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
• New Software Packages
• NEWS from new and existing packages
• Packages removed from the release

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.

• AGDEX: Agreement of Differential Expression Analysis

• BiocInstaller: Install/Update Bioconductor and CRAN Packages

• biovizBase: Basic graphic utilities for visualization of genomic data.

• CellNOptR: R version of CellNOpt, boolean features only

• CNAnorm: A normalization method for Copy Number Aberration in cancer samples.

• cn.mops: Mixture of Poisson for CNV detection in NGS data

• Cormotif: Correlation Motif Fit

• cqn: Conditional quantile normalization

• cummeRbund: cummeRbund: The finishing touch on your Tuxedo workflow. Analysis, exploration, manipulation, and visualization of Cufflinks HTS data.

• DECIPHER: Database Enabled Code for Ideal Probe Hybridization Employing R

• DEXSeq: Inference of differential exon usage in RNA-Seq

• DiffBind: Differential Binding Analysis of ChIP-Seq peak data

• dks: The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.

• DOSE: Disease Ontology Semantic and Enrichment analysis

• DTA: Dynamic Transcriptome Analysis

• EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq

• exomeCopy: Detection of CNV in exome/targeted sequencing data

• fastseg: fastseg - a fast segmentation algorithm

• flowType: Phenotyping Flow Cytometry Assays

• flowWorkspace: Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore

• GeneExpressionSignature: Gene Expression Signature based Similarity Metric

• ggbio: Static visualization for genomic data.

• GOFunction: GO-function: deriving biologcially relevant functions from statistically significant functions

• graphite: GRAPH Interaction from pathway Topological Environment

• GRENITS: Gene Regulatory Network Inference Using Time Series

• GWASTools: GWASTools: Tools for Genome Wide Association Studies

• htSeqTools: Quality Control, Visualization and Processing for High-Throughput Sequencing data

• IdMappingRetrieval: ID Mapping Data Retrieval

• inSilicoDb: Access to the InSilico Database

• iontree: Data management and analysis of ion trees from ion-trap mass spectrometry

• isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

• minfi: Analyze Illumina’s 450k methylation arrays

• MmPalateMiRNA: Murine Palate miRNA Expression Analysis

• mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

• ncdfFlow: ncdfFlow: A package that provides ncdf based storage based flow cytometry data.

• NormqPCR: Functions for normalisation of RT-qPCR data

• nucleR: Nucleosome positioning package for R

• PAN: Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

• PREDA: Position RElated Data Anlysis

• predictionet: Inference for predictive networks designed for (but not limited to) genomic data

• qtbase: Interface between R and Qt

• qtpaint: Qt-based painting infrastructure

• r3Cseq: Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)

• RamiGO: AmiGO visualize R interface

• randPack: Randomization routines for Clinical Trials

• RCASPAR: A package for survival time prediction based on a piecewise baseline hazard Cox regression model.

• ReadqPCR: Read qPCR data

• RedeR: RedeR: bridging the gap between hierarchical network representation and functional analysis.

• REDseq: Analysis of high-throughput sequencing data processed by restriction enzyme digestion

• Repitools: Epigenomic tools

• ReQON: Recalibrating Quality Of Nucleotides

• rqubic: Qualitative biclustering algorithm for expression data analysis in R

• RTopper: This package is designed to perform Gene Set Analysis across multiple genomic platforms

• stepwiseCM: Stepwise Classification of Cancer Samples using Clinical and Molecular Data

• Streamer: Enabling stream processing of large files

• sva: Surrogate Variable Analysis

• TSSi: Transcription Start Site Identification

• tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions

• VariantAnnotation: Annotation of Genetic Variants

• zlibbioc: An R packaged zlib-1.2.5

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:

• compact pdf vignette

a4Base

Changes in version 1.1.4:

• fix in limmaTwoLevels

Changes in version 1.1.3:

• update for revised glmnet package

Changes in version 1.1.1:

• on BioConductor

a4Classif

Changes in version 1.1.3:

• adapt to new lognet objects from glmnet

Changes in version 1.1.1:

• on BioConductor

a4Core

Changes in version 1.1.3:

• remove duplicated code for glmnet type of objects; add topTable method for ‘elnet’ objects and accompanying print method print.topTableElnet

Changes in version 1.1.2:

• add topTable method for ‘lognet’ objects and accompanying print method print.topTableLognet

Changes in version 1.1.1:

• on BioConductor

a4Reporting

Changes in version 1.1.1:

• fixes for latest glmnet versions

ADaCGH2

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

• Rmpi in “Enhances”, not “Suggests”, to allow for R CMD check in Mac and Windows.

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

• rsprng no longer in depends; L’Ecuyer as default random number generator.

• Using R’s registration mechanism for C routines.

• Decreased size of example to speed up R CMD check.

• SOCK is default cluster, and Rmpi not loaded by us.

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

• Output to CGHregions and input from limma and snapCGH. Changes in functions, help, vignnette.

• Can also use rlecuyer.

• Works with R-2.11 (adapted to differences in “inherits”).

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

• First fully working version for BioC. Versioning changed!

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

• Added more “Sys.sleep” to see if we can get it not to crash in Windoze.

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

• Added unloading of rlecuyer, to prevent problems with cleanEx during R CMD check.

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

• Changed “if” in stop.na.inf, as per Dundan Murdoch’s suggestion.

affxparser

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

• Maintainer email was updated.

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

• The version number was bumped for the Bioconductor devel version.

AnnotationFuncs

Changes in version 1.3:

SIGNIFICANT USER-VISIBLE CHANGES

• Added function ‘getOrthologs’ and auxcillary functions that speeds up ortholog mappings in the Inparanoid databases.

• Added parameter ‘simple’ to ‘translate’ for improved usage with lapply.

aroma.light

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

• Updated robustSmoothSpline() such that it works with the new “uniqueness” scheme of smooth.spline() in R v2.14.0 and newer. It is tricky, because robustSmoothSpline() is a reiterative algorithm which requires that the choosen “unique” x:s does not change in each iteration. Previously, ‘signif(x, 6)’ was used to identify unique x:s, which gives the same set of values when called twice, whereas this is not true for the new choice with ‘round((x - mean(x))/tol)’.

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

• Added argument ‘aspectRatio’ to plotMvsA(). It can be used to adjust the range of the ‘Mlim’ argument relative to the ‘Alim’ argument.

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

• The version number was bumped for the Bioconductor devel version.

ArrayExpressHTS

Changes in version 1.3.1:

NEW FEATURES

• Added test dataset, which is a cut version of E-GEOD-16190 experiment

• Added normalization of the reference folder

• Added automatic fixing of reference .fai index, namely duplicated chromosome entries

• Added automatic detection of quality scale where possible

• Added and option to specify quality scale for custom experiments

• Performed performance and memory optimization

• Removed options$reference_version. Since the pipeline allows processing of multi-species datasets, a single version cannot fit into multiple organism paradigm. The pipeline always runs on the latest version of reference. Support for custom versions can be added upon request.

• Added memory monitoring

BUG FIXES

• Fixes to accommodate changes in Ensembl interfaces, required for preparation of reference and annotation data.

• Fixes to accommodate changes in ENA interfaces, required for querying metadata & downloading datasets for ArrayExpress experiments.

• Fixed examples in prepareReference help page

• Fixed ArrayExpressHTSFastQ scenario without .sdrf

• Fixed production of final alignment report

Changes in version 1.3.0:

• No changes. Version changed due to package propagation.

beadarray

Changes in version 2.4:

MAJOR CHANGES

• The example data required to run examples and the vignette has been removed from the package. The experimental data package beadarrayExampleData has been created for this purpose

• Mapping of bead-level ArrayAddress IDs to Illumina IDs is now performed by loading a companion annotation package. e.g. illuminaHumanv3.db

• The addFeatureData function has been added to simplify the annotation of summary data objects

• The ggplot2 library is now used to produce boxplots of summary data with the option of including columns of featureData or phenoData as factors in the plot

• The combinedControlPlot has been added, which uses ggplot2 to consolidate the bead-level control plots into a single graphic

• BASH and HULK can now only operate on a single array at a time and accept an outlier-calling method as a parameter

OTHER CHANGES

• The imageplot function now uses ggplot2

• Accessor functions added for metrics, P95 value and signal-to-noise ratio

• The default background correction when running readIllumina with useImages = TRUE is now the medianBackground method

• getAnnotation replaced with annotation accessor function

• setAnnotation replaced with annotation <- replacement method

• checkPlatform replaced with suggestAnnotation function

• The platformSigs object was added and contains lists of ArrayAddressIDs for all know expression platforms

• The outlier calling method, squeezedVarOutlierMethod has been added, which shrinks the observed variance for a bead-type towards the predicted variance based on all bead-types on the array-section

• Errors in BASH that led to the einvasions and dinvasions arguments not being respected have been corrected

• lower-level BASH functions (e.g. BASHDiffuse) will no longer calculate a Neighbours matrix if one is not supplied (ergo one must be supplied)

• beadarray used to have problems if no outlier removal method were set in summarization (important if the outliers have already been removed by Illumina’s scanner software). The function noOutlierMethod is provided to address this

• findAllOutliersE and findAllOutliersIgnore are to be deprecated, used internally by BASH have been removed

Changes in version 2.3:

NEW FEATURES

• checkRegistration() has been completely re-written to provide a far more meaningful result in a new class, beadRegistrationData

• beadRegistrationData objects can be passed to boxplot.

• The summarize function now has a default channel parameter and useSampleFac = FALSE

BUG FIXES in 2.3.6

• Fixed problem when providing arrays argument to checkRegistration()

• Fixed problem in readIllumina when useImages = TRUE

• Patched error with analyseDirectory() (thanks to Juerg Straubhaar for this)

• Fixed problem when providing arrays argument to checkRegistration()

• Fixed problem in readIllumina when useImages = TRUE

• Patched error with analyseDirectory() (thanks to Juerg Straubhaar for this)

BUG FIXES in 2.3.5

• Added support to readIllumina() for files that use something other than a period as the decimal point character.

BUG FIXES in 2.3.4

• Fixed issues when using a combination of iScan data and a locs file to generate neighbours, manifesting as problems with imageplot and BASH.

BUG FIXES in 2.3.3

• Stopped the presence of any other .txt files in a directory resulting in undesirable behaviour of readIllumina()

BUG FIXES in 2.3.2

• readBeadLevelTextFile will now take (and use) a seperator argument.

• locs information correctly taken from a bab file if required. This effects functions such as generateNeighbours(), BASH(), HULK(), imageplot()

BUG FIXES in 2.3.1

• Image processing functions can now be passed matrices containing either integer or numeric values.

• Passed forceIScan argument to functions called by readIllumina()

BeadDataPackR

Changes in version 1.5:

BUG FIXES

• Beads with negative coordinates can now be included in the bab file

• If overlapping segments are found a warning is printed and the full locs index is used.

• Coordinate values returned by readCompressedData() are now rounded to match the precision of the original text file.

CAMERA

Changes in version 2011-28-04:

• Fix bug in getpspectra, which incorrect label isotope peaks

Changes in version 2011-24-05:

• Fix bug in findIsotopes, which could cause a crash, if maxiso was higher than 3

Changes in version 2011-23-09:

• Version 1.9.7

• Bugfix in calcIsotopes, causes groupCorr with calcIso to crash with (Error in rbind(resMat …)

• Bugfix in groupCorr with given xcmsRaw

Changes in version 2011-22-08:

• Version 1.9.6

• Bugfix in plotEICs (Error in pks[, 1] : incorrect number of dimensions)

Changes in version 2011-20-25:

• Version 1.9.9

• added some “drop=FALSE” to fix “Error in isomatrix[, 1] : incorrect number of dimensions” error

Changes in version 2011-20-10:

• Version 1.9.8

• Correct rule table extended_adducts_pos.csv (typo in proton mass)

Changes in version 2011-12-05:

• plotPsSpectrum now accepts additional parameters for plot

Changes in version 2011-04-04:

• Fix bug in findAdducts, if pseudospectrum mass list has only NA values

Changes in version 2011-02-08:

• Version 1.9.5

• Bugfix for findIsotopes if ppm was very high it could occur that one peak is assigned as two or more isotope peaks

• Version 1.9.4

• Add parameter polarity to xsAnnotate constructor

• getPeaklist and getpspectra returns now correct annotation of negative charged ions [M]-

• Add snow as additonal possibilty for parallel processing

• Add function cleanParallel to clean up with spawned slave processes

ChIPpeakAnno

Changes in version 2.2.0:

• Find the peaks with bi-directional promoters with summary statistics (peaksNearBDP).

• Summarize the occurrence of motifs in peaks (summarizePatternInPeaks).

• Add other IDs to annotated peaks or enrichedGO (addGeneIDs)The function makeVennDiagram supports 4-way venn diagram.

• Enriched Gene Ontology (GO) terms are annotated with a list of genes which can be traced back to peaks.

• FAQ: http://pgfe.umassmed.edu/ChIPpeakAnno/FAQ.html.

clusterProfiler

Changes in version 1.1.22:

• update vignette. <2011-07-23 Thu>

Changes in version 1.1.21:

• update roxygen docs. <2011-07-23 Sat>

Changes in version 1.1.20:

• update roxygen docs. <2011-07-19 Wed>

Changes in version 1.1.19:

• change to using roxygen for generating Rd file. <2011-07-19 Tue>

Changes in version 1.1.18:

• clean up some codes. <2011-07-19 Tue>

Changes in version 1.1.17:

• Remove dependence of GOstats and Category. <2011-07-18 Mon>

Changes in version 1.1.16:

• Re-implement function enrichGO. <2011-07-18 Mon>

• add parameter readable, for mapping gene IDs to gene names. <2011-07-18 Mon>

Changes in version 1.1.15:

• Modified plot method of groupGOResult, with colour coded. <2011-06-15 Wed>

cqn

Changes in version 0.99:

• Version bump as well as added to Bioconductor devel branch.

• Wrote vignette.

• Added additional manpages as well as examples.

• Added data from Montgomery et al.

• Added NAMESPACE file.

• Added manpage for cqn.

• Renamed cqn, cqn2.

• Added NEWS.Rd file.

• Added vignette skeleton.

• Added CITATION file.

cummeRbund

Changes in version 0.99.5:

• Significant speed improvements to readCufflinks() for large cuffdiff datasets.

• Tables written first then indexed.

• Added slot accessor methods to avoid using slots directly.

Changes in version 0.99.4:

• Second beta release and submission to Bioconductor

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

• First Beta release of cummeRbund and submission to Bioconductor for review and hosting.

DESeq

Changes in version 1.6.0:

• changes to dispersion estimation scheme to improve handling of outliers (see vignette for details)

• refactorized the workflow and overhauled and expanded the vignette (see there for changes to user interface)

• various changes and bug fixes (see appendix in vignette and NEWS file)

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

• fixed a bug in parametricDispersionFit. (Thanks to Alejandro Reyes for spotting and fixing this one.)

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

• method=”pooled” is now default in estimateDispersions

• added ‘fitInfo’ accessor function

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

• fitNbinomGLM no longer stops when glm.fit throws an error

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

• fixed bug in ‘nbinomTest’ again; now using a symmetric two-tailed test (i.e., the one-tailed p value is doubled)

• added warning in case of method=’blind’ if not used together with sharingMode=’fit-only’

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

• fixed bug in ‘nbinomTest’ that led to wrong p values for dispersions larger than 1

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

• minor changes to vignette

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

• fixed bug in ‘getVarianceStabilizedData’

• more informative error message if parametric fit fails

Changes in version 1.5.1:

• refactorized the way how dispersion estimation is handled, overhauled the vignette

• vignette now uses data from ‘pasilla’ package as example

• GLMs explained in vignette

• ‘estimateVarianceFunctions’ renamed to ‘estimateDispersions’

• estimateDispersions now stores intermediate results in ‘fitInfo’ slot

• new functionality for ‘estimateDispersion’: ‘sharingMode’ option with new sharing modes ‘maximum’ and ‘gene-est-only’; ‘fitType’ with new fitting type ‘parametric’; changed defaults for these; new method ‘pooled-CR’ to do edgeR-style CR estimation etc.

• several diagnostic functions removed

• lots of further small changes

DEXSeq

Changes in version 2011-10-03:

• Changes to the documentation and to the vignette. New functions added and more support for gene names and strange exonids.

Changes in version 2011-07-12:

• Parallelization possibility added to the code, with its description in the vignette and single exon genes ignored properly.

Changes in version 2011-07-01:

• ‘estimateSizeFactors’ and ‘estimatedispersions’ function added as S4 methods, no more problems when loading DESeq and DEXSeq in the same R session

DOSE

Changes in version 0.99.7:

• fixed bug in .SemVal_internal

Changes in version 0.99.6:

• Use qvalue instead of fdrtool to calculate qvalues.

EDASeq

Changes in version 0.99.1:

• The read-level EDA is now based on the classes BamFileList and FastqFileList of Rsamtools. The class ShortReadSet doesn’t exist anymore.

• Changed vignette

Changes in version 0.99.0:

• Version number changed for submission to Bioconductor

Changes in version 0.0.6:

• Fixed a bug in withinLaneNormalization to work with unnamed matrices

• Fixed a bug in biasPlot to work with a single lane experiment

• Added methods MDPlot and biasBoxplot

• Changed the vignette and added an help page for newSeqExpression function

Changes in version 0.0.5:

• Modified coerce from SeqExpressionSet to CountDataSet to treat the two class comparison in a separate way

Changes in version 0.0.4:

• Added Vignette

• Adjusted xlab in the boxplot method for signature FastqQuality

• Changed getOffset and setOffset<- methods in offst and offst<- for compatibility with edgeR

Changes in version 0.0.3:

• Added CITATION file

• Added Help pages

• Added data and extdata for the examples

edgeR

Changes in version 2.4.0:

NEW FEATURES

• New function spliceVariants for detecting alternative exon usage from exon-level count data.

• A choice of rejection regions is now implemented for exactTest, and the default is changed from one based on small probabilities to one based on doubling the smaller of the tail probabilities. This gives better results than the original conditional test when the dispersion is large (especially > 1). A Beta distribution approximation to the tail probability is also implemented when the counts are large, allowing exactTest() to be much faster and use less memory.

• exactTest now uses tagwise.dispersion by default if found in the object.

• estimateCRDisp is removed. It is now replaced by estimateGLMCommonDisp, estimateGLMTrendedDisp and estimateGLMTagwiseDisp.

• Changes to glmFit so that it automatically detects dispersion estimates if in data object. It uses tagwise if available, then trended, then common.

• Add getPriorN() to calculate the weight given to the common parameter likelihood in order to smooth (or stabilize) the dispersion estimates. Used as default for estimateTagwiseDisp and estimateGLMTagwiseDisp.

• New function cutWithMinN used in binning methods.

• glmFit now S3 generic function, and glmFit has new method argument specifying fitting algorithm.

• DGEGLM objects now subsettable.

• plotMDS.dge is retired, instead a DGEList method is now defined for plotMDS in the limma package. One advantage is that the plot can be repeated with different graphical parameters without recomputing the distances. The MDS method is also now much faster.

• Add as.data.frame method for TopTags objects.

• New function cpm to calculate counts per million conveniently.

• Adding args to dispCoxReidInterpolateTagwise to give more access to tuning parameters.

• estimateGLMTagwiseDisp now uses trended.dispersion by default if trended.dispersion is found.

• Change to glmLRT to ensure character coefficient argument will work.

• Change to maPlot so that any really extreme logFCs are brought back to a more reasonable scale.

• estimateGLMCommonDisp now returns NA when there are no residual df rather than returning dispersion of zero.

• The trend computation of the local common likelihood in dispCoxReidInterpolateTagwise is now based on moving averages rather than lowess.

• Changes to binGLMDispersion to allow trended dispersion for data sets with small numbers of genes, but with extra warnings.

BUG FIXES

• dispDeviance and dispPearson now give graceful estimates and messages when the dispersion is outside the specified interval.

• Bug fix to mglmOneWay, which was confusing parametrizations when the design matrix included negative values.

• mglmOneWay (and hence glmFit) no longer produces NA coefficients when some of the fitted values were exactly zero.

• Changes to offset behaviour in estimateGLMCommonDisp, estimateGLMTrendedDisp and estimateGLMTagwiseDisp to fix bug. Changes to several other functions on the way to fixing bugs when computing dispersions in data sets with genes that have all zero counts.

• Bug fix to mglmSimple with matrix offset.

• Bug fix to adjustedProfLik when there are fitted values exactly at zero for one or more groups.

fabia

Changes in version 2.0.0:

NEW FEATURES

• spfabia: fabia for a sparse data matrix (in sparse matrix format) and sparse vector/matrix computations in the code to speed up computations. spfabia applications: (a) detecting >identity by descent< in next generation sequencing data with rare variants, (b) detecting >shared haplotypes< in disease studies based on next generation sequencing data with rare variants

• fabia for non-negative factorization (parameter: non_negative)

• changed to C and removed dependencies to Rcpp

• improved update for lambda (alpha should be smaller, e.g. 0.03)

• introduced maximal number of row elements (lL)

• introduced cycle bL when upper bounds nL or lL are effective

• reduced computational complexity

BUG FIXES

• update formula for lambda: tighter approximation

• corrected inverse of the conditional covariance matrix of z

flowFP

• We now require that length of sampleClasses be the same as the number of instances in the flowFP object. The documentation indicated that, but the code didn’t enforce it.

• Fixed a bug regarding setting sampleClasses for a flowFPPlex. It erroneously assigned classes to only the first member of the plex.

• Setting sampleClasses for a fp or a pled to NULL or to a zero-length factor now results in removing sampleClasses from the fp or plex.

• Cleaned up documentation for flowFP-class and flowFPPlex-class.

flowWorkspace

• 0.6.0 This version supports importing of flowJo XML workspaces generated using, up to version 9.2 of the Mac OS X version of flowJo. We do not yet support workpsaces generated using the windows version of flowJo.

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:

• export to flowJo - flowWorkspace will export the correct compensation matrices, but they will need to apply manually via the menu items in flowJo.

• Navigating between graphs of populations is buggy.

• export expects to receive a workflow that contains a compensation view and a transformation view as the first two actions in the workflow.

• import from flowJ - we may not support all gating configurations. The parsing code was written based on examples. If your workspace is not being imported correctly, contact the authors. If your workspace is not being imported correctly because it’s generated by flowJo for windows, it is not supported. Are you sure you’re trying to import the XML workspace and not the .jo or .wsp file?

• flowJo 8.2 for MAC. - XML has some differences and there may be issues importing workspaces into R. We have resolved those bugs that we’ve found but we have not had the opportunity for extensive testing with this version.

• speed - import can slow for very large workspaces with many gates.

• This version supports importing of flowJo XML workspaces generated using, up to version 9.2 of the Mac OS X version of flowJo. We do not yet support workpsaces generated using the windows version of flowJo.

geneplotter

Changes in version 1.31.4:

USER VISIBLE CHANGES

• Using NEWS.Rd

• The interpretation of the argument bw by the function multidensity has been changed with the aim to make the behaviour more robust when the data ranges or sample sizes of the groups are quite different. Also, to allow more control, bw can now also be a vector, with elements corresponding to the different groups.

GenomicFeatures

Changes in version 1.6:

NEW FEATURES

• TranscriptDbs are now available as standard packages. Functions that were made available before the last release allow users to create these packages.

• TranscriptDb objects now can be used with select

• select method for TranscriptDb objects to extract data.frames of available annotations. Users can specify keys, along with the keytype, and the columns of data that they want extracted from the annotation package.

• keys now will operate on TranscriptDB objects to expose ID types as potential keys

• keytypes will show which kinds of IDs can be used as a key by select

• cols will display the kinds of data that can be extracted by select

• isActiveSeq has been added to allow entire chromosomes to be toggled active/inactive by the user. By default, everything is exposed, but if you wish you can now easily hide everything that you don’t want to see. Subsequence to this, all your accessors will behave as if only the “active” things are present in the database.

SIGNIFICANT USER-VISIBLE CHANGES

• saveDb and loadDb are here and will be replacing saveFeatures and loadFeatures. The reason for the name change is that they dispatch on (and should work with a wider range of object types than just trancriptDb objects (and their associated databases).

BUG FIXES

• ORDER BY clause has been added to SQL statements to enforce more consistent ordering of returned rows.

• bug fixes to enable DB construction to still work even after changes in schemas etc at UCSC, and ensembl sources.

• bug fixes to makeFeatureDbFromUCSC allow it to work more reliably (it was being a little too optimistic about what UCSC would actually supply data for)

GenomicRanges

Changes in version 1.6.0:

NEW FEATURES

• seqlevels() and seqinfo() setters have a new arg (‘force’, default is FALSE) to force dropping sequence levels currently in use.

• Seqinfo objects now have a genome column that can be accessed with genome() getter/setter.

• “pgap” method for c(x=”GRanges”, y=”GRanges”).

• Add comparison (==, <=, duplicated, unique, etc…) and ordering (order, sort, rank) methods for GenomicRanges objects.

• Add “flank” method for GRangesList objects.

• Add “isDisjoint” and “restrict” methods for GRanges and GRangesList objects.

• Add GRangesList constructor makeGRangesListFromFeatureFragments().

• Add “names” and “names<-“ methods for GappedAlignments objects.

• Add ‘ignore.strand’ arg to a number of methods: - findOverlaps,GRangesList,RangesList - findOverlaps,GappedAlignments,ANY - findOverlaps,ANY,GappedAlignments

• ‘shift’ and ‘weight’ arguments of “coverage” method for GenomicRanges objects now can be numeric vectors in addition to lists.

• Add “c” method for GappedAlignments objects.

SIGNIFICANT USER-VISIBLE CHANGES

• readGappedAlignments() supports 2 new arguments: (1) ‘use.names’ (default is FALSE) for using the query template names (QNAME field in a SAM/BAM file) to set the names of the returned object, and (2) ‘param’ (default is NULL, otherwise a ScanBamParam object) for controlling what fields and which records are imported. readGappedAlignments() doesn’t support the ‘which’ arg anymore.

• The names of a GRanges/GRangesList/GappedAlignments object are not required to be unique anymore.

• By default, the rownames are not set anymore on the DataFrame returned by elementMetadata() on a GRanges/GRangesList/GappedAlignments object.

• ‘width’ arg of “coverage” method for GenomicRanges objects now must be NULL or numeric vector (instead of NULL or list).

DEPRECATED AND DEFUNCT

• Deprecate countGenomicOverlaps() in favor of summarizeOverlaps().

• Deprecate grg() in favor of granges().

BUG FIXES

• Fix bug in “pintersect” methods operating on GappedAlignments objects.

genoset

1.0.0

• Object creation at user level changed so that GenoSet, BAFSet, and CNSet functions all call an internal input checker and object generator function initGenoSet rather than having GenoSet() create all 3 objects using a “type” arg.

• Segmentation functions now return DataFrame objects containing one Rle vector per sample. These give the same effect of having big matrices with repeated data matching the dimensions of the un-segmented data, but are considerably smaller. For a dataset of ~1k SNP6 arrays, the data in the lrr matrix is about 0.8% of the size using this strategy. In all regards, these can be treated as just another matrix in assayData, but in special cases it is useful to take advantage of the data in its runValue and runLength form.

• New methods defined for DataFrame to allow usage as assayData element: colMeans annotatedDataFrameFrom

• Methods that get genome information from a GenoSet now work on RangedData too. RangedData and GenoSet now share some API to make this easier. RangedData gets chr and pos, GenoSet gets names, ranges, and elementLengths. Now chrInfo, chrIndices, genoPos, etc. can work on either object type.

• pos and genoPos now defined as floor of mean of start and end positions.

1.0.6

• Substantial speed improvements for boundingIndices() and rangeSampleMeans.

1.1.7

• Added loadGC function to get local GC content and version bump for bioC2.9

1.1.8

• genomeOrder becomes toGenomeOrder which now takes and returns a GenoSet or RangedData rather than just returning the index to reorder such objects. locData<- now reorders the whole GenoSet and assures that all of the featureNames match.

1.1.9

• Added support for big.matrix objects from bigmemory as assayDataElements

1.1.10

• API Change list operator “[[” no longer used to subset by chromosome. It reverts back to extracting a column from pData like other eSets. chrIndices gains a “chr” argument that serves as a fast way to get the indices needed to subset rows by chromosome.

1.1.11

• API Addition “k” argument to “[” can be used to subset from a specific assayDataElement. Numeric and character “k”s are allowed. assayDataElement(ds,k)[i,j] is the same as ds[i,j,k], but “i” can be a RangedData or RangesList.

1.1.12

• assayDataElements can be integer matrices with levels that will serve as factors for now. Please see the help for convertToBigMatrix.

GOSemSim

Changes in version 1.11.2:

• Using methods implemented in DOSE for semantic similarity calculation.

GRENITS

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

• Initial release!

Heatplus

Changes in version 2.0.0:

• Add both row- and column annotation via annHeatmap2

• New function regHeatmap as replacement for heatmap_2

• New function annHeatmap as replacement for heatmap_plus

• Support for heatmap_2, heatmap_plus will be dropped (deprecation warning)

• Mutiple continous covariates for annotation possible (picketPlot)

• Simple legend also for annotated heatmaps (annHeatmap2)

• More detailed interface for specifiying graphical parameters (annHeatmap2)

• Green-to-red palette as new default (annHeatmap2)

HTqPCR

Changes in version 1.7:

NEW FEATURES

• Added “geometric.mean” as a normalisation method.

BUG FIXES

• Check for all-NA features in normalizeCtData rank-invariant methods.

• Modified plotCtCategory to handle cases with only 1 sample.

• Modified plotCtCategory to make colours more consistent.

• Fix in deltaCt for normalization with NAs

• Added warning in readCtData if there are NAs in input

htSeqTools

Changes in version 0.99:

• Adapted enrichedChrRegions to adapt to change in IRanges behavior

• Fixed bug in PeakLocation and stdPeakLocation when strand information was stored in variables of type factor

• Included adjustments for number of reads in each sample for giniCoverage and ssdCoverage

• Improved filterDuplReads, using mixtures of NegBinom

• Adjusted behavior of giniCoverage

• Removed readAlignedBatch, export2Aligned, export2SGR, export2SAM

Changes in version 0.2.7:

• Fixed bug in filterDuplReads method for ‘RangedDataList’ which caused it not to pass on arguments to ‘RangedData’ method

• Changed default value of ppOverAmp=.95 to .99 in filterDuplReads

• Added function rowLogRegLRT

• Fixed bug in alignPeaks caused by change in IRanges behavior.

• Added function coverageDiff to compute difference in coverage between two objects

• Fixed bug regionsCoverage caused by convertion of class “by” objects

• Added plotChrRegions function

• Added enrichedChrRegions function

• Added countHitsWindow function

• stdPeakLocation now allows to set xlim

• plot method for cmdsFit objects now automatically puts both axis on the same scale

• closestGene now allows argument genome to be of class data.frame. This avoids downloading the refflat file at each call.

• Fixed bug in enrichedRegions which caused it to crash when sample1 had more chromosomes than sample2

• Fixed bug in filterDuplReads which caused it to crash when no reads needed to be filtered

• Fixed bug in regionsCoverage which caused it to crash for empty chromosomes

• Removed functions genePlot, rangesPlot (moved to package casper)

• Added regionsCoverage, gridCoverage, stdGrid functions

• Added chipSeqQC function

• enrichedRegions was trying to load multicores library instead of multicore.

• Added ssdCoverage function

• Added enrichedRegions method for RangedDataList objects. This allows comparing proportion of reads in islands across >2 samples.

• Added islandCounts function

• Improved memory usage and speed in filterDuplReads, which no longer relies on countOverlaps from package IRanges

• Changed call to parallel to multicore::parallel to avoid confusion with other packages

Changes in version 0.2.5:

• Added arguments maxRepeats and ppOverAmp to filterDuplReads to allow it to eliminate reads appearing more than k times (before only k=1 was allowed), or with a large posterior probability of being an artifact

• Added ppEnrichedCounts function

• Modified enrichedRegions to make it compatible with new IRanges version

• Added cmds function to perform MultiDimensional Scaling on sequencing data

• Exact P-value calculation in enrichedRegions is now based on Fisher’s exact test, instead of simulations, to increase speed. Changed parameters simulate.p.value and B for exact.

• Chi-square P-value calculation in enrichedRegions is now substantially faster (reduced to about 25% of previous implementation)

• enrichedRegions now selects regions with pval <= pvalFilter, instead of pval < pvalFilter. This allows to obtain all regions by setting pvalFilter=1.

• enrichedRegions now returns reads per kilobase per million (RPKM), as well as raw counts

• Corrected enrichedRegions fold change calculation. Now it is (counts1/nsample1)/(counts2/nsample2) instead of (counts1/(nsample1-counts1))/(counts2/(nsample2-counts2))

• Reduced substantially the amount of memory required by rangesPlot

Changes in version 0.2.3:

• Fixed issue in enrichedRegions which caused it to return an object with too many spaces

• rangesPlot now produces a warning when no ranges are found in the specified region, but it still produces a plot

• Added genePlot method for signature ‘RangedData’

• Fixed issue in genePlot which caused it to ignore the … argument.

• Fixed issue in genePlot which sometimes caused it to plot additional splicing variants

• Fixed issue in ‘filterDuplReads’ which caused the returned object to have a too large number of spaces

• Added methods for signature(regions=’RangedData’, sample1=’RangedData’, sample2=’missing’) and

• Fixed bug in enrichedRegions when no hits were found. Also changed argument ‘parallelComp’ for ‘mc.cores’, so facilitate using mclapply instead of ‘parallel’ calls

• Added function tabDuplReads

• Fixed bug in filterDuplReads for RangedData signature which caused it to filter two reads from different chromosomes which had the same start and end positions

• Added extendRanges and filterDuplReads methods for RangedDataList objects. Added mc.cores argument to allow for parallel computing.

• Added export2SGR method for RangedDataList objects.

• export2SGR now uses ‘coverage’ function instead of ‘pileup’, as the latter has been deprecated

• Added export2aligned method for RangedDataList objects. Added argument dir.

• alignPeaks now returns an object of the same class as its input, instead of always returning IRangesList objects.

• Added alignPeaks method for RangedDataList objects, and parameter mc.cores to allow parallel computation.

• Major change in readAlignedBatch. Sequences from all files are now returned into a single RangedDataList object. Files are not directly saved to disk as in previous versions.

• Fixed bug in rangesPlot which caused it to plot reads longer than maxFragLength twice

• Fixed bug in genePlot which caused an error for genes with a single exon

• Added PeakLocation function. It produces the same plots as stdPeakLocation except that it doesn’t standardize the coordinates.

• Added p-value adjustment in enrichedRegions. Defined methods for the case when sample2 is missing.

• readAlignedBatch now checks for the existence of the files, and returns a warning if they don’t.

• Added listOverlap function, which allows to assess the overlap between lists e.g. two ChIP-seq experiments, or ChIP-Seq vs microarray results.

• Corrected bug in alignPeaks which could cause sequences to start at negative indexes.

Changes in version 0.2.1:

• ReadAlignedBatch now returns ‘RangedData’ objects. This required substantial structural changes, as new methods had to be defined and many existing ones needed to be adjusted.

• Added methods ‘filterDuplReads’ and ‘mergeRegions’ for signature ‘RangedData’

• Changed stdPeakLocation to a generic function and defined methods for signatures data.frame and RangedData.

• Added closestGene method for signature ‘RangedData’.

• Added enrichedPeaks function to detect peaks in sequencing experiments.

• Added enrichedRegions function to detect significantly enriched regions in sequencing experiments.

• closestGene modified: After bioC upgrade parameter multiple stoped working due to findOverlaps function that deprecated Overlaps function (which was used in previous versions).

• closestGene: Some rbinds have been removed and do.call is used insted to use less memory.

• closestGene: Better control of downloaded refflat files has been added.

• closestGene: new parameter added (promoterInOther). If it’s TRUE peaks that are in a promoter region and inside other gene will be assigned to both genes. Only works when multiple=TRUE.

Changes in version 0.2.0:

• Fixed bug in alignPeaks which caused it not to work when there were some chromosomes with no sequences. Also, now alignPeaks reports the estimated shift.

• readAlignedBatch deletes memory consuming objects after they have been saved to disk. This lowers memory requirements.

• readAlignedBatch forces the chromosome names to start by ‘chr’, to ensure compatibility with external softwares.

• Added vignette

• Added Rd file for alignPeaks

• Added export2aligned, export2SGR and rangesPlot methods for RangedData and RangedDataList objects.

• export2SGR now longer requires to specify chromosome length for IRangesList and RangedDataList objects. The range of positions where reads have been observed is used instead.

Changes in version 0.1.2:

• Added vignette

• Exported rangesPlot in NAMESPACE.

• Added function stdPeakLocation to plot peak location in ChIP-Seq and ChIP-chip experiments

• Corrected mismatching arguments in generic definition for genePlot. Also did minor changes to improve label appearance.

• closestGene did not work after upgrading to R 2.10.

Changes in version 0.1.1:

• closestGene now uses findOverlaps function instead of the deprecated ‘overlap’.

• Converted rangesPlot function to S4. Added methods for character, IRanges and IRangesList.

• Converted genePlot function to S4. Added methods for IRanges, IRangesList and CompressedIRangesList objects (additionally to the already existing one for character).

• Added alignPeaks function to align the ‘+’ and ‘-‘ reads in ChipSeq experiments

• Now readAlignedBatch returns a RangeDataList object for single end experiments instead of an IRangesList. This allows to store the strand information, which could not be done with the IRangesList object.

• Added export2SAM function

• Added export2aligned method for ‘IRanges’ objects

• Added ‘paired’ option in readAlignedBatch

• Changed default type=’Bowtie’ in readAlignedBatch

• Added genePlot function

• closestGene had an error when looking if a region falls in a promoter.

• Distance to gene added to clsoestGene function.

Changes in version 0.1.0:

• Added readAlignedBatch function

Changes in version 0.0.1:

• extendRanges now outputs an IRangesList object instead of a simple list

• Added export2aligned method.

• Added export2SGR method for IRangesList objects

• Added closestGene function.

• Changed “c” for “rbind” in “enrichedRegions.r” line 92 (needed for IRanges version 1.6.0)

• Added require(multicore) to “enrichedRegions.r” and changed mclapply to lapply for non-parallel computation

IRanges

Changes in version 1.12.0:

NEW FEATURES

• Add “relist” method that works on a List skeleton.

• Add XDoubleViews class with support of most of the functionalities available for XIntegerViews.

• c() now works on XInteger and XDouble objects (in addition to XRaw objects).

• Add min, max, mean, sum, which.min, which.max methods as synonyms for the view* functions.

SIGNIFICANT USER-VISIBLE CHANGES

• Views and RleViewsList classes don’t derive from IRanges and IRangesList classes anymore.

• When used on a List or a list, togroup() now returns an integer vector (instead of a factor) for consistency with what it does on other objects (e.g. on a Partitioning object).

• Move compact() generic from Biostrings to IRanges.

• Drop deprecated ‘multiple’ argument from “findOverlaps” methods.

• Drop deprecated ‘start’ and ‘symmetric’ arguments from “resize” method for Ranges objects.

DEPRECATED AND DEFUNCT

• Using as.data.frame() and or as( , “data.frame”) on an AtomicList object is deprecated.

• Deprecate all coercion methods from AtomicList to atomic vectors. Those methods were unlisting the object, which can still be done with unlist().

• Deprecate the Binning class.

• Remove defunct overlap() and countOverlap().

BUG FIXES

• togroup() on a List or a list does not look at the names anymore to infer the grouping, only at the shape of the list-like object.

• Fix ‘relist(IRanges(), IRangesList())’.

• Fix ‘rep.int(Rle(), integer(0))’.

• Fix some long-standing issues with the XIntegerViews code (better handling of “out of limits” or empty views, overflows, NAs).

isobar

Changes in version 1.0.0:

• first Bioconductor version (version bump to 1.0.0)!

• slot name reporterMasses is renamed to reporterTagMasses to fix clash with method reporterMasses which fetches assayData(ibspectra)[[“mass”]]

• slot name reporterNames is renamed to reporterTagNames to distinguish from deprecated Biobase::reporterNames

• added option ‘scan.lines’ to readIBSpectra: read mgf files in parts for large MGF files

• use a function for protein reporting: create.reports.R properties.conf will be replaced by properties.R

Changes in version 0.2.5:

• MSnbase support: Added functions to coerce from MSnSet to IBSpectra and vice versa. Added Msnbase to Suggests.

• support for multiple classes added

• updated Perl parsers: mascotParser2.pl and pidresParser2.pl instead of isobarXParser.pl resulting XML files can be converted to id.csv using psx2tab2.pl

• prob otion for readIBSpectra worked errornous - fixed (thanks to Xavier Robin)

• added property use.na: Use NA values for quantification

• various Analysis Report beautifications (thanks to Xavier Robin)

• varous bug fixes

Changes in version 0.2.4:

• improved Vignette descriptions, added CITATION (still UTF-8 error)

• added possibility to revert Mascot escaped TITLEs

• if proteins are excluded w/ subsetIBSpectra, exclude all it’s peptides, not only reporter-specific ones

• fix error introduced in 0.2.3: When multiple MGFs were read, an false error occured that not all id spectra could be matched

• add property ‘author’ for LaTeX reports

• section ‘Significantly regulated proteins’ not shown anymore by default added property show.significant.proteins to reenable

• added properties isotope.impurities and fragment.outlier.prob

• bug fixes:

• naming not correct when class labels contain NAs

• numeric class labels are not handled correctly

• added naRegion to noise model

• data is now stored before normalization. Those values are then used to normalize. (Thanks to observation of Chris Bielow)

Changes in version 0.2.3:

• specify combination matrix for proteinRatios and in properties.conf

• improved logging of IBSpectra creation and normalization

• fix: maplot crashed on all NA channels

• NA names in PDF report section ‘Not quantified proteins’ removed

• allow for NA class labels - they are ignored in the comuptation of ratios

Changes in version 0.2.2:

• re-added ratio vs intensity plot in QC report

• issue warning when summarize property is incorrectly defined

• create cachedir if it does not exist

• estimateRatio.group_specific_proteins renamed to quant.w.grouppeptides

• sanitize analysisname, uniprotlink, and subsection names for LaTeX

• use fancyhdr instead of fanctheadings

• added argument require.reporter.specific to reporterProteins

Changes in version 0.2.1:

• Bug fix: as.data.frame generated ions/mass colnames with a ‘X’ in front

Changes in version 0.2:

• Published online with JPR Publication

KEGGgraph

• 2011-08-23 KEGGgraph 1.9.2: Update getKGMLurl and retrieveKGML to get KGML files from HTTP pages instead of from the FTP server, which is from July 2011 only open to subscribed users. The KEGG database needs support, and users of KEGGgraph could also support by subscribing to the FTP service.

• 2011-08-23 KEGGgraph 1.9.1: Add parseKGML2DataFrame function. This function is table to convert the KGML file into a data frame recording nodes and edges in one step. For help use ‘?parseKGML2DataFrame’ in R command line.

limma

Changes in version 3.10.0:

• New function voom() allows RNA-Seq experiments to be analysed using the standard limma pipeline. An RNA-Seq case study is added to User’s Guide.

• treat(), roast() and mroast() can now estimate and work with a trend on the prior variance, bringing them into line with eBayes().

• barcodeplot() and barcodeplot2() merged into one function.

• removeBatchEffect() can now correct for two batch factors.

• plotMDS is now an S3 generic function. This allows MDS plots to be redrawn with new labels without needing to repeat the distance or scaling calculations. New S4 class “MDS” to hold the multidimensional scaling information output from plotMDS.

• getEAWP() now gets probe annotation from the expression rownames of an EList object, if no other probe annotation is available.

• topRomer() now ranks gene sets by secondary columns as well the primary criterion specified, to give a more meaningful ranking when the p-values are tied.

• wilcoxGST() now accepts signed or unsigned test statistics. Change to p-value calculation in geneSetTest() when rank.only=FALSE to avoid zero p-values and follow recommendation of Phipson and Smyth (SAGMB, 2010).

• plotMA() now recognizes ElistRaw and EList objects appropriately.

• Default span for normalizeCyclicLoess increased from 0.4 to 0.7. Speed improved when weights=NULL.

• Weaver case study (Section 11.5) in User’s Guide is updated and rewritten. Data classes ElistRaw and Elist now described in the quick start section of the User’s Guide. Other minor updates to User’s Guide.

• Bug fix for normalizeBetweenArrays() when object is an EListRaw and method=”cyclicloess”. Previously this function was applying cyclicloess to the raw intensities, then logging. Now it logs first, then applies cyclicloess.

• Bug fix to avereps() for EList objects x when x$other is not empty.

lumi

• Adding supports for Infinium 450K methylation microarrays, which\nincludes updating the color bias correction and other related\nfunctions.

minfi

Changes in version 0.99:

• Initial release to Bioconductor.

• Added NEWS file.

• Bugfix to vignette.

• readIDAT is now exported by crlmm, implying that we can import this function through NAMESPACE.

MLP

Changes in version 1.1.1:

• update using new annotation packages

• apply changes to column permutations (contributed by Heather Turner)

MSnbase

Changes in version 1.1.28:

• added pgfSweave to Suggests <2011-10-23 Sun>

Changes in version 1.1.27:

• fixed bug in readIspyData <2011-10-07 Fri>

• removed (unexported) ratio code <2011-10-12 Wed>

• added processing description when MSnSet[‘ing <2011-10-12 Wed>

• man typos corrected <2011-10-14 Fri>

• changed readMzXMLData to readMSData in tests <2011-10-14 Fri>

• expecting warning for readMzXMLData in test_io <2011-10-14 Fri>

Changes in version 1.1.26:

• extractSpectra deprecated <2011-10-05 Wed>

• small changes in cache.R functions <2011-10-05 Wed>

• changed [, extractSpectra and extractPrecSpectra to update the .cache slot <2011-10-05 Wed>

• MSnExp show method uses .cache when level==1. <2011-10-05 Wed>

• Finished level 1 cache implementation: leads to an average 11.8 times faster MSnExp show method. <2011-10-05 Wed>

Changes in version 1.1.25:

• added .cache slot to pSet class <2011-10-03 Mon>

• added pSet initialize method to set .cache and .cache$level as ‘0’. <2011-10-03 Mon>

• Check that level is defined in .cache and env is locked in pSet validity method. <2011-10-03 Mon>

• updated itraqdata.RData <2011-10-03 Mon>

• Deprecated readMzXMLData, added defunct.Rd <2011-10-03 Mon>

• changed readMzXMLData to readMSData in man <2011-10-03 Mon>

• updated show MSnExp for speed <2011-10-03 Mon>

• updated read*Data is support cache = [0

  1]. <2011-10-03 Mon>

• updated precScanNum to use sapply(spectra(…), precScanNum) instead of unlist(eapply(assayData(…), precScanNum)) to preserve splectra order. <2011-10-03 Mon>

• new cache.R file with @.cache related code <2011-10-03 Mon>

Changes in version 1.1.24:

• in readMgfData, SCANS is not used to populate acquisitionNum anymore, as several scans might have been combined upstreams <2011-09-26 Mon>

• added fillUp function in utils.R and exported <2011-09-27 Tue>

• new MSnbase-io vignette <2011-09-28 Wed>

Changes in version 1.1.23:

• fixed writeMgfData(“MSnExp”) <2011-09-21 Wed>

• readMgfData now works when mz and intensty are separated by a ‘\t’ (as exported by PRIDE Inspector) <2011-09-21 Wed>

• show(“MSnExp”) now works without retention time <2011-09-21 Wed>

• updated mgf2Spectrum2 to make it faster <2011-09-21 Wed>

• fixed missing fromFile slot in data created from readMgfData that prevented calling header <2011-09-21 Wed>

• readMgfData now creates a fData based on the peak header <2011-09-21 Wed>

• modified getCurveWidth to work with centroided data <2011-09-21 Wed>

• fixed bug getCurveWidth <2011-09-21 Wed>

Changes in version 1.1.22:

• removed (internal) Mascot query link column in readIspyData to work with latest ouput version <2011-09-12 Mon>

• removed the fillUp part in readIspyData <2011-09-14 Wed>

• exported readIspyData <2011-09-20 Tue>

• removed link to proteomics sig list <2011-09-20 Tue>

• removed url in DESCRIPTION <2011-09-20 Tue>

• Spectrum2 slot ms1scan renamed to precScanNum and populated using mzR::header()$precursorScanNum. Updated affected methods/functions and manual pages. New accessor method precScanNum is exported. THIS CHANGE IS NOT COMPATIBLE WITH PREVIOUSLY CREATED MSnSet OBJECTS! <2011-09-20 Tue>

Changes in version 1.1.21:

• updated write.exprs to add fData columns <2011-09-08 Thu>

• added write.exprs and readMSnSet unit test <2011-09-08 Thu>

Changes in version 1.1.20:

• added a readMSnSet function <2011-09-08 Thu>

• added a write.MSnSet(“MSnSet”) method <2011-09-08 Thu>

• vignette/man updates - mainly data import section documenting readMSData and readMgfData <2011-09-08 Thu>

• incorporating mzR io frame work <2011-09-05 Mon>

• use mzR’s peaksCount and header generics <2011-09-05 Mon>

• added test to check that readMzXMLData and readMSData give same output <2011-09-05 Mon>

• added readMSData.Rd doc file <2011-09-05 Mon>

• added Author@R field in DESCRIPTION <2011-09-07 Wed>

• compressed/resaved (using resaveRdaFiles) itraqdata.RData file to <2011-09-07 Wed>

Changes in version 1.1.18:

• read support for mgf files contributed by Guangchuang Yu <2011-07-06 Wed>

• added as.ExpressionSet.MSnSet and setAs methods and updated MSnSet doc <2011-07-09 Sat>

• fixed read/write mgf compatibility <2011-09-01 Thu>

• added mgf io test <2011-09-01 Thu>

• exported and document mfg read/write support <2011-09-01 Thu>

• added centroided parameter to rawToSpectrum[1|2] to set this directly at object creation in readMzXmlData <2011-09-01 Thu>

• other minor changes in Rd files <2011-09-01 Thu>

• added warning checks for combineFeatures when verbose=TRUE in test_MSnSet.R <2011-09-02 Fri>

Changes in version 1.1.17:

• updated itraqdata manual <2011-06-27 Mon>

• fixed bug in MSnSet validity method - msg was initialised to NULL when testing Biobase:::isValidVersion and Biobase::assayDataValidMembers <2011-07-02 Sat>

• added t.MSnSet method <2011-07-02 Sat>

• document t.MSnSet method <2011-07-05 Tue>

• test for t-MSnSet <2011-07-05 Tue>

• new “[“-MSnSet method to properly subset qual slot <2011-07-06 Wed>

• updated MSnSet validity method to check qual dims <2011-07-06 Wed>

• combineFeatures now drops the spectrum-specific qual slot <2011-07-06 Wed>

• test for “[“-MSnSet <2011-07-06 Wed>

Changes in version 1.1.16:

• added addVigs2WinMenu call in .onAttach <2011-06-26 Sun>

• added plotMzDelta paragraph in vignette <2011-06-26 Sun>

Changes in version 1.1.15:

• new names and description methods for ReporterIons <2011-06-16 Thu>

• added validObject() checks <2011-06-16 Thu>

• new removeReporters method <2011-06-16 Thu>

• plotMzDelta is exported and documented <2011-06-17 Fri>

Changes in version 1.1.14:

• Adding plotMzDelta QC plot (not yet exported), contributed by Guangchuang Yu <2011-06-14 Tue>

• created a locked environment to store amino.acids dataframe <2011-06-14 Tue>

• TODO plotMzDelta documentation and vignette section - man DONE in v 1.1.15 , vignette DONE in v 1.1.16

Changes in version 1.1.13:

• changed pSet [[ method <2011-06-13 Mon>

• additional updates pSet [[ method <2011-06-13 Mon>

• added MSnExp subsetting error tests <2011-06-13 Mon>

• created new plotting-dataframe.R file with former plotting utils functions, now renamed plot*.header <2011-06-13 Mon>

Changes in version 1.1.12:

• added invisible(NULL) to all show methods <2011-06-08 Wed>

• added centroided argument to plot.MSnExp <2011-06-09 Thu>

Changes in version 1.1.11:

• harmonised MSnExp and Spectrum plot axes labels <2011-05-18 Wed>

• Added plotting customisation section in vignette <2011-05-18 Wed>

• updated signature of plot2d method to “MSnExp” only <2011-05-18 Wed>

• added/exported plotDensity methods <2011-05-18 Wed>

• started QC vignette section <2011-05-18 Wed>

• added preprocSelection and preprocSelectionTable functions <2011-05-18 Wed>

• TODO document preprocSelection[Table] in vignette

• reduces plot2d-figure and plotDensity-figure sizes using png <2011-05-19 Thu>

• added plotDensity doc <2011-05-19 Thu>

• added round param to preprocSelection[Table] <2011-05-19 Thu>

• preprocSelection[Table] documented and exported <2011-05-19 Thu>

• fixed bug in plot.Spectrum1 <2011-05-24 Tue>

• changed removePeaks setGeneric explicit signature <2011-05-26 Thu>

• added MassSpectrometry biocView <2011-05-27 Fri>

Changes in version 1.1.10:

• minor updates in demo vignette <2011-05-13 Fri>

• added plot argument to plot methods <2011-05-16 Mon>

• fix in makeImpuritiesMatrix <2011-05-16 Mon>

• added meanSdPlot MSnSet method <2011-05-17 Tue>

• minor cosmetic fix in purityCorrect error message <2011-05-17 Tue>

• added method=”sum” to Spectrum/MSnExp normalisation <2011-05-17 Tue>

• typo in MSnSet-class.Rd corrected <2011-05-17 Tue>

Changes in version 1.1.9:

• exporting normali[s|z]e methods for MSnSet, Spectrum and MSnExp <2011-05-12 Thu>

• added quantile normalisation <2011-05-12 Thu>

• added quantile.robust normalisation <2011-05-12 Thu>

• added vsn2 normalisation <2011-05-12 Thu>

• added normalise manual <2011-05-12 Thu>

• included normalisation section in vignette <2011-05-13 Fri>

• more vignette updates <2011-05-13 Fri>

• updated plotting methods to round MZ in title <2011-05-13 Fri>

Changes in version 1.1.8:

• added writeMgfData method from spectra and experiment <2011-05-09 Mon>

• added writeMgfData manual <2011-05-09 Mon>

• added itraqdata data set and updated vignette to use it <2011-05-11 Wed>

• updated man pages to use tiny dummyiTRAQ.mzXML <2011-05-11 Wed>

• added makeImpuritiesMatrix function <2011-05-11 Wed>

Changes in version 1.1.7:

• reporter ions purity correction method, man and test <2011-05-09 Mon>

• updated vignette <2011-05-09 Mon>

Changes in version 1.1.6:

• added incomplete dissociation and spectral counting sections to demo vignette <2011-05-06 Fri>

• added bioc-sig-proteomics link to foreword <2011-05-06 Fri>

• type in foreword <2011-05-06 Fri>

Changes in version 1.1.5:

• added combineFeatures example in demo vignette <2011-05-05 Thu>

Changes in version 1.1.4:

• readIspyData updated to return updated factors <2011-05-03 Tue>

• added unexported/undocumented combineFeatures function for MSnSets <2011-05-03 Tue>

• added basic tests for combineFeatures <2011-05-03 Tue>

• added combineFeatures manual <2011-05-04 Wed>

• exportig combineFeatures <2011-05-04 Wed>

Changes in version 1.1.3:

• as.data.frame.Spectrum columns now are (first) mz and (second) intensity <2011-04-27 Wed>

• exporting as.data.frame.Spectrum and coerce <2011-04-27 Wed>

Changes in version 1.1.2:

• Simplified quantify generic signature - now only object argument <2011-04-19 Tue>

• Added strict parameter to quantify method, man updated, added relevant test

• Added illustrative plot for quantitation methods in MSnbase-demo vignette <2011-04-19 Tue>

• Added illustrative plot for data pre-processing (removePeaks and clean) in MSnbase-demo vignette <2011-04-20 Wed>

• No warnings are issued anymore when peaks expands outside of mz(reporters) +/- width(reporters). See ?quantify on how to check this manually. <2011-04-19 Tue>

• No warnings are issued anymore when reporter peaks are missing. See ?quantify on how to check this manually. <2011-04-20 Wed>

• pSet validity warns if length(unique(msLevel(object))) > 1, rather than != 1. The latter triggered a warning for a new(“MSnExp”). <2011-04-20 Wed>

Changes in version 1.1.1:

• added setAs data.frame and as.data.frame methods for Spectrum objects <2011-03-29 Tue>

• support for uncentroided MS2 spectra plots <2011-03-31 Thu> <2011-04-02 Sat>

• support for uncentroided MS1 spectra plots <2011-04-02 Sat>

• minor modification to readIspyData <2011-04-04 Mon>

• removed centroided slot from MSnProcess and added to individial Spectrum instances. Relevant for Velos HCD (profile)/CID (uncentroided) data <2011-04-04 Mon>

• modified readMzXmlData accordingly <2011-04-04 Mon>

• added validObject(new(…)) tests for each class <2011-04-04 Mon>

• added centroided[<-] methods to Spectrum and pSet <2011-04-04 Mon>

• added ‘keepAll’ parameter to readIspyData <2011-04-11 Mon>

Mulcom

Changes in version 1.3.0:

• Mulcom subroutines are substantially rewritten in C.

ncdfFlow

0.1.0

FEATURES:

• netCDF support for large data sets.

• support all the related methods for flowSet

KNOWN ISSUES:

• write meta data - ncdfFlow allows user to save the entire ncdfFlowSet object in ncdf file. Currently the meta data is first serialized in R and stored as raw vector in cdf. It can fail when the meta data size exceeds the limit of serialization function.

netresponse

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

• removed compiler package and functions as they are included in R-2.14

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

• added options for read.network

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

• compiler added

• corrected weight estimation from vdp.mixt

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

• updated toydata

• compute.weights: now operating in log-domain to avoid occasional floating point errors

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

• added plot.pca function to visualize subnets in 2D with ellipsoid confidence intervals and annotation colors

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

BUG FIXES

• fixed discretization NAMESPACE issues

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

SIGNIFICANT USER-VISIBLE CHANGES

• added speedup option speedup.max.edges in detect.responses. To consider only this many most similar neighborghs in merging, similarity is evaluated by empirical mutual information estimate with sqrt(n) bins where n is data sample size

• changed AIC to default information criterion (previously BIC). Both remain to be available through information.criterion argument

pdInfoBuilder

Changes in version 1.18:

USER VISIBLE CHANGES

• The annotation packages for SNP chips no longer have a ‘fragment_length*’ column in the featureSet/featureSetCNV tables. Fragment length now has its own table, ‘fragmentLength’ (for SNP probes) and ‘fragmentLengthCNV’ (for CN probes).

• Rda files available through annotation packages created by pdInfoBuilder > 1.17 are compressed using ‘xz’.

• Fixed License field on the template.

• Added an additional template for SNP arrays supported by CRLMM.

pint

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

• Fixed bugs with GenomeModels accessors

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

• changed the default match.probes to TRUE in screen.cgh.mrna; now also checks with match.probes = FALSE that the probes are matched

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

• now artificially adding arm information if it is missing, to avoid halts

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

• screen.cgh.mrna option segmented changed into match.probes

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

BUG FIXES

• Fixed a bug in plot.ChromosomeModels

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

BUG FIXES

• fixed a bug which prevented screeningn while missing values were present

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

• added interpretation tools in report.R

qpgraph

Changes in version 1.10:

NEW FEATURES

• estimation of mixed interactions for genetical genomics data via mixed graphical model theory.

• qpBoundary() to explore sparsity in graphs estimated from non-rejection rates.

• MLE of covariance matrices via the Hastie-Tibshirani-Friedman (HTF) algorithm (Hastie, Tibshirani and Friedman, 2009, pg. 634), which enables a much faster simulation of these matrices via qpG2Sigma() than with the previous version based on the IPF algorithm, and much faster MLE of partial correlations via qpPAC().

• uniform sampling of d-regular graphs in qpRndGraph() with the algorithm of Steger and Wormald (1990)

BUG FIXES

• proper handling of master node identification with snow so that parallel computations work again with snow versions > 0.3-3

RPA

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

• removed compiler and corrected the broken compiler function references

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

• added bg correction in rpa.online

• accurate and relatively fast variance hyperparameter update function added (see update.hyperparameters, update.s2)

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

• speedups in hyperparameter estimation; alpha treated as scalar

• removed affinity.method

• added quantiles.online normalization method BUG FIXES

• alpha, beta updates fixed

• rpa.fit did not return updated alpha, beta: now corrected.

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

• rpa.fit-class: added alpha, beta prior parameters for the inverse Gamma conjugate prior for the probe-specific variances

• modified RPA.iteration, RPA.update.sigma2 so as to directly utilize priors everywhere.

• added set.alpha, set.beta and update.hyperparameters, update.alpha, update.beta in internal functions

• added toydata generator function sample.probeset

• rpa.plot: added comparison of toydata and fitted data by adding the toydata.object argument

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

• corrected AffyCompII result note

• polished plot functions in rpa.plot and plot-methods

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

• added compiler to betahat in RPA.sigma2.update.R to speed up

• added NA/NaN check to RPA.iteration after a defected affybatch with NA values was found to cause crash

rqubic

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

• Fix errors in documentations

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

• Submission to Bioconductor

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

• Rename quantile.discritize to quantileDiscritize in order to avoid conflicts with the S3 method nomenclature

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

• Re-starting version indexing due to submission to the Bioc repository

Rsamtools

Changes in version 1.6.0:

NEW FEATURES

• TabixFile, indexTabix, scanTabix, yieldTabix index (sorted, compressed) and parse tabix-indexed files

• readBamGappedReads(), bamFlagAsBitMatrix(), bamFlagAND()

• Add use.names and param args to readBamGappedAlignments(); dropped which and … args.

• PileupFiles, PileupParam, applyPileup for visiting several BAM files and calculating pile-ups on each.

• Provide a zlib for Windows, as R does not currently do this

• BamFileList, BcfFileList, TabixFileList, FaFileList clases extend IRanges::SimpleList, for managings lists of file references

• razfFa creates random access compressed fasta files.

• count and scanBam support input of larger numbers of records; countBam nucleotide count is now numeric() and subject to rounding error when large.

• Update to samtools 0.1.17

• asBcf and indexBcf coerces VCF files to BCF, and indexes BCF

• Update to samtools 0.1.18

• scanVcf parses VCF files; use scanVcf,connection,missing-method to stream, scanVcf,TabixFile,*-method to select subsets. Use unpackVcf to expand INFO and GENO fields.

SIGNIFICANT USER-VISIBLE CHANGES

• ScanBamParam argument ‘what’ defaults to character(0) (nothing) rather than scanBamWhat() (everything)

• bamFlag returns a user-friendly description of flags by default

BUG FIXES

• scanBam (and readBamGappedAlignments) called with an invalid or character(0) index no longer segfaults.

• scanBcfHeader parses values with embedded commas or =

• scanFa fails, rather than returns incorrect sequences, when file is compressed and file positions are not accessed sequentially

• scanBcf parses VCF files with no genotype information.

• scanBam called with the first range having no reads returned invalid results for subsequent ranges; introduced in svn r57138

• scanBamFlag isPrimaryRead changed to isNotPrimaryRead, correctly reflecting the meaning of the flag.

Rsubread

Changes in version 1.4.0:

NEW FEATURES

• Detect exon junctions (subjunc function).

• Make detection calls for each genes to tell whether or not they are expressed (detectionCall function).

• Count number of reads falling into each gene or each exon (featureCounts function).

RTCA

Changes in version 2009-07-13:

• combineRTCA(list): Additional column is renamed into Plate. The vlues is evaluated from list item names. When the list has no name, an integer index beginning from 1 is used. Special attentions to list partially with names is noted in the documentation.

• parseRTCA(file, dec=”.”,phenoData, skipWell,…): Example is added in the documentation how to import pre-configured phenoData. Details section in the documentation is re-written to describe the process of parsing.

• RTCA-class: Experiment ID added to RTCA class

• Makefile: add Makefile to simplify common tasks like check and install

• plotGridEffect: takes ‘column’ instead of ‘col’ as mode parameter, and renders the mode as the title of the legend. Documentation updated.

• plotRTCA: is removed from the package and is substituted by the plot function.

ShortRead

Changes in version 1.11:

NEW FEATURES

• trimTails to trim low quality trailing nucleotides

• trimEnds to remove arbitrary (vectors of) letters from reads or qualities

• FastqStreamer to iterate over a fastq file

• FastqFile, FastqFileList to represent fastq files

SIGNIFICANT USER-VISIBLE CHANGES

• writeFastq has argument full, default value FALSE, disabling printing of identifier a second time in ‘+’ line

• srapply requires that options(srapply_fapply=”parallel”) or options(srapply_fapply=”Rmpi”) to enable parallel processing via fapply

BUG FIXES

• SolexaRealign, SolexaAlign, and SolexaResult transposed strand inforamtion

• FastqSampler segfaulted on some files

• writeFasta had a semi-documented argument mode; it is now documented and as a consequence dis-allows argument ‘append’ that would previously have been passed to underlying methods.

TargetSearch

Changes in version 1.10.0:

NEW FEATURES

• New function “writeLibText” to save “tsLib” objects in a tab-delimited text file (which can consecuently be re-imported). It might be also used to convert a MSP file into a TEXT file.

BUG FIXES

• Added some ‘drop=FALSE’ in plotSpectra function.

• Calls to ‘pdf’ are now followed by ‘on.exit(dev.off())’ to make sure that the device is closed after unexpected errors or user interruption.

Changes in version 1.8.2:

BUG FIXES

• bug fixed error due to changes in TargetSearch object definitions in function writeMSP.

Changes in version 1.8.1:

BUG FIXES

• ‘sampleRI’ and ‘Profile’ functions would return NA if the minPairCor parameter was greater than the number of samples.

• Change GUI message to a more suitable one.

• ‘FAMEoutliers’ failed if only one sample was analyzed.

• ‘ProfileCleanUP’ accepts a minPairObs parameter like ‘Profile’

• The parameter minPairObs is now checked so that cannot take a value lower than 5 in ‘sampleRI’, ‘Profile’, and ‘ProfileCleanUP’ functions.

TEQC

Changes in version 2.0.0:

• new function ‘TEQCreport’ creates an html report with standard TEQC analysis results

• besides bed files, now also BAM files can be used as input for ‘get.reads’

• ‘get.reads’ and ‘get.targets’ now only read the columns required for the analysis from the respective bed files

• when read IDs include ‘#0/1’ and ‘#0/2’ (to indicate read 1 and read 2 of a pair), those characters will be removed from the IDs within ‘get.reads’. The reason is that in ‘reads2pairs’ the two IDs of a read pair have to be identical.

• the package now depends on packages Rsamtools and hwriter

• ‘chrom.barplot’,’ fraction.reads.target’, ‘insert.size.hist’, and ‘duplicates.barplot’ now also can deal with with ‘reads2pairs’ output having the two elements ‘singleReads’ and ‘readpairs’

Changes in version 1.1.2:

• bug fix in ‘coverage.target’ and ‘coverage.GC’ (in very large datasets, global coverage average and standard deviation were not calculated)

Changes in version 1.1.0:

• fix in ‘reads2pairs’: when the two reads of a read pair map to different chromosomes, they will be returned within the ‘singleReads’ element of the output (before function gave en error in case of such read pairs)

• added optional argument ‘max.distance’ to ‘reads2pairs’; when the reads of a read pair are further apart than ‘max.dist’ bases, they will be added to the ‘singleReads’ element of the output instead to the ‘readpairs’ element

tigre

Changes in version 1.8.0:

NEW FEATURES

• Direct support for variances for Illumina Bead Array data from lumi.

• Prettier default plot style

BUG FIXES

• Fix to variance scaling in plots of models with TF mRNA measurements

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

BUG FIXES

• Fix: target ranking now works with >= 10 known targets (thanks to Jake Michaelson for the report)

VariantAnnotation

Changes in version 1.0.0:

NEW FEATURES

• readVcf() for reading and parsing VCF files into a SummarizedExperiment

• locateVariants() and predictCoding() for identifying amino acid coding changes in nonsynonymous variants

• dbSNPFilter() and regionFilter() for filtering variants on membership in dbSNP or on a particular location in the genome

• access to PolyPhen and SIFT predictions through keys() , cols() and select() methods. See ?SIFT or ?PolyPhen.

BUG FIXES

• No changes classified as ‘bug fixes’ (package under active development)

xps

Changes in version 1.14.0:

VERSION xps-1.13.10

• update function xpsQAReport() to replace “_” with “_” for *.Rnw

VERSION xps-1.13.9

• add quality report function xpsQAReport()

• update vignette xps.Rnw

VERSION xps-1.13.8

• add functions attachProbe(), removeProbe(), etc.

• add functions contentGC(), probeSequence()

• add functions inten2GCplot(), plotInten2GC()

• update vignette xps.Rnw

VERSION xps-1.13.7

• add function unitID2symbol()

• add function plotProbeset()

• update vignette xps.Rnw

VERSION xps-1.13.6

• update function indexUnits() for exon probesets

• add function symbol2unitID()

• add function probesetplot()

VERSION xps-1.13.5

• update script4schemes.R to include schemes with annotation na32

• update script4xps.R and script4exon.R

VERSION xps-1.13.4

• move to ROOT version 5.30/00, update README

• update vignettes xps.Rnw and xpsClasses.Rnw

VERSION xps-1.13.3

• correct problem in unitID2affyID() on Linux caused by sQuote()

VERSION xps-1.13.2

• add functions plotXXX()

• function hist() no longer requires to attachInten()

• add functions indexUnits(), pmindex(), mmindex()

• add functions probesetID2unitID(), unitID2probesetID(), etc

• add functions attachUnitNames(), removeUnitNames()

• add functions attachDataXY(), removeDataXY()

VERSION xps-1.13.1

• update function plotImage() to draw background images

Packages removed from the release

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