[BioC] [Bioc-sig-seq] Bioconductor 2.8 is released

[Dan Tenenbaum]

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/
>>
>> _______________________________________________
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>>
>