November 1, 2011

Bioconductors:

We are pleased to announce Bioconductor 2.9, consisting of 517 software packages and more than 500 up-to-date annotation packages. There are 60 new software packages, and many updates and improvements to existing packages; 10 packages have been removed from this release. Bioconductor 2.9 is compatible with R 2.14.0, 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 2.9

To install Bioconductor 2.9:

  1. Install R 2.14.0. Bioconductor 2.9 has been designed expressly for this version of R.

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

New Software Packages

There are 60 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:

a4

Changes in version 1.1.2:

a4Base

Changes in version 1.1.4:

Changes in version 1.1.3:

Changes in version 1.1.1:

a4Classif

Changes in version 1.1.3:

Changes in version 1.1.1:

a4Core

Changes in version 1.1.3:

Changes in version 1.1.2:

Changes in version 1.1.1:

a4Reporting

Changes in version 1.1.1:

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):

Changes in version 1.3.3 (2011-10-19):

Changes in version 1.3.2 (2011-10-18):

Changes in version 1.2.1 (2011-06-06):

affxparser

Changes in version 1.25.1 (2011-09-27):

Changes in version 1.25.0 (2011-04-13):

AnnotationFuncs

Changes in version 1.3:

SIGNIFICANT USER-VISIBLE CHANGES

aroma.light

Changes in version 1.21.2 (2011-10-10):

Changes in version 1.21.1 (2011-06-26):

Changes in version 1.21.0 (2011-04-13):

ArrayExpressHTS

Changes in version 1.3.1:

NEW FEATURES

BUG FIXES

Changes in version 1.3.0:

beadarray

Changes in version 2.4:

MAJOR CHANGES

OTHER CHANGES

Changes in version 2.3:

NEW FEATURES

BUG FIXES in 2.3.6

BUG FIXES in 2.3.5

BUG FIXES in 2.3.4

BUG FIXES in 2.3.3

BUG FIXES in 2.3.2

BUG FIXES in 2.3.1

BeadDataPackR

Changes in version 1.5:

BUG FIXES

CAMERA

Changes in version 2011-28-04:

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 2011-12-05:

Changes in version 2011-04-04:

Changes in version 2011-02-08:

ChIPpeakAnno

Changes in version 2.2.0:

clusterProfiler

Changes in version 1.1.22:

Changes in version 1.1.21:

Changes in version 1.1.20:

Changes in version 1.1.19:

Changes in version 1.1.18:

Changes in version 1.1.17:

Changes in version 1.1.16:

Changes in version 1.1.15:

cqn

Changes in version 0.99:

cummeRbund

Changes in version 0.99.5:

Changes in version 0.99.4:

Changes in version 0.1.3 (2011-08-18):

DESeq

Changes in version 1.6.0:

Changes in version 1.5.29 (2011-10-10):

Changes in version 1.5.27 (2011-10-18):

Changes in version 1.5.24 (2011-08-10):

Changes in version 1.5.23 (2011-07-14):

Changes in version 1.5.22 (2011-07-14):

Changes in version 1.5.21 (2011-07-14):

Changes in version 1.5.20 (2011-07-07):

Changes in version 1.5.1:

DEXSeq

Changes in version 2011-10-03:

Changes in version 2011-07-12:

Changes in version 2011-07-01:

DOSE

Changes in version 0.99.7:

Changes in version 0.99.6:

EDASeq

Changes in version 0.99.1:

Changes in version 0.99.0:

Changes in version 0.0.6:

Changes in version 0.0.5:

Changes in version 0.0.4:

Changes in version 0.0.3:

edgeR

Changes in version 2.4.0:

NEW FEATURES

BUG FIXES

fabia

Changes in version 2.0.0:

NEW FEATURES

BUG FIXES

flowFP

flowWorkspace

FEATURES:

-import flowJo XML workspace from the Mac version. (Greg Finak)

-convert GatingHierarchy objects to workflows. (Mike Jiang)

-export workflows to flowJo XML workspace readable by Mac version of flowJo (Mose Andre)

-netCDF support for large data sets. Based on code contributed by Nisat Gopalakrishnan.

KNOWN ISSUES:

geneplotter

Changes in version 1.31.4:

USER VISIBLE CHANGES

GenomicFeatures

Changes in version 1.6:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

GenomicRanges

Changes in version 1.6.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

genoset

1.0.0

1.0.6

1.1.7

1.1.8

1.1.9

1.1.10

1.1.11

1.1.12

GOSemSim

Changes in version 1.11.2:

GRENITS

Changes in version 0.99.1 (2011-08-07):

Heatplus

Changes in version 2.0.0:

HTqPCR

Changes in version 1.7:

NEW FEATURES

BUG FIXES

htSeqTools

Changes in version 0.99:

Changes in version 0.2.7:

Changes in version 0.2.5:

Changes in version 0.2.3:

Changes in version 0.2.1:

Changes in version 0.2.0:

Changes in version 0.1.2:

Changes in version 0.1.1:

Changes in version 0.1.0:

Changes in version 0.0.1:

IRanges

Changes in version 1.12.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

isobar

Changes in version 1.0.0:

Changes in version 0.2.5:

Changes in version 0.2.4:

Changes in version 0.2.3:

Changes in version 0.2.2:

Changes in version 0.2.1:

Changes in version 0.2:

KEGGgraph

limma

Changes in version 3.10.0:

lumi

minfi

Changes in version 0.99:

MLP

Changes in version 1.1.1:

MSnbase

Changes in version 1.1.28:

Changes in version 1.1.27:

Changes in version 1.1.26:

Changes in version 1.1.25:

Changes in version 1.1.24:

Changes in version 1.1.23:

Changes in version 1.1.22:

Changes in version 1.1.21:

Changes in version 1.1.20:

Changes in version 1.1.18:

Changes in version 1.1.17:

Changes in version 1.1.16:

Changes in version 1.1.15:

Changes in version 1.1.14:

Changes in version 1.1.13:

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:

Mulcom

Changes in version 1.3.0:

ncdfFlow

0.1.0

FEATURES:

KNOWN ISSUES:

netresponse

Changes in version 1.5.14 (2011-10-28):

Changes in version 1.5.12 (2011-06-29):

Changes in version 1.5.11 (2011-06-28):

Changes in version 1.5.09 (2011-06-13):

Changes in version 1.5.08 (2011-05-27):

Changes in version 1.5.04 (2011-05-27):

BUG FIXES

Changes in version 1.5.02 (2011-05-18):

SIGNIFICANT USER-VISIBLE CHANGES

pdInfoBuilder

Changes in version 1.18:

USER VISIBLE CHANGES

pint

Changes in version 1.5.35 (2011-10-13):

Changes in version 1.5.34 (2011-08-15):

Changes in version 1.5.33 (2011-08-02):

Changes in version 1.5.30 (2011-07-15):

Changes in version 1.5.29 (2011-05-09):

BUG FIXES

Changes in version 1.5.28 (2011-05-09):

BUG FIXES

Changes in version 1.5.06 (2011-04-16):

qpgraph

Changes in version 1.10:

NEW FEATURES

BUG FIXES

RPA

Changes in version 1.9.19 (2011-10-29):

Changes in version 1.9.17 (2011-06-27):

Changes in version 1.9.11 (2011-06-02):

Changes in version 1.9.06 (2011-05-29):

Changes in version 1.9.03 (2011-05-14):

Changes in version 1.9.02 (2011-04-21):

rqubic

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

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

Changes in version 0.99.1 (2011-08-11):

Changes in version 0.99.0 (2011-08-05):

Rsamtools

Changes in version 1.6.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Rsubread

Changes in version 1.4.0:

NEW FEATURES

RTCA

Changes in version 2009-07-13:

ShortRead

Changes in version 1.11:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

TargetSearch

Changes in version 1.10.0:

NEW FEATURES

BUG FIXES

Changes in version 1.8.2:

BUG FIXES

Changes in version 1.8.1:

BUG FIXES

TEQC

Changes in version 2.0.0:

Changes in version 1.1.2:

Changes in version 1.1.0:

tigre

Changes in version 1.8.0:

NEW FEATURES

BUG FIXES

Changes in version 1.6.1 (2011-04-26):

BUG FIXES

VariantAnnotation

Changes in version 1.0.0:

NEW FEATURES

BUG FIXES

xps

Changes in version 1.14.0:

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

Packages removed from the release

The following packages are no longer in the release: GeneSpring, GeneTraffic, makePlatformDesign, Rdbi, RdbiPgSQL, rflowcyt, Rredland, Ruuid, simulatorAPMS.

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