April 2, 2012

Bioconductors:

We are pleased to announce Bioconductor 2.10, consisting of 554 software packages and more than 600 up-to-date annotation packages. There are 45 new software packages, and many updates and improvements to existing packages; 5 packages have been removed from this release. Bioconductor 2.10 is compatible with R 2.15.0, 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 2.10

To install Bioconductor 2.10:

  1. Install R 2.15.0. Bioconductor 2.10 has been designed expressly for this version of R.

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

New Software Packages

There are 45 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:

a4Base

Changes in version 1.2.4:

Changes in version 1.2.3:

Changes in version 1.2.2:

Changes in version 1.2.1:

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):

affxparser

Changes in version 1.28.0 (2012-03-30):

Changes in version 1.27.5 (2012-03-19):

Changes in version 1.27.4 (2012-03-05):

Changes in version 1.27.3 (2011-11-18):

Changes in version 1.27.1 (2011-11-01):

Changes in version 1.27.0 (2011-10-31):

Changes in version 1.26.4 (2012-03-06):

Changes in version 1.26.2 (2011-11-16):

Changes in version 1.26.1 (2011-11-01):

aroma.light

Changes in version 1.24.0 (2012-03-30):

Changes in version 1.23.0 (2011-10-31):

ArrayExpressHTS

Changes in version 1.5.2:

UPDATES

Changes in version 1.5.1:

UPDATES

biovizBase

Changes in version 1.1.16:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

CAMERA

Changes in version 2012-03-19:

Changes in version 2012-02-29:

Changes in version 2012-02-17:

Changes in version 2012-02-15:

Changes in version 2012-02-10:

Changes in version 2011-29-11:

Changes in version 2011-28-04:

Changes in version 2011-24-11:

Changes in version 2011-24-05:

Changes in version 2011-23-09:

Changes in version 2011-22-08:

Changes in version 2011-20-25:

Changes in version 2011-20-10:

Changes in version 2011-12-12:

Changes in version 2011-12-05:

Changes in version 2011-10-11:

Changes in version 2011-04-04:

Changes in version 2011-02-08:

Changes in version 2010-29-09:

Changes in version 2010-23-11:

Changes in version 2010-20-09:

Changes in version 2010-11-10:

Changes in version 2010-11-06:

Changes in version 2010-08-11:

Changes in version 2010-05-03:

Changes in version 2010-04-20:

Changes in version 2010-04-19:

Changes in version 2010-03-17:

Changes in version 2010-01-11:

Changes in version 2009-11-24:

Changes in version 2009-11-20:

Changes in version 2009-08-26:

Changes in version 2009-08-24:

Changes in version 2009-08-12:

Changes in version 2009-08-04:

Changes in version 2009-06-03:

Changes in version 2009-05-22:

Changes in version 2009-05-06:

Changes in version 2009-03-30:

Changes in version 2009-03-18:

Changes in version 2009-03-10:

Changes in version 2009-02-24:

Changes in version 2009-02-20:

Changes in version 2009-02-18:

Changes in version 2009-01-19:

Changes in version 2008-10-15:

Changes in version 2008-10-13:

Changes in version 2007-10-12:

categoryCompare

Changes in version 0.99.0:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.7.8:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.7.4:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.7.3:

SIGNIFICANT USER-VISIBLE CHANGES

cellGrowth

Changes in version 0.99.0:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.4.0:

SIGNIFICANT USER-VISIBLE CHANGES

clusterProfiler

Changes in version 1.4.0:

Changes in version 1.3.15:

Changes in version 1.3.14:

Changes in version 1.3.13:

Changes in version 1.3.12:

Changes in version 1.3.11:

Changes in version 1.3.10:

Changes in version 1.3.9:

Changes in version 1.3.8:

Changes in version 1.3.7:

Changes in version 1.3.6:

Changes in version 1.3.5:

Changes in version 1.3.4:

Changes in version 1.3.3:

Changes in version 1.3.2:

Changes in version 1.3.1:

CNAnorm

Changes in version 1.1.8:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.1.7:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.1.6:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.1.5:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.1.4:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.1.3:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.1.2:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.1.1:

SIGNIFICANT USER-VISIBLE CHANGES

codelink

Changes in version 1.23.2:

Changes in version 1.23.1:

cqn

Changes in version 1.1:

Changes in version 1.0.1:

cummeRbund

Changes in version 1.1.5:

BUG FIXES

Changes in version 1.1.4:

NEW FEATURES

BUG FIXES

Changes in version 1.1.3:

NEW FEATURES

BUG FIXES

NOTES

Changes in version 1.1.1:

BUG FIXES

NEW FEATURES

NOTES

deepSNV

Changes in version 1.1.4:

BUG FIXES

Changes in version 1.0.0:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.99.2:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.99.1:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.99.0:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.9.5:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 0.9.4:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.9.3:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.9.2:

BUG FIXES

Changes in version 0.9.1:

BUG FIXES

Changes in version 0.9.0:

SIGNIFICANT USER-VISIBLE CHANGES

DESeq

Changes in version 1.7.10 (2011-03-26):

Changes in version 1.7.9 (2011-03-16):

Changes in version 1.7.8 (2011-03-15):

Changes in version 1.7.7 (2011-03-15):

Changes in version 1.7.6:

Changes in version 1.7.1:

DEXSeq

Changes in version 2011-10-03:

Changes in version 2011-07-12:

Changes in version 2011-07-01:

DiffBind

Changes in version 1.2.0 (2012-03-30):

DOSE

Changes in version 1.1.12:

Changes in version 1.1.11:

Changes in version 1.1.10:

Changes in version 1.1.9:

Changes in version 1.1.8:

Changes in version 1.1.7:

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:

easyRNASeq

Changes in version 1.1.10:

NEW FEATURES

BUG FIXES

Changes in version 1.1.9:

BUG FIXES

Changes in version 1.1.8:

BUG FIXES

Changes in version 1.1.7:

BUG FIXES

Changes in version 1.1.6:

BUG FIXES

Changes in version 1.1.5:

BUG FIXES

Changes in version 1.1.4:

EDASeq

Changes in version 1.2.0:

edgeR

Changes in version 2.6.0:

ExiMiR

Changes in version 1.3.1:

exomeCopy

Changes in version 1.2.0 (2012-02-26):

flowCore

Changes in version 1.21.5:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.21.1:

SIGNIFICANT USER-VISIBLE CHANGES

GeneGroupAnalysis

Changes in version 1.1:

GeneticsPed

Changes in version 2007-09-12:

Changes in version 2007-04-25:

Changes in version 2007-04-19:

Changes in version 2007-04-18:

Changes in version 2007-04-06:

Changes in version 2007-04-01:

Changes in version 2007-04:

Changes in version 2007-03-02:

Changes in version 2006-03-29:

Changes in version 2006-03-16:

GenomicFeatures

Changes in version 1.8:

NEW FEATURES

GenomicRanges

Changes in version 1.8.0:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

BUG FIXES

genoset

Changes in version 1.4.19:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.4.10:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.4.9:

ggbio

Changes in version 1.1.8:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

Notes

GOSemSim

Changes in version 1.13.6:

Changes in version 1.13.5:

Changes in version 1.13.4:

Changes in version 1.13.3:

Changes in version 1.13.2:

Changes in version 1.13.1:

gprege

Changes in version 0.99.1 (2011-07-26):

Changes in version 0.99.0 (2011-07-11):

GRENITS

Changes in version 1.7.1 (2012-03-15):

GSVA

Changes in version 1.4:

USER VISIBLE CHANGES

BUG FIXES

GWASTools

Changes in version 1.1.9:

Changes in version 1.1.8:

Changes in version 1.1.7:

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:

HTqPCR

Changes in version 1.9:

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

BUG FIXES

htSeqTools

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:

IRanges

Changes in version 1.14.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

isobar

Changes in version 1.1.3:

Changes in version 1.1.2:

Changes in version 1.1.1:

NEW FEATURES

KEGGgraph

Changes in version 1.11.1:

SIGNIFICANT USER-VISIBLE CHANGES

limma

Changes in version 3.12.0:

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):

minfi

Changes in version 1.1:

MinimumDistance

Changes in version 1.0:

USER VISIBLE CHANGES

MLP

Changes in version 1.3.0:

Changes in version 1.2.1:

mosaics

Changes in version 1.3.4:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.3.2:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.2.5:

Changes in version 1.2.4:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.2.3:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

MSnbase

Changes in version 1.3.15:

Changes in version 1.3.14:

Changes in version 1.3.13:

Changes in version 1.3.12:

Changes in version 1.3.11:

Changes in version 1.3.10:

Changes in version 1.3.9:

Changes in version 1.3.8:

Changes in version 1.3.7:

Changes in version 1.3.6:

Changes in version 1.3.5:

Changes in version 1.3.4:

Changes in version 1.3.3:

Changes in version 1.3.2:

Changes in version 1.3.1:

Changes in version 1.3.0:

ncdfFlow

Changes in version 1.1.2:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.1.1:

SIGNIFICANT USER-VISIBLE CHANGES

KNOWN ISSUES

netresponse

Changes in version 1.7.38 (2012-03-28):

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.7.34 (2012-03-28):

Changes in version 1.7.33 (2012-03-13):

Changes in version 1.7.32 (2012-02-21):

Changes in version 1.7.03 (2012-02-02):

Changes in version 1.7.02 (2012-02-01):

oligo

Changes in version 1.20:

USER VISIBLE CHANGES

BUG FIXES

oneChannelGUI

Changes in version 1.21.11:

SIGNIFICANT USER-VISIBLE CHANGES

pdInfoBuilder

Changes in version 1.20:

USER VISIBLE CHANGES

phyloseq

Changes in version 0.99:

pint

Changes in version 1.7.03 (2012-03-22):

Changes in version 1.7.01 (2012-01-16):

procoil

Changes in version 1.5.1:

qpgraph

Changes in version 1.12:

NEW FEATURES

QUALIFIER

Changes in version 1.0.0:

FEATURES

KNOWN ISSUES

R453Plus1Toolbox

Changes in version 1.5.2:

RCytoscape

Changes in version 1.6.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

ReactomePA

Changes in version 0.99.0:

Changes in version 0.2.3:

Changes in version 0.2.2:

Changes in version 0.2.1:

Changes in version 0.2.0:

Changes in version 0.1.1:

Changes in version 0.1.0:

RedeR

Changes in version 1.1.16:

NEW FEATURES

BUG FIXES

ReQON

Changes in version 1.2.0:

NEW FEATURES

RPA

Changes in version 1.11.13 (2012-02-25):

Changes in version 1.11.12 (2011-12-13):

Changes in version 1.11.05 (2011-11-11):

rqubic

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

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

Changes in version 1.1-3 (2012-01-05):

Changes in version 1.1-2 (2012-01-03):

Changes in version 1.1-1 (2011-12-22):

Rsamtools

Changes in version 1.8.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Rsubread

Changes in version 1.6.0:

NEW FEATURES

RTCA

Changes in version 2009-07-13:

rtracklayer

Changes in version 1.15:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

ShortRead

Changes in version 1.13:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

TargetSearch

Changes in version 1.12.0:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

VariantAnnotation

Changes in version 1.2.0:

NEW FEATURES

xps

Changes in version 2.15.0:

VERSION xps-1.15.2

VERSION xps-1.15.1

Changes in version 2.14.0:

VERSION xps-1.13.10

VERSION xps-1.13.9

VERSION xps-1.13.8

VERSION xps-1.13.7

VERSION xps-1.13.6

VERSION xps-1.13.5

VERSION xps-1.13.4

VERSION xps-1.13.3

VERSION xps-1.13.2

VERSION xps-1.13.1

Changes in version 2.13.0:

VERSION xps-1.11.12

VERSION xps-1.11.11

VERSION xps-1.11.10

VERSION xps-1.11.9

VERSION xps-1.11.8

VERSION xps-1.11.7

VERSION xps-1.11.6

VERSION xps-1.11.5

VERSION xps-1.11.4

VERSION xps-1.11.3

VERSION xps-1.11.1

Changes in version 2.12.0:

VERSION xps-1.9.9

VERSION xps-1.9.8

VERSION xps-1.9.7

VERSION xps-1.9.6

VERSION xps-1.9.5

VERSION xps-1.9.4

VERSION xps-1.9.3

VERSION xps-1.9.2

VERSION xps-1.9.1

Changes in version 2.11.0:

VERSION xps-1.7.9

VERSION xps-1.7.8

VERSION xps-1.7.7

VERSION xps-1.7.6

VERSION xps-1.7.4

VERSION xps-1.7.3

VERSION xps-1.7.2

VERSION xps-1.7.1

Changes in version 2.10.0:

VERSION xps-1.5.19

VERSION xps-1.5.18

VERSION xps-1.5.17

VERSION xps-1.5.16

VERSION xps-1.5.15

VERSION xps-1.5.14

VERSION xps-1.5.13

VERSION xps-1.5.12

VERSION xps-1.5.9

VERSION xps-1.5.8

VERSION xps-1.5.7

VERSION xps-1.5.4

VERSION xps-1.5.3

VERSION xps-1.5.1

Changes in version 2.9.0:

VERSION xps-1.3.13

VERSION xps-1.3.12

VERSION xps-1.3.11

VERSION xps-1.3.8

VERSION xps-1.3.6

VERSION xps-1.3.5

VERSION xps-1.3.4

VERSION xps-1.3.3

VERSION xps-1.3.1

Changes in version 2.8.0:

VERSION xps-1.1.9

VERSION xps-1.1.8

VERSION xps-1.1.7

VERSION xps-1.1.6

VERSION xps-1.1.5

VERSION xps-1.1.4

VERSION xps-1.1.3

VERSION xps-1.1.2

VERSION xps-1.1.1

Changes in version 2.7.0:

VERSION xps-0.99.11

VERSION xps-0.99.10

VERSION xps-0.99.9

VERSION xps-0.99.8

VERSION xps-0.99.3

VERSION xps-0.4.3

VERSION xps-0.4.2

VERSION xps-0.4.1

VERSION xps-0.4.0

yaqcaffy

Changes in version 1.15.1:

Packages removed from the release

The following packages are no longer in the release: edd, ontoTools, GeneR, RMAGEML, RTools4TB

Fred Hutchinson Cancer Research Center