October 3, 2012

Bioconductors:

We are pleased to announce Bioconductor 2.11, consisting of 610 software packages and more than 650 up-to-date annotation packages. There are 58 new software packages, and many updates and improvements to existing packages; Bioconductor 2.11 is compatible with R 2.15.1, 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 2.11

To install Bioconductor 2.11:

  1. Install R 2.15.1. Bioconductor 2.11 has been designed expressly for this version of R.

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

  3. If you have already been using Bioconductor 2.10 (with R-2.15), you can upgrade as follows:

    source("http://bioconductor.org/biocLite.R")

    biocLite("BiocUpgrade")

New Software Packages

There are 58 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 1.4.1:

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 1.29.13 (2012-09-26):

Changes in version 1.29.12 (2012-09-12):

Changes in version 1.29.11 (2012-09-01):

Changes in version 1.29.10 (2012-08-29):

Changes in version 1.29.9 (2012-08-29):

Changes in version 1.29.8 (2012-08-14):

Changes in version 1.29.7 (2012-08-14):

Changes in version 1.29.6 (2012-06-26):

Changes in version 1.29.5 (2012-06-19):

Changes in version 1.29.4 (2012-06-14):

Changes in version 1.29.3 (2012-05-22):

Changes in version 1.29.2 (2012-05-22):

Changes in version 1.29.1 (2012-05-18):

Changes in version 1.29.0 (2012-03-30):

Changes in version 1.28.1 (2012-06-26):

affyPara

Changes in version 1.17.1:

annmap

Changes in version 0.99.3:

Changes in version 0.99.2:

Changes in version 0.99.1:

Changes in version 0.99.0:

Changes in version 0.9.16:

Changes in version 0.9.15:

Changes in version 0.9.14:

Changes in version 0.9.13:

Changes in version 0.9.12:

Changes in version 0.9.11:

Changes in version 0.9.10:

Changes in version 0.9.9:

Changes in version 0.9.8:

Changes in version 0.9.7:

Changes in version 0.9.6:

Changes in version 0.9.5:

AnnotationForge

Changes in version 1.9.5:

NEW FEATURES

NOTEWORTHY CHANGES BETWEEN THIS version and 1.3.11

aroma.light

Changes in version 1.27.1 (2012-09-12):

Changes in version 1.27.0 (2012-08-30):

Changes in version 1.26.1 (2012-08-30):

Changes in version 1.26.0 (2012-08-19):

Changes in version 1.25.4 (2012-08-19):

Changes in version 1.25.3 (2012-04-16):

Changes in version 1.25.2 (2012-04-16):

Changes in version 1.25.1 (2012-04-16):

Changes in version 1.25.0 (2012-03-30):

arrayQualityMetrics

Changes in version 3.13.2:

USER VISIBLE CHANGES

bigmemoryExtras

Version Date Category Text 0.1.8

Biobase

Changes in version 2.17:

USER VISIBLE CHANGES

BitSeq

Version: 1.2.0 (27.9.2012)

CAMERA

Changes in version 2012-06-12:

Changes in version 2012-06-11:

Changes in version 2012-05-25:

Changes in version 2012-04-12:

ChemmineR

Changes in version 2.10.0:

NEW FEATURES

clusterProfiler

Changes in version 1.5.1:

Changes in version 1.5.0:

cqn

Changes in version 1.3:

cummeRbund

v1.99.6 Notes: - 'annotation' and "annotation<-" generics were moved to BiocGenerics 0.3.2. Now using appropriate generic function, but requiring BiocGenerics >= 0.3.2 v1.99.5 Bugfixes: - Added replicates argument to csDistHeat to view distances between individual replicate samples. - Appropriately distinguish now between 'annotation' (external attributes) and features (gene-level sub-features). - csHeatmap now has 'method' argument to pass function for any dissimilarity metric you desire. You must pass a function that returns a 'dist' object applied to rows of a matrix. Default is still JS-distance.

v1.99.3 New Features: - Added diffTable() method to return a table of differential results broken out by pairwise comparison. (more human-readable) - Added sigMatrix() method to CuffSet objects to draw heatmap showing number of significant genes by pairwise comparison at a given FDR. - A call to fpkm() now emits calculated (model-derived) standard deviation field as well. - Can now pass a GTF file as argument to readCufflinks() to integrate transcript model information into database backend * Added requirement for rtracklayer and GenomicFeatures packages. * You must also indicate which genome build the .gtf was created against by using the 'genome' argument to readCufflinks. - Integration with Gviz: * CuffGene objects now have a makeGeneRegionTrack() argument to create a GeneRegionTrack() from transcript model information * Can also make GRanges object * ONLY WORKS IF YOU READ .gtf FILE IN WITH readCufflinks() - Added csScatterMatrix() and csVolcanoMatrix() method to CuffData objects. - Added fpkmSCVPlot() as a CuffData method to visualize replicate-level coefficient of variation across fpkm range per condition. - Added PCAplot() and MDSplot() for dimensionality reduction visualizations (Principle components, and multi-dimensional scaling respectively) - Added csDistHeat() to create a heatmap of JS-distances between conditions.

Bugfixes: - Fixed diffData 'features' argument so that it now does what it's supposed to do. - added DB() with signature(object="CuffSet") to NAMESPACE

Notes: - Once again, there have been modifications to the underlying database schema so you will have to re-run readCufflinks(rebuild=T) to re-analyze existing datasets. - Importing 'defaults' from plyr instead of requiring entire package (keeps namespace cleaner). - Set pseudocount=0.0 as default for csDensity() and csScatter() methods (This prevents a visual bias for genes with FPKM <1 and ggplot2 handles removing true zero values).

v1.99.2 Bugfixes: - Fixed bug in replicate table that did not apply make.db.names to match samples table. - Fixed bug for missing values in .count_tracking files. - Now correctly applying make.db.names to .read_group_tracking files. - Now correctly allows for empty .count_tracking and .read_group_tracking files v1.99.1 - This represents a major set of improvements and feature additions to cummeRbund. - cummeRbund now incorporates additional information emitted from cuffdiff 2.0 including: - run parameters and information. - sample-level information such as mass and scaling factors. - individual replicate fpkms and associated statistics for all features. - raw and normalized count tables and associated statistics all features.

New Features: - Please see updated vignette for overview of new features. - New dispersionPlot() to visualize model fit (mean count vs dispersion) at all feature levels. - New runInfo() method returns cuffdiff run parameters. - New replicates() method returns a data.frame of replicate-level parameters and information. - getGene() and getGenes() can now take a list of any tracking_id or gene_short_name (not just gene_ids) to retrieve a gene or geneset. - Added getFeatures() method to retrieve a CuffFeatureSet independent of gene-level attributes. This is ideal for looking at sets of features outside of the context of all other gene-related information (i.e. facilitates feature-level analysis) - Replicate-level fpkm data now available. - Condition-level raw and normalized count data now available. - repFpkm(), repFpkmMatrix, count(), and countMatrix are new accessor methods to CuffData, CuffFeatureSet, and CuffFeature objects. - All relevant plots now have a logical 'replicates' argument (default = F) that when set to TRUE will expose replicate FPKM values in appropriate ways. - MAPlot() now has 'useCount' argument to draw MA plots using count data as opposed to fpkm estimates.

Notes: - Changed default csHeatmap colorscheme to the much more pleasing 'lightyellow' to 'darkred' through 'orange'. - SQLite journaling is no longer disabled by default (The benefits outweigh the moderate reduction in load times).

Bugfixes: - Numerous random bug fixes to improve consistency and improve performance for large datasets. v1.2.1 Bugfixes: -Fixed bug in CuffFeatureSet::expressionBarplot to make compatible with ggplot2 v0.9. New Features: - Added 'distThresh' argument to findSimilar. This allows you to retrieve all similar genes within a given JS distance as specified by distThresh. - Added 'returnGeneSet' argument to findSimilar. [default = T] If true, findSimilar returns a CuffGeneSet of genes matching criteria (default). If false, a rank-ordered data frame of JS distance values is returned. - findSimilar can now take a 'sampleIdList' argument. This should be a vector of sample names across which the distance between genes should be evaluated. This should be a subset of the output of samples(genes(cuff)). Notes: - Added requirement for 'fastcluster' package. There is very little footprint, and it makes a significant improvement in speed for the clustering analyses.

DART

Version Date Category Text 1.3.1 Dependency changed from igraph to igraph0

ddgraph

Changes in version 1.0.3:

Changes in version 1.0.2:

Changes in version 1.0.1:

Changes in version 1.0.0:

deepSNV

Changes in version 1.3.3 (2012-09-14):

Updates

Changes in version 1.3.2 (2012-04-10):

Updates

Changes in version 1.2.3 (2012-04-10):

Bugfixes

DESeq

Changes in version 1.9.12 (2012-09-05):

Changes in version 1.9.7 (2012-05-25):

Changes in version 1.9.6:

Changes in version 1.9.5:

Changes in version 1.9.4 (2012-04-24):

Changes in version 1.9.2 (2012-04-05):

Changes in version 1.9.1 (2012-04-01):

DEXSeq

Changes in version 2012-06-26:

Changes in version 2012-05-21:

Changes in version 2011-10-03:

Changes in version 2011-07-12:

Changes in version 2011-07-01:

DiffBind

Changes in version 1.4.0:

Changes in version 1.2.3 (2012-09-01):

DOSE

Changes in version 1.3.2:

Changes in version 1.3.1:

DSS

Changes in version 0.99-1:

Changes in version 0.99:

NEW FEATURES

EasyqpcR

Changes in version 1.0.0:

easyRNASeq

Changes in version 1.3.14:

NEW FEATURES

BUG FIXES

Changes in version 1.3.13:

BUG FIXES

Changes in version 1.3.12:

Changes in version 1.3.11:

BUG FIXES

Changes in version 1.3.10:

Changes in version 1.3.9:

Changes in version 1.3.8:

NEW FEATURES

Changes in version 1.3.7:

NEW FEATURES

BUG FIXES

Changes in version 1.3.6:

NEW FEATURES

BUG FIXES

Changes in version 1.3.5:

NEW FEATURES

BUG FIXES

Changes in version 1.3.4:

NEW FEATURES

Changes in version 1.3.3:

Changes in version 1.3.2:

BUG FIXES

Changes in version 1.3.1:

NEW FEATURES

Changes in version 1.3.0:

Changes in version 1.2.5:

BUG FIXES

Changes in version 1.2.4:

Changes in version 1.2.3:

NEW FEATURES

Changes in version 1.2.2:

BUG FIXES

Changes in version 1.2.1:

NEW FEATURES

EBImage

Changes in version 4.0.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

EDASeq

Changes in version 1.3:

edgeR

Changes in version 3.0.0:

ExiMiR

Changes in version 1.99.1:

Changes in version 1.99.0:

fabia

Changes in version 2.3.1:

NEW FEATURES

flowCore

flowViz

CHANGES IN VERSION 1.21.1

1.add modified lattice theme to flowViz and change the default color scheme for non-smoothed xyplot 2.add stat=TRUE to display population % in xyplot and add abs=FALSE and pos=0.5 to control the position of gate labels 3.made change to prepanel.xyplot.flowset so that it return an empty list instead of NULL value for empty panels.This was causing the error thrown by lattice:::limits.and.aspect which calculates the scales for each panel and expects non-null return value from prepanel function 4.remove the old src and R code for hexbin and add hexbin package based hexagon plot support within panel.xyplot.flowframe 5.add binTrans argument to xyplot that gets passed to hexin to transform the raw counts. sqrt is the default,NULL value means no transformation. 6.add new classes "filters", "filtersList" to allow flowViz to plot multiple filters/gates for one flowFrame

fmcsR

Changes in version 0.99.0:

FunciSNP

Changes in version 0.99.0 (2012-05-25):

Changes in version 0.2.0 (2012-05-18):

Changes in version 0.1.0 (2012-02-12):

GeneAnswers

Changes in version 1.14:

NEW FEATURES

GeneNetworkBuilder

Changes in version 1.0.0:

NEW FEATURES

BUG FIXES

GenomicFeatures

Changes in version 1.10:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

GenomicRanges

Changes in version 1.10.0:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

genoset

1.9.8 GRanges everywhere! GenoSet now supports GRanges in the locData slot. All functions that take RangedData now also take GRanges. I have unified the API for GRanges, RangedData, and GenoSet to the point that GenoSet classes and the functions in the package are agnostic to the type of range object. I have not, however, fixed the contentious issue of using the "$" operator with GRanges to access elementMetadata.

1.9.10 Subsetting by location now only with GRanges and RangedData. Dropped RangesList to avoid weird errors about the RangedDataOrRangesListOrGRanges class union. Apparently the RangedDataOrGRanges class union is fine. I think RangesLists are not used often anyway.

1.9.11 GenoSet creation and featureNames<- no longer do make.names.

1.9.12 GenoSet creation and sampleNames<- no longer do make.names.

GGBase

Changes in version 3.20.0:

ggbio

Changes in version 1.5.16:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

Notes

GGtools

Changes in version 4.6:

GOSemSim

Changes in version 1.15.3:

Changes in version 1.15.2:

Changes in version 1.15.1:

GSEABase

Changes in version 1.19:

NEW FEATURES

Gviz

Changes in version 1.2.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

GWASTools

Changes in version 1.3.16:

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:

HiTC

Changes in version 1.1.3:

NEW FEATURES

DEPRECATED AND DEFUNCT

Changes in version 1.1.2:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

Changes in version 1.1.1:

NEW FEATURES

hpar

Changes in version 0.99.1:

Changes in version 0.99.0:

Changes in version 0.1.0:

htSeqTools

Changes in version 1.3.1:

iPAC

Changes in version 0.3.0:

IRanges

Changes in version 1.16.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

iSeq

Changes in version 1.9.0:

isobar

KEGGprofile

2012-09-19 KEGGprofile 0.99.2: Improvement in processing expression matrix with only one time point

2012-06-29 KEGGprofile 0.99.1: Add the param lwd when type='lines'

limma

Changes in version 3.14.0:

lmdme

Changes in version 0.99.1:

MINOR CHANGES

DOCUMENTATION

minfi

Changes in version 1.3:

MLInterfaces

Changes in version 1.37.1:

MLP

Changes in version 1.5.2:

Changes in version 1.5.0:

Changes in version 1.4.2:

Changes in version 1.4.1:

mosaics

Changes in version 1.5.3:

BUG FIXES

Changes in version 1.5.2:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.5.1:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.4.1:

BUG FIXES

motifStack

Changes in version 1.0.0:

NEW FEATURES

BUG FIXES

MSnbase

Changes in version 1.5.25:

Changes in version 1.5.24:

Changes in version 1.5.23:

Changes in version 1.5.22:

Changes in version 1.5.21:

Changes in version 1.5.20:

Changes in version 1.5.19:

Changes in version 1.5.18:

Changes in version 1.5.17:

Changes in version 1.5.16:

Changes in version 1.5.15:

Changes in version 1.5.14:

Changes in version 1.5.13:

Changes in version 1.5.12:

Changes in version 1.5.11:

Changes in version 1.5.10:

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:

Changes in version 1.5.0:

ncdfFlow

1.optimize [[ accessor by merging two routines into [[ method and\nremoving some unnecessary check or subsetting

netresponse

Changes in version 1.9.17 (2012-06-28):

Changes in version 1.9.15 (2012-05-23):

Changes in version 1.9.14 (2012-05-14):

Changes in version 1.9.13 (2012-05-04):

USER-VISIBLE CHANGES

Changes in version 1.9.12 (2012-05-03):

USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.9.10 (2012-04-30):

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.9.07 (2012-04-25):

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.9.05 (2012-04-24):

Changes in version 1.9.04 (2012-04-21):

oligo

Changes in version 1.22:

USER VISIBLE CHANGES

BUG FIXES

phyloseq

phyloseq 1.1.50

phyloseq 1.1.45

phyloseq 1.1.44

phyloseq 1.1.43

phyloseq 1.1.42

phyloseq 1.1.41

phyloseq 1.1.40

Huge Update and Renaming Event.

phyloseq 1.1.33

phyloseq 1.1.29

phyloseq 1.1.28

phyloseq 1.1.27

phyloseq 1.1.23-26

phyloseq 1.1.19-22

phyloseq 1.1.18

phyloseq 1.1.17

phyloseq 1.1.15

phyloseq 1.1.14

phyloseq 1.1.10

phyloseq 1.1.8-9

phyloseq 1.1.7

phyloseq 1.1.6

phyloseq 1.1.5

phyloseq 1.1.4

phyloseq 1.1.1-3

PWMEnrich

Changes in version 1.0.2:

Changes in version 1.0.1:

Changes in version 1.0.0:

qpgraph

Changes in version 1.14:

NEW FEATURES

R453Plus1Toolbox

Changes in version 1.7.4:

ReactomePA

Changes in version 1.1.1:

RedeR

Version Date Category Text 2011-03-23

ReQON

Changes in version 1.3.4:

NEW FEATURES

BUG FIXES

Changes in version 1.3.2:

NEW FEATURES

Rgraphviz

Changes in version 2.1:

Risa

This is the first release version of the package. It contains functionality to parse ISAtab datasets into an R object from the ISAtab class. It also provides functionality to save the ISA-tab dataset, or each of its individual files. Additionally, it is also possible to update assay files. Currently, metadata associated to proteomics and metabolomics-based assays (i.e. mass spectrometry) can be processed into an xcmsSet object (from the xcms R package

rols

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:

Changes in version 0.2.2:

Changes in version 0.2.1:

Changes in version 0.2.0:

RPA

Changes in version 1.13.06 (2012-09-09):

Changes in version 1.13.02 (2012-05-27):

NEW FEATURES

BUG FIXES

Rsamtools

Changes in version 1.10.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Rsubread

Changes in version 1.8.0:

NEW FEATURES

ShortRead

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

BUG FIXES

synapter

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:

TargetSearch

Changes in version 1.14.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

tigre

Changes in version 1.12.0:

TransView

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

BUG FIXES

xcms

CHANGES IN VERSION 1.33.16

USER VISIBLE CHANGES

o diffreport and plotEIC have a new parameter mzdec, with is the
  number of decimal places of the m/z values in the EIC plot title

CHANGES IN VERSION 1.33.16

UPDATED FEATURES:

o Lock mass gap filler now works with netCDF lock mass function
  file to find the exact times of the scans and works with the
  newer Waters MS instruments.

CHANGES IN VERSION 1.33.15

BUG FIXES

o scanrage is now honoured in xcmsSet, also when in parallel mode

CHANGES IN VERSION 1.33.14

BUG FIXES

o scanrage is now honoured in xcmsRaw, and consequently 
  also in xcmsSet(matchedFilter), where previously 
  it was ignored.

CHANGES IN VERSION 1.33.13

BUG FIXES

o write.cdf() has been fixed to write files AMDIS can read

CHANGES IN VERSION 1.33.12

BUG FIXES

o write.mzData adds Polarity to the file if available

CHANGES IN VERSION 1.33.11

USER VISIBLE CHANGES

o centWave uses a new method to estimate local noise which
improves detection of closely spaced peaks

NEW FEATURES

o placeholder

BUG FIXES

o group.mzClust was failing when result had one peak

For more details and all changes before May 2012 please see the (now discontinued) CHANGELOG in the source package (inst/ folder).

CHANGED BEHAVIOUR since Version 1.32:

Other Changes since Version 1.32:

yaqcaffy

Changes in version 1.17.2:

Changes in version 1.17.1:

Packages removed from the release

No packages have been removed from the release.

Fred Hutchinson Cancer Research Center