April 4, 2013

Bioconductors:

We are pleased to announce Bioconductor 2.12, consisting of 671 software packages and more than 675 up-to-date annotation packages. There are 65 new software packages, and many updates and improvements to existing packages; Bioconductor 2.12 is compatible with R 3.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release includes an updated Bioconductor Amazon Machine Image. Visit http://bioconductor.org for details and downloads.

Contents

Getting Started with Bioconductor 2.12

To install Bioconductor 2.12:

  1. Install R 3.0. Bioconductor 2.12 has been designed expressly for this version of R.

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

New Software Packages

There are 65 new packages in this release of Bioconductor.

NEWS from new and existing packages

Package maintainers can add NEWS files describing changes to their packages. The following package NEWS is available:

ADaCGH2

Changes in version 2.1.3 (2010-10-06):

Changes in version 2.1.2 (2010-10-04):

Changes in version 2.1.1 (2010-09-30):

Changes in version 2.1.0 (2010-09-23):

Changes in version 1.9.0 (2013-03-23):

affxparser

Changes in version 1.31.4 (2013-03-19):

Changes in version 1.31.3 (2013-03-18):

Changes in version 1.31.2 (2013-01-07):

Changes in version 1.31.1 (2012-10-18):

Changes in version 1.31.0 (2012-10-01):

Changes in version 1.30.2 (2013-01-07):

affyPara

Changes in version 1.19.2:

Changes in version 1.19.1:

annmap

Changes in version 1.1.1:

AnnotationDbi

Changes in version 1.22:

NEW FEATURES

BUG FIXES AND CODE MAINTENANCE

aroma.light

Changes in version 1.29.0 (2012-10-01):

ASEB

Changes in version 1.4.0:

Changes in version 1.3.2:

Changes in version 1.3.1:

Changes in version 1.3.0:

BaseSpaceR

Changes in version 1.0.0:

PACKAGE FEATURES

PACKAGE FEATURES

PACKAGE FEATURES

PACKAGE FEATURES

Biobase

Changes in version 2.19:

USER VISIBLE CHANGES

BiocInstaller

Changes in version 1.10.0:

NEW FEATURES

USER-VISIBLE CHANGES

biomvRCNS

Changes in version 0.99.3:

NEW FEATURES

BUG FIXES

Changes in version 0.99.2:

NEW FEATURES

BUG FIXES

Changes in version 0.99.1:

NEW FEATURES

BitSeq

Changes in version 1.3.11 (2013-04-02):

NEW FEATURES

NEW FEATURES

Changes in version 1.3.10 (2013-03-30):

NEW FEATURES

Changes in version 1.3.6 (2013-03-19):

NEW FEATURES

BUG FIXES

Changes in version 1.2.2 (2013-01-29):

Changes in version 1.2.1 (2012-11-06):

BSgenome

Changes in version 1.28.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

MISCELLANEOUS

bsseq

Changes in version 0.7:

CellNOptR

Changes in version 1.6.0 (2013-03-12):

CGEN

Changes in version 2.0:

USER VISIBLE CHANGES

BUG FIXES

PLANS

ChemmineR

Changes in version 2.12.0:

NEW FEATURES

NEW FEATURES

NEW FEATURES

cisPath

Changes in version 1.0.0:

Changes in version 0.99.10:

Changes in version 0.99.9:

Changes in version 0.99.8:

Changes in version 0.99.7:

Changes in version 0.99.6:

Changes in version 0.99.5:

Changes in version 0.99.4:

Changes in version 0.99.3:

Changes in version 0.99.2:

Changes in version 0.99.1:

Changes in version 0.99.0:

clusterProfiler

Changes in version 1.7.1:

cqn

Changes in version 1.5:

ddgraph

Changes in version 1.3.1:

Changes in version 1.3.0:

DEGseq

Changes in version 1.14.0:

Changes in version 1.13.3:

Changes in version 1.13.2:

Changes in version 1.13.1:

Changes in version 1.13.0:

DESeq2

Changes in version 1.0.0:

DEXSeq

Changes in version 2013-02-27:

Changes in version 2012-11-28:

DiffBind

Changes in version 1.6.0:

DOSE

Changes in version 1.5.1:

DSS

Changes in version 1.2.0-1:

easyRNASeq

Changes in version 1.5.1:

Changes in version 1.5.0:

Changes in version 1.4.2:

BUG FIXES

Changes in version 1.4.1:

EBImage

Changes in version 4.2.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

edgeR

Changes in version 3.2.0:

eiR

Changes in version 1.0.0:

NEW FEATURES

ExiMiR

Changes in version 2.0.1:

exomeCopy

Changes in version 1.6.0 (2013-03-05):

fmcsR

Changes in version 1.1.3:

Changes in version 1.1.2:

Changes in version 1.1.1:

gage

Changes in version 2.9.4:

Changes in version 2.9.2:

Changes in version 2.9.1:

GeneAnswers

Changes in version 2.0.0:

NEW FEATURES

BUG FIXES

geNetClassifier

Changes in version 1.0:

NEW FEATURES

genomeIntervals

Changes in version 1.15.3:

Changes in version 1.15.2:

Changes in version 1.15.1:

GenomicFeatures

Changes in version 1.12:

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

GenomicRanges

Changes in version 1.12.0:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

GGtools

Changes in version 4.7:

gmapR

Changes in version 1.2.0:

NEW FEATURES

USER-VISIBLE CHANGES

BUG FIXES

GOSemSim

Changes in version 1.17.1:

GraphPAC

Changes in version 1.0.0:

GSEABase

Changes in version 1.21:

SIGNIFICANT USER-VISIBLE CHANGES

Gviz

Changes in version 1.4.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

GWASTools

Changes in version 1.5.9:

Changes in version 1.5.8:

Changes in version 1.5.7:

Changes in version 1.5.6:

Changes in version 1.5.5:

Changes in version 1.5.4:

Changes in version 1.5.3:

Changes in version 1.5.2:

Changes in version 1.5.1:

hapFabia

Changes in version 1.2.0:

Changes in version 1.0.5:

Changes in version 1.0.4:

Changes in version 1.0.3:

Changes in version 1.0.2:

NEW FEATURES

NEW FEATURES

NEW FEATURES

Changes in version 1.0.1:

NEW FEATURES

NEW FEATURES

HiTC

Changes in version 1.3.3:

NEW FEATURES

BUG FIXES

Changes in version 1.3.2:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.3.1:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

hpar

Changes in version 1.1.2:

Changes in version 1.1.1:

Changes in version 1.1.0:

HTSeqGenie

Changes in version 3.9.25:

Changes in version 3.9.24:

Changes in version 3.9.23:

Changes in version 3.9.22:

Changes in version 3.9.21:

Changes in version 3.9.20:

Changes in version 3.9.19:

Changes in version 3.9.18:

Changes in version 3.9.17:

Changes in version 3.9.16:

Changes in version 3.9.15:

Changes in version 3.9.14:

Changes in version 3.9.13:

Changes in version 3.9.12:

Changes in version 3.9.11:

Changes in version 3.9.10:

Changes in version 3.9.9:

Changes in version 3.9.8:

Changes in version 3.9.7:

Changes in version 3.9.6:

Changes in version 3.9.5:

Changes in version 3.9.4:

Changes in version 3.9.3:

Changes in version 3.9.2:

Changes in version 3.9.1:

Changes in version 3.9.0:

htSeqTools

Changes in version 1.5.1:

iPAC

Changes in version 1.1.2:

IRanges

Changes in version 1.18.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

isobar

Changes in version 1.5.2:

Changes in version 1.5.1:

Changes in version 1.5:

KEGGREST

Changes in version 1.0.0:

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

limma

Changes in version 3.16.0:

MANOR

Changes in version 2011-03-18 (2011-03-18):

Changes in version 2010-10-01 (2010-10-01):

Changes in version 2010-01-24 (2010-01-24):

Changes in version 2009-01-15 (2009-01-15):

Changes in version 2009-01-13 (2009-01-13):

Changes in version 2009-01-06 (2009-01-06):

Changes in version 2009-01-04 (2009-01-04):

Changes in version 2009-01-02 (2009-01-02):

Changes in version 2009-01-01 (2009-01-01):

Changes in version 2008-12-31 (2008-12-31):

Changes in version 2008-11-26 (2008-11-26):

Changes in version 2008-09-23 (2008-09-23):

Changes in version 2008-09-04 (2008-09-04):

metagenomeSeq

Changes in version 1.0.0 (2013-03-29):

minfi

Changes in version 1.5:

MLInterfaces

Changes in version 1.39.5:

Changes in version 1.39.4:

Changes in version 1.39.3:

Changes in version 1.39.2:

Changes in version 1.39.1:

MotifDb

Changes in version 1.1.3:

NEW FEATURES

motifStack

Changes in version 1.2.12:

NEW FEATURES

BUG FIXES

Changes in version 1.2.10:

NEW FEATURES

BUG FIXES

Changes in version 1.2.9:

NEW FEATURES

BUG FIXES

Changes in version 1.2.8:

NEW FEATURES

BUG FIXES

Changes in version 1.2.7:

NEW FEATURES

BUG FIXES

Changes in version 1.2.6:

NEW FEATURES

BUG FIXES

Changes in version 1.2.5:

NEW FEATURES

BUG FIXES

Changes in version 1.2.4:

NEW FEATURES

BUG FIXES

Changes in version 1.2.3:

NEW FEATURES

BUG FIXES

Changes in version 1.2.2:

NEW FEATURES

BUG FIXES

Changes in version 1.2.0:

NEW FEATURES

BUG FIXES

MSnbase

Changes in version 1.7.25:

Changes in version 1.7.24:

Changes in version 1.7.23:

Changes in version 1.7.22:

Changes in version 1.7.21:

Changes in version 1.7.20:

Changes in version 1.7.19:

Changes in version 1.7.18:

Changes in version 1.7.17:

Changes in version 1.7.16:

Changes in version 1.7.15:

Changes in version 1.7.14:

Changes in version 1.7.13:

Changes in version 1.7.12:

Changes in version 1.7.11:

Changes in version 1.7.10:

Changes in version 1.7.9:

Changes in version 1.7.8:

Changes in version 1.7.7:

Changes in version 1.7.6:

Changes in version 1.7.5:

Changes in version 1.7.4:

Changes in version 1.7.3:

Changes in version 1.7.2:

Changes in version 1.7.1:

Changes in version 1.7.0:

mzR

Changes in version 1.5.9:

Changes in version 1.5.8:

Changes in version 1.5.7:

Changes in version 1.5.6:

Changes in version 1.5.5:

Changes in version 1.5.4:

Changes in version 1.5.3:

NarrowPeaks

Changes in version 1.3.2:

ncdfFlow

1.5.32: 1.add "file" argument to allow user to specify file path 2.add "rbind" method to allow combining more than two ncdfFlowSets once,

NOISeq

Changes in version 1.1.5 (2013-01-28):

Changes in version 1.1.4 (2013-01-21):

Changes in version 1.1.3 (2013-01-18):

Changes in version 1.1.2 (2012-11-30):

Changes in version 1.1.1:

oligo

Changes in version 1.24:

BUG FIXES

pathview

Changes in version 1.0.0:

piano

Changes in version 0.99-1:

Changes in version 0.99-0:

plgem

Changes in version 1.31.2:

Changes in version 1.31.1:

pRoloc

Changes in version 0.99.17:

Changes in version 0.99.16:

Changes in version 0.99.15:

Changes in version 0.99.14:

Changes in version 0.99.13:

Changes in version 0.99.12:

Changes in version 0.99.11:

Changes in version 0.99.10:

Changes in version 0.99.9:

Changes in version 0.99.8:

Changes in version 0.99.7:

Changes in version 0.99.6:

Changes in version 0.99.5:

Changes in version 0.99.4:

Changes in version 0.99.3:

Changes in version 0.99.2:

Changes in version 0.99.1:

Changes in version 0.99.0:

PWMEnrich

Changes in version 2.0.0:

Changes in version 1.3.0:

qpgraph

Changes in version 1.16:

NEW FEATURES

USER VISIBLE CHANGES

BUG FIXES

QuasR

Changes in version 1.0.0:

INITIAL RELEASE

INITIAL RELEASE

INITIAL RELEASE

r3Cseq

Changes in version 1.5.0 (2012-10-25):

R453Plus1Toolbox

Changes in version 1.9.2:

rBiopaxParser

Changes in version 0.99.10:

Changes in version 0.99.9:

Changes in version 0.99.8:

Changes in version 0.99.7:

Changes in version 0.99.6:

Changes in version 0.99.5:

Changes in version 0.99.3:

Changes in version 0.99.0:

Changes in version 0.23:

Changes in version 0.21:

Changes in version 0.15:

Changes in version 0.14:

Changes in version 0.13:

Changes in version 0.12:

Changes in version 0.11:

Changes in version 0.10:

Changes in version 0.09:

Changes in version 0.08:

Changes in version 0.06:

Changes in version 0.04:

Changes in version 0.01:

Rbowtie

Changes in version 1.0.0:

INITIAL RELEASE

BUG FIXES

RCytoscape

Changes in version 1.9.8:

BUG FIXES

ReactomePA

Changes in version 1.3.1:

ReportingTools

Changes in version 2013-4-1:

ReQON

Changes in version 1.5.0:

BUG FIXES

Rgraphviz

Changes in version 2.3:

rhdf5

Changes in version 2.4.0:

NEW FEATURES

USER VISIBLE CHANGES

Risa

1.1.0: 1. The ISAtab-class was extended to include the definition of assay.names, factors, treatments and groups. 2. The previous processAssayXcmsSet method was split into processAssayXcmsSet.1factor and processAssayXcmsSet to consider the first factor only (as it was in the previous definition) or all the factors, respectively. 3. More methods for processing mass spectrometry assays were added: - the method getMSAssayFilenames retrieves a list with the mass spectrometry assay filenames - the method getRawDataFiles retrieves a list with all the files listed under the column 'Raw Spectral Data File' within the mass spectrometry assays. - the method is.ms receives an object from the ISAtab-class and an assay filename as parameter, and retrieves TRUE if the assay filename is a mass spectrometry assay, or FALSE otherwise. 4. A method called suggestBiocPackage was added, which retrieves a list of packages in Bioconductor that might be relevant to the ISAtab dataset, according to its assays' mesaurement and technology types. This method relies on the BiocViews annotations for each of the packages available in Bioconductor in a specific version. 5. Added AssayTab-class and subclasses for MS, Microarray, Seq and NMR. 6. Defined method getAssayRawDataFilenames and getRawDataFilenames 7. Defined method getExpressionSet for microarray assays relying on affy package.

RNASeqPower

Changes in version 0.99-2:

rols

Changes in version 1.1.6:

Changes in version 1.1.5:

Changes in version 1.1.4:

Changes in version 1.1.3:

Changes in version 1.1.2:

Changes in version 1.1.1:

Changes in version 1.1.0:

RPA

Changes in version 1.15.34 (2013-03-07):

rqubic

Changes in version 1.8.1 (2011-08-02):

Changes in version 1.8.0 (2011-07-11):

Rsamtools

Changes in version 1.12.0:

NEW FEATURES

USER-VISIBLE CHANGES

BUG FIXES

Rsubread

Changes in version 1.10.0:

NEW FEATURES

NEW FEATURES

RTCA

Changes in version 2009-07-13:

rtracklayer

Changes in version 1.20:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

SeqArray

Changes in version 0.99.1:

ShortRead

Changes in version 1.17:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

SSPA

Changes in version 1.99.0:

NEW FEATURES

BUG FIXES

synapter

Changes in version 1.1.5:

Changes in version 1.1.4:

Changes in version 1.1.3:

Changes in version 1.1.2:

Changes in version 1.1.1:

Changes in version 1.1.0:

TargetSearch

Changes in version 1.16.0:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

TEQC

Changes in version 2.7.2:

TransView

Changes in version 1.2.11:

BUG FIXES

Changes in version 1.2.9:

BUG FIXES

Changes in version 1.2.8:

NEW FEATURES

NEW FEATURES

Changes in version 1.2.7:

NEW FEATURES

BUG FIXES

Changes in version 1.2.6:

BUG FIXES

Changes in version 1.2.5:

BUG FIXES

Changes in version 1.2.4:

BUG FIXES

Changes in version 1.2.3:

NEW FEATURES

NEW FEATURES

NEW FEATURES

Changes in version 1.2.2:

BUG FIXES

Changes in version 1.2.1:

BUG FIXES

Changes in version 1.2.0:

NEW FEATURES

BUG FIXES

TurboNorm

Changes in version 1.7.2:

BUG FIXES

Changes in version 1.7.1:

NEW FEATURES

BUG FIXES

VariantAnnotation

Changes in version 1.6.0:

NEW FEATURES

MODIFICATIONS

DEPRECATED and DEFUNCT

BUG FIXES

VariantTools

Changes in version 1.2.0:

NEW FEATURES

USER-VISIBLE CHANGES

BUG FIXES

wateRmelon

0.99.16: seabird() no longer takes a vector for the stop argument

0.99.15: temporarily removed dependency on ROCR (and thus gdata)

0.99.14: normalized intensities as well as betas fixed a bug in as.methylumi

0.99.13:

0.99.12: Sentrix IDs should work (thanks to Elodie Portales-Casamar for bug report).

0.99.11:

0.99.10:

0.9.8: new MethyLumiSet method for pfilter RGtoy2 removed from data(minfitoy). This is because minfi now expects the manifest to be a package. swan function patched so that it can process subsets of array data (provided by Jovana Maksimovic). Now works with melon data set. as.methylumi generic function added. Gets fData from package:IlluminaHumanMethylation450k.db . The MethyLumiSet method is useful for ensuring methylumi objects contain this data. Andrew Teschendorff's BMIQ function and a MethyLumiSet method added minfi 1.4.0 has a changed manifest structure resulting in SNP probes being left out of the MethylSet. This breaks genki() for the minfi objects and also the minfitoy data() set.

xcms

Changes in version 1.35.7:

BUG FIXES

Changes in version 1.35.6:

BUG FIXES

Changes in version 1.35.4:

NEW FEATURES

USER VISIBLE CHANGES

Changes in version 1.35.3:

BUG FIXES

Changes in version 1.35.2:

UPDATED FEATURES

BUG FIXES

Changes in version 1.35.1:

UPDATED FEATURES

xps

Changes in version 2.16:

VERSION xps-1.19.10

VERSION xps-1.19.9

VERSION xps-1.19.8

VERSION xps-1.19.7

VERSION xps-1.19.2 - 6

VERSION xps-1.19.1

Packages removed from the release

The following packages are no longer in the release: cosmo, cosmoGUI, gene2pathway

Fred Hutchinson Cancer Research Center