvolution for Protein Mass >> ?Spectrometry by template matching >> >> joda >> >> ?JODA algorithm for quantifying gene deregulation using knowledge >> >> lol >> >> ?Lots Of Lasso >> >> mcaGUI >> >> ?Microbial Community Analysis GUI >> >> mgsa >> >> ?Model-based gene set analysis >> >> MLP >> >> ?Mean Log P Analysis >> >> mosaics >> >> ?MOdel-based one and two Sample Analysis and Inference for ChIP-Seq >> >> MSnbase >> >> ?Base Functions and Classes for MS-based Proteomics >> >> NCIgraph >> >> ?Pathways from the NCI Pathways Database >> >> phenoDist >> >> ?Phenotypic distance measures >> >> phenoTest >> >> ?Tools to test correlation between gene expression and phenotype >> >> procoil >> >> ?Prediction of Oligomerization of Coiled Coil Proteins >> >> pvac >> >> ?PCA-based gene filtering for Affymetrix arrays >> >> qrqc >> >> ?Quick Read Quality Control >> >> RNAinteract >> >> ?Estimate Pairwise Interactions from multidimensional features >> >> Rsubread >> >> ?a super fast, sensitive and accurate read aligner for mapping >> ?next-generation sequencing reads >> >> seqbias >> >> ?Estimation of per-position bias in high-throughput sequencing data >> >> snm >> >> ?Supervised Normalization of Microarrays >> >> snpStats >> >> ?SnpMatrix and XSnpMatrix classes and methods >> >> survcomp >> >> ?Performance Assessment and Comparison for Survival Analysis >> >> TDARACNE >> >> ?Network reverse engineering from time course data >> >> TEQC >> >> ?Quality control for target capture experiments >> >> TurboNorm >> >> ?A fast scatterplot smoother suitable for microarray normalization >> >> Vega >> >> ?An R package for copy number data segmentation >> >> >> Using Bioconductor in the cloud >> =============================== >> >> This release features the Bioconductor Amazon Machine >> Image (AMI), which allows easy access to R and Bioconductor >> within the Elastic Compute Cloud (EC2). It's easy to run >> parallelizable tasks on MPI clusters, run R from within >> your web browser using RStudio Server, and more. No >> installation required. Information available at: >> >> http://bioconductor.org/help/bioconductor-cloud-ami/ >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> Bioc-sig-sequencing at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> >
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Survival • 1.8k views
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@ivan-gregoretti-3975
Last seen 9.5 years ago
Canada
Great. Would you mind showing how you can update the packages using any of those mirrors? Thank you, Ivan On Fri, Apr 15, 2011 at 11:34 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > On Fri, Apr 15, 2011 at 8:10 AM, Ivan Gregoretti <ivangreg at="" gmail.com=""> wrote: >> Hello Dan, >> >> Updating Bioconductor devel packages as instructed in >> >> http://bioconductor.org/install/ >> >> usually leads to stalled downloads when it retrieves large packages. >> The BSgenome packages are notorious for this. >> >> Can you or anybody recommend a solution that does not involve manually >> downloading the tar balls one by one? (Perhaps the is a mirror for >> devel.) > > Hi Ivan, > > There are mirrors for release and devel here: > > http://bioconductor.org/about/mirrors/ > > Dan > > >> >> Thank you, >> >> Ivan >> >> >> >> On Thu, Apr 14, 2011 at 5:33 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >>> Bioconductors: >>> >>> We are pleased to announce Bioconductor 2.8, consisting of 466 >>> software packages and more than 500 up-to-date annotation packages. >>> There are 48 new software packages, and many updates and improvements >>> to existing packages. Two software packages that were in the previous >>> version have been removed. Bioconductor 2.8 is compatible with >>> R 2.13.0, and is supported on Linux, 32- and 64-bit Windows, and Mac >>> OS. ?Visit >>> >>> http://bioconductor.org >>> >>> for details and downloads. >>> >>> Contents >>> ======== >>> >>> * Getting Started with Bioconductor 2.8 >>> * New Software Packages >>> * Using Bioconductor in the cloud >>> >>> Getting Started with Bioconductor 2.8 >>> ===================================== >>> >>> To install Bioconductor 2.8: >>> >>> 1. Install R 2.13.0. ?Bioconductor 2.8 has been designed expressly for >>> this version of R. >>> >>> 2. Follow the instructions here: >>> >>> http://bioconductor.org/install/ >>> >>> Please visit http://bioconductor.org for details and downloads. >>> >>> New Software Packages >>> ===================== >>> >>> There are 48 new packages in this release of Bioconductor. >>> >>> a4 >>> >>> ?Automated Affymetrix Array Analysis Umbrella Package >>> >>> a4Base >>> >>> ?Automated Affymetrix Array Analysis Base Package >>> >>> a4Classif >>> >>> ?Automated Affymetrix Array Analysis Classification Package >>> >>> a4Core >>> >>> ?Automated Affymetrix Array Analysis Core Package >>> >>> a4Preproc >>> >>> ?Automated Affymetrix Array Analysis Preprocessing Package >>> >>> a4Reporting >>> >>> ?Automated Affymetrix Array Analysis Reporting Package >>> >>> AnnotationFuncs >>> >>> ?Annotation translation functions >>> >>> anota >>> >>> ?ANalysis Of Translational Activity >>> >>> chopsticks >>> >>> ?The snp.matrix and X.snp.matrix classes >>> >>> Clonality >>> >>> ?Clonality testing >>> >>> clst >>> >>> ?Classification by local similarity threshold >>> >>> clstutils >>> >>> ?Tools for performing taxonomic assignment >>> >>> clusterProfiler >>> >>> ?statistical analysis and visulization of >>> ?functional profiles for genes and gene clusters >>> >>> cn.farms >>> >>> ?Factor Analysis for copy number estimation >>> >>> ENVISIONQuery >>> >>> ?Retrieval from the ENVISION bioinformatics data portal into R >>> >>> ExiMiR >>> >>> ?R functions for the normalization of Exiqon miRNA array data >>> >>> flowPhyto >>> >>> ?Methods for Continuous Flow Cytometry >>> >>> flowPlots >>> >>> ?analysis plots and data class for gated flow cytometry data >>> >>> gaia >>> >>> ?An R package for genomic analysis of significant >>> ?chromosomal aberrations >>> >>> genefu >>> >>> ?Relevant Functions for Gene Expression Analysis, >>> ?Especially in Breast Cancer >>> >>> genoset >>> >>> ?Provides classes similar to ExpressionSet for copy number analysis >>> >>> GSVA >>> >>> ?Gene Set Variation Analysis >>> >>> ibh >>> >>> ?Interaction Based Homogeneity for Evaluating Gene Lists >>> >>> inveRsion >>> >>> ?Inversions in genotype data >>> >>> IPPD >>> >>> ?Isotopic peak pattern deconvolution for Protein Mass >>> ?Spectrometry by template matching >>> >>> joda >>> >>> ?JODA algorithm for quantifying gene deregulation using knowledge >>> >>> lol >>> >>> ?Lots Of Lasso >>> >>> mcaGUI >>> >>> ?Microbial Community Analysis GUI >>> >>> mgsa >>> >>> ?Model-based gene set analysis >>> >>> MLP >>> >>> ?Mean Log P Analysis >>> >>> mosaics >>> >>> ?MOdel-based one and two Sample Analysis and Inference for ChIP- Seq >>> >>> MSnbase >>> >>> ?Base Functions and Classes for MS-based Proteomics >>> >>> NCIgraph >>> >>> ?Pathways from the NCI Pathways Database >>> >>> phenoDist >>> >>> ?Phenotypic distance measures >>> >>> phenoTest >>> >>> ?Tools to test correlation between gene expression and phenotype >>> >>> procoil >>> >>> ?Prediction of Oligomerization of Coiled Coil Proteins >>> >>> pvac >>> >>> ?PCA-based gene filtering for Affymetrix arrays >>> >>> qrqc >>> >>> ?Quick Read Quality Control >>> >>> RNAinteract >>> >>> ?Estimate Pairwise Interactions from multidimensional features >>> >>> Rsubread >>> >>> ?a super fast, sensitive and accurate read aligner for mapping >>> ?next-generation sequencing reads >>> >>> seqbias >>> >>> ?Estimation of per-position bias in high-throughput sequencing data >>> >>> snm >>> >>> ?Supervised Normalization of Microarrays >>> >>> snpStats >>> >>> ?SnpMatrix and XSnpMatrix classes and methods >>> >>> survcomp >>> >>> ?Performance Assessment and Comparison for Survival Analysis >>> >>> TDARACNE >>> >>> ?Network reverse engineering from time course data >>> >>> TEQC >>> >>> ?Quality control for target capture experiments >>> >>> TurboNorm >>> >>> ?A fast scatterplot smoother suitable for microarray normalization >>> >>> Vega >>> >>> ?An R package for copy number data segmentation >>> >>> >>> Using Bioconductor in the cloud >>> =============================== >>> >>> This release features the Bioconductor Amazon Machine >>> Image (AMI), which allows easy access to R and Bioconductor >>> within the Elastic Compute Cloud (EC2). It's easy to run >>> parallelizable tasks on MPI clusters, run R from within >>> your web browser using RStudio Server, and more. No >>> installation required. Information available at: >>> >>> http://bioconductor.org/help/bioconductor-cloud-ami/ >>> >>> _______________________________________________ >>> Bioc-sig-sequencing mailing list >>> Bioc-sig-sequencing at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>> >> >
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João Moura ▴ 160
@joao-moura-4505
Last seen 9.6 years ago
Hi Ivan, Just look at the output of the source() > source("http://bioconductor.org/biocLite.R") BioC_mirror = http://bioconductor.org Change using chooseBioCmirror(). Cheers On Fri, Apr 15, 2011 at 5:41 PM, Ivan Gregoretti <ivangreg@gmail.com> wrote: > Great. > > Would you mind showing how you can update the packages using any of > those mirrors? > > Thank you, > > Ivan > > > > On Fri, Apr 15, 2011 at 11:34 AM, Dan Tenenbaum <dtenenba@fhcrc.org> > wrote: > > On Fri, Apr 15, 2011 at 8:10 AM, Ivan Gregoretti <ivangreg@gmail.com> > wrote: > >> Hello Dan, > >> > >> Updating Bioconductor devel packages as instructed in > >> > >> http://bioconductor.org/install/ > >> > >> usually leads to stalled downloads when it retrieves large packages. > >> The BSgenome packages are notorious for this. > >> > >> Can you or anybody recommend a solution that does not involve manually > >> downloading the tar balls one by one? (Perhaps the is a mirror for > >> devel.) > > > > Hi Ivan, > > > > There are mirrors for release and devel here: > > > > http://bioconductor.org/about/mirrors/ > > > > Dan > > > > > >> > >> Thank you, > >> > >> Ivan > >> > >> > >> > >> On Thu, Apr 14, 2011 at 5:33 PM, Dan Tenenbaum <dtenenba@fhcrc.org> > wrote: > >>> Bioconductors: > >>> > >>> We are pleased to announce Bioconductor 2.8, consisting of 466 > >>> software packages and more than 500 up-to-date annotation packages. > >>> There are 48 new software packages, and many updates and improvements > >>> to existing packages. Two software packages that were in the previous > >>> version have been removed. Bioconductor 2.8 is compatible with > >>> R 2.13.0, and is supported on Linux, 32- and 64-bit Windows, and Mac > >>> OS. Visit > >>> > >>> http://bioconductor.org > >>> > >>> for details and downloads. > >>> > >>> Contents > >>> ======== > >>> > >>> * Getting Started with Bioconductor 2.8 > >>> * New Software Packages > >>> * Using Bioconductor in the cloud > >>> > >>> Getting Started with Bioconductor 2.8 > >>> ===================================== > >>> > >>> To install Bioconductor 2.8: > >>> > >>> 1. Install R 2.13.0. Bioconductor 2.8 has been designed expressly for > >>> this version of R. > >>> > >>> 2. Follow the instructions here: > >>> > >>> http://bioconductor.org/install/ > >>> > >>> Please visit http://bioconductor.org for details and downloads. > >>> > >>> New Software Packages > >>> ===================== > >>> > >>> There are 48 new packages in this release of Bioconductor. > >>> > >>> a4 > >>> > >>> Automated Affymetrix Array Analysis Umbrella Package > >>> > >>> a4Base > >>> > >>> Automated Affymetrix Array Analysis Base Package > >>> > >>> a4Classif > >>> > >>> Automated Affymetrix Array Analysis Classification Package > >>> > >>> a4Core > >>> > >>> Automated Affymetrix Array Analysis Core Package > >>> > >>> a4Preproc > >>> > >>> Automated Affymetrix Array Analysis Preprocessing Package > >>> > >>> a4Reporting > >>> > >>> Automated Affymetrix Array Analysis Reporting Package > >>> > >>> AnnotationFuncs > >>> > >>> Annotation translation functions > >>> > >>> anota > >>> > >>> ANalysis Of Translational Activity > >>> > >>> chopsticks > >>> > >>> The snp.matrix and X.snp.matrix classes > >>> > >>> Clonality > >>> > >>> Clonality testing > >>> > >>> clst > >>> > >>> Classification by local similarity threshold > >>> > >>> clstutils > >>> > >>> Tools for performing taxonomic assignment > >>> > >>> clusterProfiler > >>> > >>> statistical analysis and visulization of > >>> functional profiles for genes and gene clusters > >>> > >>> cn.farms > >>> > >>> Factor Analysis for copy number estimation > >>> > >>> ENVISIONQuery > >>> > >>> Retrieval from the ENVISION bioinformatics data portal into R > >>> > >>> ExiMiR > >>> > >>> R functions for the normalization of Exiqon miRNA array data > >>> > >>> flowPhyto > >>> > >>> Methods for Continuous Flow Cytometry > >>> > >>> flowPlots > >>> > >>> analysis plots and data class for gated flow cytometry data > >>> > >>> gaia > >>> > >>> An R package for genomic analysis of significant > >>> chromosomal aberrations > >>> > >>> genefu > >>> > >>> Relevant Functions for Gene Expression Analysis, > >>> Especially in Breast Cancer > >>> > >>> genoset > >>> > >>> Provides classes similar to ExpressionSet for copy number analysis > >>> > >>> GSVA > >>> > >>> Gene Set Variation Analysis > >>> > >>> ibh > >>> > >>> Interaction Based Homogeneity for Evaluating Gene Lists > >>> > >>> inveRsion > >>> > >>> Inversions in genotype data > >>> > >>> IPPD > >>> > >>> Isotopic peak pattern deconvolution for Protein Mass > >>> Spectrometry by template matching > >>> > >>> joda > >>> > >>> JODA algorithm for quantifying gene deregulation using knowledge > >>> > >>> lol > >>> > >>> Lots Of Lasso > >>> > >>> mcaGUI > >>> > >>> Microbial Community Analysis GUI > >>> > >>> mgsa > >>> > >>> Model-based gene set analysis > >>> > >>> MLP > >>> > >>> Mean Log P Analysis > >>> > >>> mosaics > >>> > >>> MOdel-based one and two Sample Analysis and Inference for ChIP- Seq > >>> > >>> MSnbase > >>> > >>> Base Functions and Classes for MS-based Proteomics > >>> > >>> NCIgraph > >>> > >>> Pathways from the NCI Pathways Database > >>> > >>> phenoDist > >>> > >>> Phenotypic distance measures > >>> > >>> phenoTest > >>> > >>> Tools to test correlation between gene expression and phenotype > >>> > >>> procoil > >>> > >>> Prediction of Oligomerization of Coiled Coil Proteins > >>> > >>> pvac > >>> > >>> PCA-based gene filtering for Affymetrix arrays > >>> > >>> qrqc > >>> > >>> Quick Read Quality Control > >>> > >>> RNAinteract > >>> > >>> Estimate Pairwise Interactions from multidimensional features > >>> > >>> Rsubread > >>> > >>> a super fast, sensitive and accurate read aligner for mapping > >>> next-generation sequencing reads > >>> > >>> seqbias > >>> > >>> Estimation of per-position bias in high-throughput sequencing data > >>> > >>> snm > >>> > >>> Supervised Normalization of Microarrays > >>> > >>> snpStats > >>> > >>> SnpMatrix and XSnpMatrix classes and methods > >>> > >>> survcomp > >>> > >>> Performance Assessment and Comparison for Survival Analysis > >>> > >>> TDARACNE > >>> > >>> Network reverse engineering from time course data > >>> > >>> TEQC > >>> > >>> Quality control for target capture experiments > >>> > >>> TurboNorm > >>> > >>> A fast scatterplot smoother suitable for microarray normalization > >>> > >>> Vega > >>> > >>> An R package for copy number data segmentation > >>> > >>> > >>> Using Bioconductor in the cloud > >>> =============================== > >>> > >>> This release features the Bioconductor Amazon Machine > >>> Image (AMI), which allows easy access to R and Bioconductor > >>> within the Elastic Compute Cloud (EC2). It's easy to run > >>> parallelizable tasks on MPI clusters, run R from within > >>> your web browser using RStudio Server, and more. No > >>> installation required. Information available at: > >>> > >>> http://bioconductor.org/help/bioconductor-cloud-ami/ > >>> > >>> _______________________________________________ > >>> Bioc-sig-sequencing mailing list > >>> Bioc-sig-sequencing@r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > >>> > >> > > > > _______________________________________________ > Bioc-sig-sequencing mailing list > Bioc-sig-sequencing@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > -- João Moura [[alternative HTML version deleted]]
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Hi Jo?o, Your suggestion works as advertised. Just to keep it handy on the record, this is an example source("http://bioconductor.org/biocLite.R") chooseBioCmirror("http://watson.nci.nih.gov/bioc_mirror") biocLite("BSgenome.Hsapiens.UCSC.hg19") Thank you, Ivan On Fri, Apr 15, 2011 at 12:18 PM, Jo?o Moura <palerma at="" gmail.com=""> wrote: > Hi Ivan, > Just look at the output of the source() >> source("http://bioconductor.org/biocLite.R") > BioC_mirror = http://bioconductor.org > Change using chooseBioCmirror(). > Cheers > On Fri, Apr 15, 2011 at 5:41 PM, Ivan Gregoretti <ivangreg at="" gmail.com=""> wrote: >> >> Great. >> >> Would you mind showing how you can update the packages using any of >> those mirrors? >> >> Thank you, >> >> Ivan >> >> >> >> On Fri, Apr 15, 2011 at 11:34 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> wrote: >> > On Fri, Apr 15, 2011 at 8:10 AM, Ivan Gregoretti <ivangreg at="" gmail.com=""> >> > wrote: >> >> Hello Dan, >> >> >> >> Updating Bioconductor devel packages as instructed in >> >> >> >> http://bioconductor.org/install/ >> >> >> >> usually leads to stalled downloads when it retrieves large packages. >> >> The BSgenome packages are notorious for this. >> >> >> >> Can you or anybody recommend a solution that does not involve manually >> >> downloading the tar balls one by one? (Perhaps the is a mirror for >> >> devel.) >> > >> > Hi Ivan, >> > >> > There are mirrors for release and devel here: >> > >> > http://bioconductor.org/about/mirrors/ >> > >> > Dan >> > >> > >> >> >> >> Thank you, >> >> >> >> Ivan >> >> >> >> >> >> >> >> On Thu, Apr 14, 2011 at 5:33 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> >> wrote: >> >>> Bioconductors: >> >>> >> >>> We are pleased to announce Bioconductor 2.8, consisting of 466 >> >>> software packages and more than 500 up-to-date annotation packages. >> >>> There are 48 new software packages, and many updates and improvements >> >>> to existing packages. Two software packages that were in the previous >> >>> version have been removed. Bioconductor 2.8 is compatible with >> >>> R 2.13.0, and is supported on Linux, 32- and 64-bit Windows, and Mac >> >>> OS. ?Visit >> >>> >> >>> http://bioconductor.org >> >>> >> >>> for details and downloads. >> >>> >> >>> Contents >> >>> ======== >> >>> >> >>> * Getting Started with Bioconductor 2.8 >> >>> * New Software Packages >> >>> * Using Bioconductor in the cloud >> >>> >> >>> Getting Started with Bioconductor 2.8 >> >>> ===================================== >> >>> >> >>> To install Bioconductor 2.8: >> >>> >> >>> 1. Install R 2.13.0. ?Bioconductor 2.8 has been designed expressly for >> >>> this version of R. >> >>> >> >>> 2. Follow the instructions here: >> >>> >> >>> http://bioconductor.org/install/ >> >>> >> >>> Please visit http://bioconductor.org for details and downloads. >> >>> >> >>> New Software Packages >> >>> ===================== >> >>> >> >>> There are 48 new packages in this release of Bioconductor. >> >>> >> >>> a4 >> >>> >> >>> ?Automated Affymetrix Array Analysis Umbrella Package >> >>> >> >>> a4Base >> >>> >> >>> ?Automated Affymetrix Array Analysis Base Package >> >>> >> >>> a4Classif >> >>> >> >>> ?Automated Affymetrix Array Analysis Classification Package >> >>> >> >>> a4Core >> >>> >> >>> ?Automated Affymetrix Array Analysis Core Package >> >>> >> >>> a4Preproc >> >>> >> >>> ?Automated Affymetrix Array Analysis Preprocessing Package >> >>> >> >>> a4Reporting >> >>> >> >>> ?Automated Affymetrix Array Analysis Reporting Package >> >>> >> >>> AnnotationFuncs >> >>> >> >>> ?Annotation translation functions >> >>> >> >>> anota >> >>> >> >>> ?ANalysis Of Translational Activity >> >>> >> >>> chopsticks >> >>> >> >>> ?The snp.matrix and X.snp.matrix classes >> >>> >> >>> Clonality >> >>> >> >>> ?Clonality testing >> >>> >> >>> clst >> >>> >> >>> ?Classification by local similarity threshold >> >>> >> >>> clstutils >> >>> >> >>> ?Tools for performing taxonomic assignment >> >>> >> >>> clusterProfiler >> >>> >> >>> ?statistical analysis and visulization of >> >>> ?functional profiles for genes and gene clusters >> >>> >> >>> cn.farms >> >>> >> >>> ?Factor Analysis for copy number estimation >> >>> >> >>> ENVISIONQuery >> >>> >> >>> ?Retrieval from the ENVISION bioinformatics data portal into R >> >>> >> >>> ExiMiR >> >>> >> >>> ?R functions for the normalization of Exiqon miRNA array data >> >>> >> >>> flowPhyto >> >>> >> >>> ?Methods for Continuous Flow Cytometry >> >>> >> >>> flowPlots >> >>> >> >>> ?analysis plots and data class for gated flow cytometry data >> >>> >> >>> gaia >> >>> >> >>> ?An R package for genomic analysis of significant >> >>> ?chromosomal aberrations >> >>> >> >>> genefu >> >>> >> >>> ?Relevant Functions for Gene Expression Analysis, >> >>> ?Especially in Breast Cancer >> >>> >> >>> genoset >> >>> >> >>> ?Provides classes similar to ExpressionSet for copy number analysis >> >>> >> >>> GSVA >> >>> >> >>> ?Gene Set Variation Analysis >> >>> >> >>> ibh >> >>> >> >>> ?Interaction Based Homogeneity for Evaluating Gene Lists >> >>> >> >>> inveRsion >> >>> >> >>> ?Inversions in genotype data >> >>> >> >>> IPPD >> >>> >> >>> ?Isotopic peak pattern deconvolution for Protein Mass >> >>> ?Spectrometry by template matching >> >>> >> >>> joda >> >>> >> >>> ?JODA algorithm for quantifying gene deregulation using knowledge >> >>> >> >>> lol >> >>> >> >>> ?Lots Of Lasso >> >>> >> >>> mcaGUI >> >>> >> >>> ?Microbial Community Analysis GUI >> >>> >> >>> mgsa >> >>> >> >>> ?Model-based gene set analysis >> >>> >> >>> MLP >> >>> >> >>> ?Mean Log P Analysis >> >>> >> >>> mosaics >> >>> >> >>> ?MOdel-based one and two Sample Analysis and Inference for ChIP-Seq >> >>> >> >>> MSnbase >> >>> >> >>> ?Base Functions and Classes for MS-based Proteomics >> >>> >> >>> NCIgraph >> >>> >> >>> ?Pathways from the NCI Pathways Database >> >>> >> >>> phenoDist >> >>> >> >>> ?Phenotypic distance measures >> >>> >> >>> phenoTest >> >>> >> >>> ?Tools to test correlation between gene expression and phenotype >> >>> >> >>> procoil >> >>> >> >>> ?Prediction of Oligomerization of Coiled Coil Proteins >> >>> >> >>> pvac >> >>> >> >>> ?PCA-based gene filtering for Affymetrix arrays >> >>> >> >>> qrqc >> >>> >> >>> ?Quick Read Quality Control >> >>> >> >>> RNAinteract >> >>> >> >>> ?Estimate Pairwise Interactions from multidimensional features >> >>> >> >>> Rsubread >> >>> >> >>> ?a super fast, sensitive and accurate read aligner for mapping >> >>> ?next-generation sequencing reads >> >>> >> >>> seqbias >> >>> >> >>> ?Estimation of per-position bias in high-throughput sequencing data >> >>> >> >>> snm >> >>> >> >>> ?Supervised Normalization of Microarrays >> >>> >> >>> snpStats >> >>> >> >>> ?SnpMatrix and XSnpMatrix classes and methods >> >>> >> >>> survcomp >> >>> >> >>> ?Performance Assessment and Comparison for Survival Analysis >> >>> >> >>> TDARACNE >> >>> >> >>> ?Network reverse engineering from time course data >> >>> >> >>> TEQC >> >>> >> >>> ?Quality control for target capture experiments >> >>> >> >>> TurboNorm >> >>> >> >>> ?A fast scatterplot smoother suitable for microarray normalization >> >>> >> >>> Vega >> >>> >> >>> ?An R package for copy number data segmentation >> >>> >> >>> >> >>> Using Bioconductor in the cloud >> >>> =============================== >> >>> >> >>> This release features the Bioconductor Amazon Machine >> >>> Image (AMI), which allows easy access to R and Bioconductor >> >>> within the Elastic Compute Cloud (EC2). It's easy to run >> >>> parallelizable tasks on MPI clusters, run R from within >> >>> your web browser using RStudio Server, and more. No >> >>> installation required. Information available at: >> >>> >> >>> http://bioconductor.org/help/bioconductor-cloud-ami/ >> >>> >> >>> _______________________________________________ >> >>> Bioc-sig-sequencing mailing list >> >>> Bioc-sig-sequencing at r-project.org >> >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> >>> >> >> >> > >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> Bioc-sig-sequencing at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > -- > Jo?o Moura >
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