[BioC] Bioconductor 2.9 is released

[Dan Tenenbaum]

Bioconductors:

We are pleased to announce Bioconductor 2.9, consisting of 517
software packages and more than 500 up-to-date annotation packages.
There are 60 new software packages, and many updates and improvements
to existing packages; 10 packages have been removed from this
release. Bioconductor 2.9 is compatible with R 2.14.0, and is
supported on Linux, 32- and 64-bit Windows, and Mac OS.  This release
includes an updated Bioconductor Amazon Machine Image.  Visit
http://bioconductor.org for details and downloads.


Contents
--------

* Getting Started with Bioconductor 2.9
* New Software Packages

For the full release announcement, including package NEWS and a list
of packages removed from the release, please visit the BioC 2.9 release
page:

http://bioconductor.org/news/bioc_2_9_release/


Getting Started with Bioconductor 2.9
=====================================

To install Bioconductor 2.9:

1. Install R 2.14.0.  Bioconductor 2.9 has been designed expressly for
this version of R.

2. Follow the instructions at http://bioconductor.org/install/.

New Software Packages
=====================

There are 60 new packages in this release of Bioconductor.

- AGDEX: Agreement of Differential Expression Analysis

- BiocInstaller: Install/Update Bioconductor and CRAN Packages

- biovizBase: Basic graphic utilities for visualization of genomic
  data.

- CellNOptR: R version of CellNOpt, boolean features only

- CNAnorm: A normalization method for Copy Number Aberration in
  cancer samples.

- cn.mops: Mixture of Poisson for CNV detection in NGS data

- Cormotif: Correlation Motif Fit

- cqn: Conditional quantile normalization

- cummeRbund: cummeRbund: The finishing touch on your Tuxedo
  workflow. Analysis, exploration, manipulation, and visualization of
  Cufflinks HTS data.

- DECIPHER: Database Enabled Code for Ideal Probe Hybridization
  Employing R

- DEXSeq: Inference of differential exon usage in RNA-Seq

- DiffBind: Differential Binding Analysis of ChIP-Seq peak data

- dks: The double Kolmogorov-Smirnov package for evaluating multiple
  testing procedures.

- DOSE: Disease Ontology Semantic and Enrichment analysis

- DTA: Dynamic Transcriptome Analysis

- EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq

- exomeCopy: Detection of CNV in exome/targeted sequencing data

- fastseg: fastseg - a fast segmentation algorithm

- flowType: Phenotyping Flow Cytometry Assays

- flowWorkspace: Import flowJo Workspaces into BioConductor and
  replicate flowJo gating with flowCore

- GeneExpressionSignature: Gene Expression Signature based Similarity
  Metric

- ggbio: Static visualization for genomic data.

- GOFunction: GO-function: deriving biologcially relevant functions
  from statistically significant functions

- graphite: GRAPH Interaction from pathway Topological Environment

- GRENITS: Gene Regulatory Network Inference Using Time Series

- GWASTools: GWASTools: Tools for Genome Wide Association Studies

- htSeqTools: Quality Control, Visualization and Processing for
  High-Throughput Sequencing data

- IdMappingRetrieval: ID Mapping Data Retrieval

- inSilicoDb: Access to the InSilico Database

- iontree: Data management and analysis of ion trees from ion-trap
  mass spectrometry

- isobar: Analysis and quantitation of isobarically tagged MSMS
  proteomics data

- minfi: Analyze Illumina's 450k methylation arrays

- MmPalateMiRNA: Murine Palate miRNA Expression Analysis

- mzR: parser for netCDF, mzXML, mzData and mzML files (mass
  spectrometry data)

- ncdfFlow: ncdfFlow: A package that provides ncdf based storage
  based flow cytometry data.

- NormqPCR: Functions for normalisation of RT-qPCR data

- nucleR: Nucleosome positioning package for R

- PAN: Posterior association networks and functional modules inferred
  from rich phenotypes of gene perturbations

- PREDA: Position RElated Data Anlysis

- predictionet: Inference for predictive networks designed for (but
  not limited to) genomic data

- qtbase: Interface between R and Qt

- qtpaint: Qt-based painting infrastructure

- r3Cseq: Analysis of Chromosome Conformation Capture and
  Next-generation Sequencing (3C-seq)

- RamiGO: AmiGO visualize R interface

- randPack: Randomization routines for Clinical Trials

- RCASPAR: A package for survival time prediction based on a
  piecewise baseline hazard Cox regression model.

- ReadqPCR: Read qPCR data

- RedeR: RedeR: bridging the gap between hierarchical network
  representation and functional analysis.

- REDseq: Analysis of high-throughput sequencing data processed by
  restriction enzyme digestion

- Repitools: Epigenomic tools

- ReQON: Recalibrating Quality Of Nucleotides

- rqubic: Qualitative biclustering algorithm for expression data
  analysis in R

- RTopper: This package is designed to perform Gene Set Analysis
  across multiple genomic platforms

- stepwiseCM: Stepwise Classification of Cancer Samples using
  Clinical and Molecular Data

- Streamer: Enabling stream processing of large files

- sva: Surrogate Variable Analysis

- TSSi: Transcription Start Site Identification

- tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family
  of distributions

- VariantAnnotation: Annotation of Genetic Variants

- zlibbioc: An R packaged zlib-1.2.5