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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
