[BioC] Bioconductor 2.7 is released

[Martin Morgan]

Bioconductors:

We are pleased to announce Bioconductor 2.7, consisting of 419
software packages. There are 34 new packages, and many updates and
improvements to existing packages. Bioconductor 2.7 is compatible with
R 2.12.0, and is supported on Linux, 32- and 64-bit Windows, and Mac
OS.  Visit

  http://bioconductor.org

for details and downloads.

Contents
========

o Getting Started with Bioconductor 2.7
o New Software Packages
o Web Site Updates

Getting Started with Bioconductor 2.7
=====================================

To install Bioconductor 2.7:

1. Install R 2.12.0.  Bioconductor 2.7 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 34 new packages in this release of Bioconductor.

ADaCGH2

  Analysis of aCGH experiments using parallel computing and ff objects

attract

  Methods to find gene expression modules representing drivers in
  Kauffman's Attractor Landscape

BHC

  Bayesian Hierarchical Clustering

BioNet

  Functional analysis of biological networks

CGEN

  Case-control studies in genetic epidemiology

CoGAPS

  Coordinated Gene Activity in Pattern Sets

coRNAi

  Analysis of co-knock-down RNAi data

CRImage

  Classify cells and calculate tumor cellularity

DEgraph

  Two-sample tests on a graph

fabia

  Factor Analysis for Bicluster Acquisition

farms

  Factor Analysis for Robust Microarray Summarization

gage

  Generally Applicable Gene-set Enrichment for Pathway Analysis

GeneGA

  Design gene based on both mRNA secondary structure and codon usage
  bias using Genetic algorithm

HTSanalyzeR

  Network and gene set enrichment analysis pipeline for high
  throughput screens.

imageHTS

  Analysis of high-throughput microscopy-based screens

iSeq

  Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising
  Models

IsoGeneGUI

  A graphical user interface to dose-response analysis of microarray
  data

les

  Identifying Loci of Enhanced Significance in Tiling Microarray Data

LVSmiRNA

  LVS normalization for Agilent miRNA data

MBCB

  Model-based Background Correction for Beadarray

MEDIPS

  MeDIP-Seq data analysis

Mulcom

  Differential expression and false discovery rate calculation through
  multiple comparison

netresponse

  Functional network analysis

NTW

  Predict gene network using an Ordinary Differential Equation (ODE)
  based method

NuPoP

  Nucleosome positioning prediction

ontoCAT

  Ontology parsing

OTUbase

  Deals with OTU data

PatientGeneSets

  Patient-oriented gene-set analysis

R453Plus1Toolbox

  Import and analyze data from Roche's Genome Sequencer System.

RCytoscape

  Display and manipulate graphs in Cytoscape

RDRToolbox

  Nonlinear dimension reduction with Isomap and LLE.

RMAPPER

  Interface to the MAPPER database of transcription factor binding
  sites

rnaSeqMap

  rnaSeq analyses using xmapcore database

SQUADD

  Add-on to Standardized Qualitative Dynamical Systems software for
  the logical models approach to analysis of complex dynamic systems

Web Site Updates
================

The Bioconductor web site underwent significant changes during the last
release cycle. The web site includes extensive help resources for both
users and package developers, in addition to information on package
installation. One particularly useful feature in navigating the large
numbers of available packages is the updated biocViews widget

  http://bioconductor.org/help/bioc-views/release/BiocViews.html


On behalf of the Bioconductor team,


Martin Morgan
-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793