[BioC] Bioconductor 2.3 is released

[Patrick Aboyoun]

Bioconductors:

We are pleased to announce the release of Bioconductor 2.3. This release 
includes 36 new software packages, and many changes to existing 
packages. Bioconductor 2.3 is comprised of 294 software packages and is 
compatible with the recently released R 2.8.0.

Please visit http://bioconductor.org for details and downloads.


IMPORTANT NOTE FOR MAC USERS:  R 2.8.0 is using a new Mac OS X binary 
package distribution system and the CRAN and BioC repositories need to 
catch up with this change. If you are using Mac OS X, please refrain 
from migrating to R-2.8.0 until these new binary package repositories 
are put in place, or use 'type="source"' when installing packages using 
biocLite.


Contents
========

  o Release Highlight
  o Getting Started with Bioconductor 2.3
  o New Software Packages
  o Software Packages in 2.2 that didn't make it to 2.3


Release Highlight
=================

This release contains a septet of packages (BSgenome, Biostrings, 
ShortRead, IRanges, HilbertVis, HilbertVisGUI, and rtracklayer) that are 
suited to analyze 'next generation' high-throughput DNA sequence data. 
The BSgenome package provides the backbone for representing genome 
sequences from many different organisms including human, mouse, rat, 
dog, chimp, chicken, cow, fruit fly, honey bee, yeast, E. coli, C. 
elegans, and arabidopsis. The Biostrings package performs fast or 
flexible alignments between reads and genomes. The ShortRead package 
provides tools for importation/exportation and quality assurance of 
common data formats. The IRanges package offers an emerging 
infrastructure for managing very large data objects and for range-based 
data representation. The packages HilbertVis and HilbertVisGUI display 
data with space-filling (Hilbert) curves that maintain the spatial 
information implied by the linearity of chromosomes. The rtracklayer 
package provides an interface to genome browsers and their annotation 
tracks.


Getting Started with Bioconductor 2.3
=====================================

IMPORTANT: MAC USERS: see the important note above.

To install Bioconductor 2.3

1. Install R 2.8.0.  Bioconductor 2.3 has been designed expressly for 
this version of R.

2. Follow the instructions here:

   http://bioconductor.org/docs/install

Please visit http://bioconductor.org for details and downloads.


New 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.


affyContam
 Structured corruption of cel file data to demonstrate QA effectiveness

Agi4x44PreProcess
 Preprocesses Agilent 4x44 array data

ArrayExpress
 Accesses the ArrayExpress microarray database at EBI

arrayMvout
 Analyzes AffyBatch instances

ArrayTools
 Quality assessment and differentially gene expression detection for 
Affymetrix GeneChips

BicARE
 Biclustering Analysis and Results Exploration

CGHbase
 Base functions and classes for arrayCGH data analysis

CGHregions
 Dimension reduction for arrayCGH data with minimal information loss

ChemmineR
 Compound Data Mining Framework

CMA
 Synthesis of microarray-based classification

DFP
 Supervised technique for identifying differentially expressed genes 
using Fuzzy Patterns (FPs).

domainsignatures
 Finds significantly enriched gene classifications based on their 
InterPro domain structure

dualKS
 Training and classifying gene expression data sets using a 
Kolmogorov-Smirnov rank-sum based algorithm

edgeR
 Estimates and tests for differential expression in multiple digital 
gene expression libraries

HELP
 Pipeline for analyzing HELP microarray data that includes graphical and 
mathematical tools

HilbertVis
 Functions to visualize long vectors of integer data by means of Hilbert 
curves

HilbertVisGUI
 An interactive tool to visualize long vectors of integer data by means 
of Hilbert curves

IRanges
 Infrastructure for managing large data objects and range-based data 
representations

ITALICS
 Normalizes Affymetrix GeneChip Human Mapping 100K and 500K set

iterativeBMA
 Bayesian Model Averaging (BMA) of classification models of 2-class 
microarray samples

iterativeBMAsurv
 Uses Bayesian Model Averaging (BMA) of survival analysis models of 
microarray data

KCsmart
 Multi-sample aCGH analysis package using kernel convolution

logitT
 Implements the Logit-t algorithm

LPEadj
 Extends the LPE algorithm

MEDME
 Determines absolute and relative DNA methylation scores from MeDIP 
enrichment measurements
 
miRNApath
 Provides pathway enrichment techniques for miRNA expression data

microRNA
 Accesses different data resources for microRNAs

minet
 Implements methods for inferring mutual information networks from data.

multiscan
 Estimates gene expressions from several laser scans of the same microarray

parody
 Provides routines for univariate and multivariate outlier detection

PLPE
 Performs tests for paired high-throughput data

RNAither
 Analyzes cell-based RNAi screens

RpsiXML
 Queries, data structure and interface to visualization of interaction 
datasets

SIM
 Finds associations between DNA copy number and gene expression

ShortRead
 Representation of high-throughput, short-read sequencing data

xmapbridge
 Plots graphs in the X:Map genome browser


Software Packages in 2.2 that didn't make it to 2.3
===================================================

1. SemSim
2. widgetInvoke



    Thanks to all who contributed to this release and made it a reality!


        The Biocore Team