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Bioconductor 2.10 Released

April 2, 2012

Bioconductors:

We are pleased to announce Bioconductor 2.10, consisting of 554 software packages and more than 600 up-to-date annotation packages. There are 45 new software packages, and many updates and improvements to existing packages; 5 packages have been removed from this release. Bioconductor 2.10 is compatible with R 2.15.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS. This release includes an updated Bioconductor Amazon Machine Image. Visit http://bioconductor.org for details and downloads.

Getting Started with Bioconductor 2.10
New Software Packages
NEWS from new and existing packages
Packages removed from the release

Getting Started with Bioconductor 2.10

To install Bioconductor 2.10:

Install R 2.15.0. Bioconductor 2.10 has been designed expressly for this version of R.
Follow the instructions at http://bioconductor.org/install/.

New Software Packages

There are 45 new packages in this release of Bioconductor.

AffyRNADegradation: Analyze and correct probe positional bias in microarray data due to RNA degradation
ASEB: Predict Acetylated Lysine Sites
BiocGenerics: Generic functions for Bioconductor
birta: Bayesian Inference of Regulation of Transcriptional Activity
BitSeq: Transcript expression inference and differential expression
BRAIN: Baffling Recursive Algorithm for Isotope distributioN calculations
BrainStars: query gene expression data and plots from BrainStars (B*)
CancerMutationAnalysis: Cancer mutation analysis
categoryCompare: Meta-analysis of high-throughput experiments using feature annotations
cellGrowth: Fitting cell population growth models
cnvGSA: Gene Set Analysis of (Rare) Copy Number Variants
coGPS: cancer outlier Gene Profile Sets
DART: Denoising Algorithm based on Relevance network Topology
deepSNV: Test for subclonal SNVs in deep sequencing experiments.
easyRNASeq: Count summarization and normalization for RNA-Seq data.
EBcoexpress: EBcoexpress for Differential Co-Expression Analysis
ffpe: Quality assessment and control for FFPE microarray expression
GeneGroupAnalysis: Gene Functional Class Analysis
GEWIST: Gene Environment Wide Interaction Search Threshold
gprege: Gaussian Process Ranking and Estimation of Gene Expression time-series
Gviz: Plotting data and annotation information along genomic coordinates
gwascat: representing and modeling data in the NHGRI GWAS catalog
HiTC: High Throughput Chromosome Conformation Capture analysis
HybridMTest: Hybrid Multiple Testing
iASeq: iASeq: integrating multiple sequencing datasets for detecting allele-specific events
iBBiG: Iterative Binary Biclustering of Genesets
IdMappingAnalysis: ID Mapping Analysis
inSilicoMerging: Collection of Merging Techniques for Gene Expression Data
manta: Microbial Assemblage Normalized Transcript Analysis
maskBAD: Masking probes with binding affinity differences
MinimumDistance: A package for de novo CNV detection in case-parent trios
motifRG: A package for discriminative motif discovery, designed for high throughput sequencing dataset
NarrowPeaks: Functional Principal Component Analysis to Narrow Down Transcription Factor Binding Site Candidates
pcaGoPromoter: pcaGoPromoter is used to analyze DNA micro array data
phyloseq: Handling and analysis of high-throughput phylogenetic sequence data.
PING: Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
QUALIFIER: Qualitiy Control of Gated Flow Cytometry Experiments
RchyOptimyx: Optimyzed Cellular Hierarchies for Flow Cytometry
ReactomePA: Reactome Pathway Analysis
rhdf5: HDF5 interface to R
sigaR: statistics for integrative genomics analyses in R
spade: SPADE – An analysis and visualization tool for Flow Cytometry
ternarynet: Ternary Network Estimation
VegaMC: VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
virtualArray: Build virtual array from different microarray platforms

NEWS from new and existing packages

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

a4Base

Changes in version 1.2.4:

throw error in case ‘group’ variable contains missing values in spectalMap

Changes in version 1.2.3:

circumvent build issues on certain versions of windows

Changes in version 1.2.2:

more appropriate handling of the dots argument in plot1gene

Changes in version 1.2.1:

fix in legend for spectralMap

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!

affxparser

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

The version number was bumped for the Bioconductor 2.10 release version.

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

ROBUSTNESS: Now the native code throws R errors, instead of printing an error message to stdout/stderr and then returning null, that is translated to errors at the R level.

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

BUG FIX: affxparser would not build on Windows with the new Rtools toolchain (Rtools 2.15.0.1915-1919).

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

ROBUSTNESS: Added sanity checks asserting that the internal readers did indeed read something and not just returned NULL. It should be very unlikely that this occurs, but there is still a small risk that after asserting that a file exists, but before the internal Fusion SDK parsers access the file, the file has been removed.

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

Same updates as in v1.26.1.

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

The version number was bumped for the Bioconductor devel version.

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

BUG FIX: affxparser would not build on Windows with the new Rtools toolchain (Rtools 2.15.0.1915-1919), which is for R (> 2.14.1), i.e. also for R v2.14.2 (but not v2.14.1). This is the same bug fix that was first done in v1.27.4.

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

The version number was bumped by Bioconductor to trigger a build.

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

FIX: Fixed warning on “In readBin(con, what = “integer”, size = 4, n = 1, signed = FALSE, ‘signed = FALSE’ is only valid for integers of sizes 1 and 2” that some read methods would generated.

aroma.light

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

The version number was bumped for the Bioconductor release version.

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

The version number was bumped for the Bioconductor devel version.

ArrayExpressHTS

Changes in version 1.5.2:

UPDATES

fixed trace names, cleanup
updated the code downloading SDRFs to rename seq.srdf.txt to .sdrf.txt
unified the functions providing default options
exposed the options that are used in the process
changed errors to warnings where process can still be completed
fixed improper tools detection on the external R Cloud, added detection using elements in PATH.
simplified setting of tools options, removed the need to invoke initEnvironmentVariables after the options are set, made it automatic
updated help pages
composed all options related pages into “package options” page and “processing options” page. Exposed all options.
removed the initEnvironmentVariables
removed outdated references

Changes in version 1.5.1:

UPDATES

improved error handling within the ArrayExpressHTS
added stop.on.warnings that allows detection of possible failures earlier. However if used it would narrow the amount of experiments that can be successfully processed.
added log.error instead of log.info where necessary
reorganised pipeline options, made them visible to users in the command syntax.
reorganised R Cloud parameters into a single set of visible/usable options
made the pipeline automatically detect “Organism” from SDRF and filter using a selected value.
reworked reading from SDRF to cover most of the “flexible formatting” cases
improved creation of R Cloud computation cluster, widened usage of retries.
added proper functions to work with environment variables
updated package help pages
updated the annotation processing following Ensembl update.
updated help pages, descriptions and references
updated package vignette documentation
slightly reorganised the structure of the document
rewritten some sections
added a few new sections
added examples where needed
reimplemented problematic searching and downloading of .seq.sdrf.txt files
fixed problematic handling of “NA” or “missing” nominal length values from ENA
made a number of reference preparation tasks be able to run in parallel and not affect each other.
fixed the “count” method to properly read fields of bam files

biovizBase

Changes in version 1.1.16:

NEW FEATURES

addSteping add extra arugments group.selfish to control stepping method
add estimateCoverage method for fast estimate coverage

SIGNIFICANT USER-LEVEL CHANGES

addStepings rename to addStepping

CAMERA

Changes in version 2012-03-19:

Version 1.11.10
Bugfix in groupCorr, where the function throws an error if argument xraw is not null
Version 1.11.9
Bugfix in findAdducts, where adduct annotation filtering was to stringent, if ips score is higher 1.5

Changes in version 2012-02-29:

Version 1.11.8
Bugfix in findAdducts parallel mode, where wrong psgrp indices were stored in annoGrp

Changes in version 2012-02-17:

Version 1.11.7
Bugfix in findAdducts, where the ruleset is not saved within a xsAnnotate object with user defined rules
Changed a general groupCorr behaviour. If no edge is above correlation threshold, all peaks are seperated in pspecs of size 1

Changes in version 2012-02-15:

Version 1.11.6
Fix error in groupCorr: If sample is set to something other than 1 or NA, it result in a crash

Changes in version 2012-02-10:

Version 1.11.5
Bugfix in groupCorr where parameter cor_eic_th doesn’t influence correlation across samples
Add new parameter for groupCorr cor_exp_th

Changes in version 2011-29-11:

Version 1.11.3
Add new function combinexsAnnos. It allows checking and reannotation of sample with a coressponding sample from the opposite ion mode

Changes in version 2011-28-04:

Fix bug in getpspectra, which incorrect label isotope peaks

Changes in version 2011-24-11:

Version 1.11.2
Bugfix in annotateDiffreport: Since 1.7.7 mismatch of the peaklist from CAMERA and the diffreport function results in false ordered peaktable

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 2011-12-12:

Version 1.11.4
Add missing Rd page combinexsAnnos

Changes in version 2011-12-05:

plotPsSpectrum now accepts additional parameters for plot

Changes in version 2011-10-11:

Version 1.11.1
add the possibility to extract multiple isotope intensity from different samples with getIsotopeCluster

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

Changes in version 2010-29-09:

Add function findNeutralLoss and findNeutralLossSpecs

Changes in version 2010-23-11:

Fix bug in findAdducts. Function failed, if run in parallel mode.

Changes in version 2010-20-09:

Add function getIsotopeCluster for retrival of isotope cluster

Changes in version 2010-11-10:

Rewrite Vignette

Changes in version 2010-11-06:

Speed up in findAdducts
Fix unit tests

Changes in version 2010-08-11:

Add intval parameter to groupFWHM and findIsotopes
Change getPeaklist to S4 Methods.
Add getPeaklist parameter intval, where the intensity value can be selected
Additional bugfix for findIsotopes. Could occur with 1.7.1, that all isotopes will be deleted.

Changes in version 2010-05-03:

Fix bug in findIsotopes, crashed with dim error

Changes in version 2010-04-20:

Fix bug in annotate function

Changes in version 2010-04-19:

Last changes for the next BioC release
Rewrite of the vignette

Changes in version 2010-03-17:

Hugh changes in CAMERA for working with multiple sample
Add check constrains in groupCorr for isotopes and primary adducts

Changes in version 2010-01-11:

Fix bug in findIsotopes. Occurs if the first isotope peak, could be assigned from two different monoisotopic peaks.
Reduce slightly the number of found isotopes

Changes in version 2009-11-24:

Add experimental parallel mode with MPI

Changes in version 2009-11-20:

Fix bug in setting ruletable

Changes in version 2009-08-26:

add nSlaves as argument to findAdducts (for parallel annotation with MPI)

Changes in version 2009-08-24:

small bugfixes in getPeaklist
add neutral losses to rule set

Changes in version 2009-08-12:

Fixed plotEICs for 1 peak groups

Changes in version 2009-08-04:

Add ips Score to annoGrp

Changes in version 2009-06-03:

Add adduct labels to plotPeaks()
Add adduct labels to plotEICs()

Changes in version 2009-05-22:

Add first visualisation function plotEICs() and plotPeaks()

Changes in version 2009-05-06:

bump for devel 2.5

Changes in version 2009-03-30:

add combine_xsanno
small refactoring
changes in scoring schemata

Changes in version 2009-03-18:

after groupCorr every peak is now member of a group
bugfix: remove xM-xH clones
remove dependency on Hmisc

Changes in version 2009-03-10:

speed-up of findAdducts

Changes in version 2009-02-24:

refactoring findAdducts
add methods for pos/neg polarity comparison

Changes in version 2009-02-20:

replace na.omit with naOmit

Changes in version 2009-02-18:

add neutral losses into ruleset
other bugfixes

Changes in version 2009-01-19:

Change isotope nomination
add lists for fragments, ions and neutral losses

Changes in version 2008-10-15:

Lot of bugfixes and speed up the correlation

Changes in version 2008-10-13:

First build for version 0.1.1

Changes in version 2007-10-12:

Inital release & collection of stuff

categoryCompare

Changes in version 0.99.0:

SIGNIFICANT USER-VISIBLE CHANGES

First review in Bioconductor

Changes in version 0.7.8:

SIGNIFICANT USER-VISIBLE CHANGES

Updated the vignette. Removed long lines, added links to figures, fixed some errors

Changes in version 0.7.4:

SIGNIFICANT USER-VISIBLE CHANGES

changed category in ccCompare to categoryName for GENccEnrichResults-class

Changes in version 0.7.3:

SIGNIFICANT USER-VISIBLE CHANGES

First commit

cellGrowth

Changes in version 0.99.0:

SIGNIFICANT USER-VISIBLE CHANGES

no dontrun in examples
use system.file() instead of installed.packages() in examples
renamed the example_files directory to extdata

Changes in version 0.4.0:

SIGNIFICANT USER-VISIBLE CHANGES

first submission

clusterProfiler

Changes in version 1.4.0:

bump up version to 1.4.0 for 2.10 release
add URL in DESCRIPTION

Changes in version 1.3.15:

add support to organsims other than human, mouse, and yeast. <2012-03-22, Thu>
add GFFparser.R, which provide function Gff2GeneTable to parse Gff files and build gene information table.<2012-03-22, Thu>
add function buildGOmap for building GO mapping files for unsurported organisms, which can be analyzed now. <2012-03-22, Thu>
add vignette explaining how to run GO analysis for unsupported organism. <2012-03-12, Thu>

Changes in version 1.3.14:

re-implement enrichGO by import enrich.internal in DOSE implement S3 methods for mapping IDs for GO analysis. <2012-03-18, Sun>
re-implement enrichKEGG by import enrich.internal in DOSE implement S3 methods for mapping IDs for KEGG analysis. <2012-03-19, Mon>
re-implement groupGOResult class by extended from enrichResult, and modified groupGO by using S3 methods designed for enrichGO. <2012-03-19,Mon>
bug fixed for importing setReadable<- instead of setReadable. <2012-03-20, Tue>
bug fixed of TERM2NAME.GO. <2012-03-21, Wed>

Changes in version 1.3.13:

import plot summary from stats4, for BiocGenerics (version 0.1.10) removed them <2012-03-03, Sat>

Changes in version 1.3.12:

fixed BibTeX database file .bib. month = , must be month = someMonth, or totally deleted, leave it blank will cause texi2dvi failed. <2012-03-01, Thu>

Changes in version 1.3.11:

update vignette. <2012-02-28, Tue>

Changes in version 1.3.10:

fixed warnings concerning documents of plot generics. <2012-02-27, Mon>
import summary generic from BiocGenerics instead of stats4. <2012-02-27, Mon>

Changes in version 1.3.9:

fixed build error in bioc repos <2012-02-26 Sun>

Changes in version 1.3.8:

add visualization section in vignette <2012-02-16 Thu>

Changes in version 1.3.7:

@exportMethod plot <2012-02-15 Wed>
fix bug when calling summary method from plot, for summary defined in base is S3 method, instead import summary generic from stats4 <2012-02-15 Wed>

Changes in version 1.3.6:

remove generic definition of show, summary and plot, add NAMESPACE import show from methods and plot from graphics. summary need not to import, for is defined in the base package. <2012-02-13 Mon>
rewrite vignette <2012-02-13 Mon>

Changes in version 1.3.5:

update plot codes accompany with new version of ggplot2(>=0.9.0) <2012-02-07 Tue>

Changes in version 1.3.4:

using apply instead of mdply to improve speed <2012-02-03 Fri>
add citation of clusterProfiler <2012-02-03 Fri>

Changes in version 1.3.3:

add showCategory parameter for plot functions <2011-01-11 Wed>

Changes in version 1.3.2:

add qvalueCutoff parameter. <2011-01-05 Thu>

Changes in version 1.3.1:

add plot.categoryNet for enrichGOResult. <2011-11-10 Thu>

CNAnorm

Changes in version 1.1.8:

SIGNIFICANT USER-VISIBLE CHANGES

Fixed plotGenome so that, when fixVaxes = TRUE horizontal lines are drawn even if there are no points in a certain area.

Changes in version 1.1.7:

SIGNIFICANT USER-VISIBLE CHANGES

Removed arguments ‘adjust’ and ‘n’ from plotPeaks as it needs to retrieve the same values used in peakPloidy
Added option fixVAxes to plotGenome to fix vertical axes to maxRatio and minRatio
Fixed plotGenome so that the line from superimpose = “DNACopy” is actually a line and not a series of dots
If plotting only one chromosome, instead of plotting chr name, it plots chromosome position.

Changes in version 1.1.6:

SIGNIFICANT USER-VISIBLE CHANGES

Added method ‘closest’ to function peakPloidy for a “standard” normalisation
Fixed the ‘mode’ method
Internal tiding

Changes in version 1.1.5:

SIGNIFICANT USER-VISIBLE CHANGES

Added methods ‘median’ and ‘mode’ to to function peakPloidy for a “standard” normalisation

Changes in version 1.1.4:

SIGNIFICANT USER-VISIBLE CHANGES

Fixed an error in exportTable which was providing a meaningless value for SegMean

Changes in version 1.1.3:

SIGNIFICANT USER-VISIBLE CHANGES

Changed the provided data (LS041 and CN) to match what bam2windows.pl version 0.3.4

Changes in version 1.1.2:

SIGNIFICANT USER-VISIBLE CHANGES

Added an option to plot more colorful genome plots

Changes in version 1.1.1:

SIGNIFICANT USER-VISIBLE CHANGES

Corrected a bug in exportTable that crashed if smoothed ratio was not available.

codelink

Changes in version 1.23.2:

Improvements on how codPlotScatter() manages labels. Renamed generic scatter plot function plotma() to plotxy(), which better reflects the current status.

Changes in version 1.23.1:

Implemented missing function codPlotScatter() for CodelinkSet objects (accessible via codPlot(…, what = “scatter”)). The implementation reuses the plotma() function used by codPlotMA(). By default the first array is plotted against the median. Thanks to William Michels for reporting this and testing the CodelinkSet framework.
Minor improvements to linear model section in CodelinkSet-vignette. Now the code is evaluated.

cqn

Changes in version 1.1:

Same fixes as in 1.0.1
Resaved the data files, so they take up less space.
Added edgeR as a Suggests: since the vignette uses it.

Changes in version 1.0.1:

The function alpha has been moved from ggplot2 to the new package scales. Vignette and Suggests: fields have been changed accordingly.
sizeFactors = NULL should now work for cqn and cq.fixedlength. Thanks to Maria Chikina for reporting this

cummeRbund

Changes in version 1.1.5:

BUG FIXES

Fixed minor bug in database setup that caused instability with cuffdiff –no-diff argument. oFixed bug in csDendro method for CuffData objects.

Changes in version 1.1.4:

NEW FEATURES

Added MAplot() method to CuffData objects.

BUG FIXES

Finished abrupt migration to reshape2. As a result fixed a bug in which ‘cast’ was still required for several functions and could not be found. Now appropriately using ‘dcast’ or ‘acast’.
Fixed minor bug in CuffFeature::fpkmMatrix

Changes in version 1.1.3:

NEW FEATURES

getSig() has been split into two functions: getSig() now returns a vector of ids (no longer a list of vectors), and getSigTable() returns a ‘testTable’ of
binary values indicating whether or not a gene was significant in a particular comparison.
Added ability in getSig() to limit retrieval of significant genes to two provided conditions (arguments x & y). (reduces time for function call if you have a specific comparison in mind a priori)
When you specify x & y with getSig(), q-values are recalculated from just those selected tests to reduce impact of multiple testing correction.
If you do not specificy x & y getSig() will return a vector of tracking_ids for all comparisons (with appropriate MTC).
You can now specify an ‘alpha’ for getSig() and getSigTable() [ 0.05 by default to match cuffdiff default ] by which to filter the resulting significance calls.
Added csSpecificity() method: This method returns a feature-X-condition matrix (same shape as fpkmMatrix) that provides a ‘condition-specificity’ score defined as 1-(JSdist(p,q)) where p is is the density of expression (probability vector of log(FPKM+1)) of a given gene across all conditions, and q is the unit vector for that condition (ie. perfect expression in that particular condition)
specificity = 1.0 if the feature is expressed exclusively in that condition
Created csDendro() method: This method returns a object of class ‘dendrogram’ (and plots using grid) of JS distances between conditions for all genes in a CuffData, CuffGeneSet, or CuffFeatureSet object.
Useful for identifying relationships between conditions for subsets of features
New visual cues in several plot types that indicates the quantification status (‘quant_stat’ field) of a particular gene:condition. This information is useful to indicate whether or not to trust the expression values for a given gene under a specific condition, and may provide insight into outlier expression values. This feature can be disabled by setting showStatus=F.
csDensity() is now available for CuffFeatureSet and CuffGeneSet objects

BUG FIXES

Fixed bug in getGenes that may have resulted in long query lag for retrieving promoter diffData. As a result all calls to getGenes should be significantly faster.
CuffData fpkm argument ‘features’ now returns appropriate data.frame (includes previously un-reported data fields).
Replaced all instances of ‘ln_fold_change’ with the actual ‘log2_fold_change’. Values were previously log2 fold change but database headers were not updated to reflect this.
Fixed bug that could cause readCufflinks() to die with error when using reshape2::melt instead of reshape::melt.

NOTES

The structure of the underlying database has changed in this version. As a consequence, you must rebuild you cuffData.db file to use new version. readCufflinks(rebuild=T)
Updated vignette
‘fullnames’ logical argument was added to fpkmMatrix. If True, rownames for fpkmMatrix will be a concatenation of gene_short_name and tracking_id. This has the added benefit of making row labels in csHeatmap easier to read, as well as preserving uniqueness.
Slight speed improvements to JSdist (noticeable when using csCluster on large feature sets).
‘testTable’ argument to getSig() has been dropped in lieu of new getSigTable() method.

Changes in version 1.1.1:

BUG FIXES

fixed issue in which there was no graceful error handling of missing CDS or TSS data in cuffdiff output.
Fixed issue in which distribution test data (promoters, splicing, relCDS) were not appropriately added to objects on creation. oFixed bug that would sometimes cause csBoxplot() to throw an error when log-transforming fpkm data. Also added pseudocount argument.
Fixed bug that would cause diffData() to return a filtered subset of results by default.
Adjusted indexing of tables to improve performance on large datasets.
Fixed bug that caused diffData method to not be registered with CuffFeature and CuffGene objects.
Fixed bug that sometimes caused over-plotting of axis labels in csBarplots.

NEW FEATURES

added getSig method to CuffSet class for rapid retrieval of significant features from all pairwise tests (as a list of IDs).
By default the level is ‘genes’ but any feature level can be queried.
csCluster now uses Jensen-Shannon distance by default (as opposed to Euclidean)
Added ‘xlimits’ argument to csVolcano to constrain plot dimensions.
Enforced requirement in csVolcano for x and y arguments (as sample names).

NOTES

Changed dependency ‘reshape’ to ‘reshape2’
Changed the default orientation of expressionBarplot() for CuffFeatureSet objects.
Changed output of csCluster to a list format that includes clustering information. As a result, I created the function csClusterPlot to replace the previous default drawing behavior of csCluster. This allows for stable cluster analysis.
For consistency, the ‘testId’ slot for CuffDist objects was renamed to ‘idField’. This brings the CuffDist class in line with the CuffData class.
CuffGene and CuffGeneSet now include slots for promoter, splicing, and relCDS distribution test results.

deepSNV

Changes in version 1.1.4:

BUG FIXES

Fixed error in summary() when there were no significant SNVs.
Some fixes if only a single column of the alignment is selected

Changes in version 1.0.0:

SIGNIFICANT USER-VISIBLE CHANGES

Added CITATION file
Made NEWS (this file) R-readable
Changed Vignette

Changes in version 0.99.2:

SIGNIFICANT USER-VISIBLE CHANGES

Changed plot to S3 method (to avoid warning in R-devel)

Changes in version 0.99.1:

SIGNIFICANT USER-VISIBLE CHANGES

Added small .bam example files test.bam, control.bam with 100 positions.
Modified man pages for bam2R()
Modified man page for coordinates()
Corrected example of consensusSequence()
Compressed .RData files with tools::resaveRdaFiles
Changed vignette to attach data, rather than load remotely.
Argument “regions” of deepSNV can be a GRanges object.

Changes in version 0.99.0:

SIGNIFICANT USER-VISIBLE CHANGES

Added BiocViews field
Added HIVmix data
Added new examples
Registered bam2R with R_registerRoutines
New accessor functions “test”, “control”, “p.val”, and “coordinates”
Updated vignette

Changes in version 0.9.5:

SIGNIFICANT USER-VISIBLE CHANGES

“summary” now reports additional columns from regions slot.

BUG FIXES

drop=FALSE in subsetting and summary.

Changes in version 0.9.4:

SIGNIFICANT USER-VISIBLE CHANGES

Directly link to static samtools library provided by Rsamtools
Load example .bam files over http

Changes in version 0.9.3:

SIGNIFICANT USER-VISIBLE CHANGES

Added beta-binomial model
Extended documentation
Use summary instead of significantSNV

Changes in version 0.9.2:

BUG FIXES

Minor bugfixes

Changes in version 0.9.1:

BUG FIXES

Minor bugfixes

Changes in version 0.9.0:

SIGNIFICANT USER-VISIBLE CHANGES

Pre-release

DESeq

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

Added pooled-CR method.
Fixed error message for insufficient replication.

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

Fixed error in vignette.
Silenced warnings from nbinomFitGLM about convergence; this information is given in the result anyway.

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

The VST is now roughly equal to log2 for local dispersion fits, too.

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

changed the variance stabilizing transformation once more; this time it is hopefully correct. The derivation of the formula is now documented in the new file vst.pdf.

Changes in version 1.7.6:

fixed regression bug in getVarianceStabilizedData: the formula for parametric dispersion fit was wrong since I “fixed” the factor to get log2 asymptotic behaviour.

Changes in version 1.7.1:

various changes to vignette by whuber

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

DiffBind

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

GRanges is default class for peaksets and reports instead of RangedData, controlled by DataType parameter.
Both analysis methods (edgeR and DESeq) use generalized linear models (GLMs) for two-group contrasts by default.
Blocking factors (for two-factor analysis) can be specified flexibly such that arbitrary blocking factors can be used. Section added to vignette showing an ananalysis using a blocking factor.
Added new metadata type, DBA_TREATMENT.
New DBA_SCORE_ options for specifying scoring method, including TMM normalized counts, and ability to change scoring method on the fly in dba.plotHeatmap and dba.plotPCA when plotting global binding matrix.
bRemoveDuplicates parameter in dba.count allows duplicate reads to be discarded when computing counts
More efficient use of memory when analyzing (controlled by bReduceObjects parameter in dba.analyze).
various bugs fixed, man pages updated, and warning messages added.

DOSE

Changes in version 1.1.12:

implement barplot for enrichResult <2012-03-18, Sun>
bug fixed for setReadable method <2012-03-19, Mon>
add logFC parameter for cnet plot, support color gene nodes by their expression value (log fold change) <2012-03-21, Wed>
add mapping entrezgene ID and gene Name for organisms other than human, mouse and yeast. <2012-03-22, Thu>
bug fixed for attempt to name logFC, when it is NULL. <2012-03-22, Thu>
optimized readable method. <2012-03-26, Mon>

Changes in version 1.1.11:

setReadable method for mapping gene ID to gene Symbol in enrichResult instance. <2012-03-12, Mon>
export method show. <2012-03-12, Mon>

Changes in version 1.1.10:

import plot summary from stats4, for BiocGenerics (version 0.1.10) removed them <2012-03-03, Sat>
Add DO2ALLEG and EG2ALLDO, for mapping undirecte annotation. <2012-03-03, Sat>
update vignette <2012-03-06, Tue>

Changes in version 1.1.9:

fixed BibTeX database file .bib. month = , must be month = someMonth, or totally deleted, leave it blank will cause texi2dvi failed. <2012-03-01, Thu>
update IC data and DO-EG mapping data. <2012-03-01, Thu>

Changes in version 1.1.8:

update vignette, add semantic similarity algorithms’ details. <2012-02-28, Tue>

Changes in version 1.1.7:

fixed warnings concerning documents of plot generics. <2012-02-27, Mon>
import summary generic from BiocGenerics instead of stats4. <2012-02-27, Mon>

Changes in version 1.1.6:

defined S3 generic for ALLEXTID, EXTID2NAME, EXTID2TERMID, TERM2NAME, and TERMID2EXTID. <2012-02-26, Sun>
update roxygen and regenerate man file. <2012-02-26, Sun>
import S4 generics of plot from BiocGenerics. <2012-02-26, Sun>

Changes in version 1.1.5:

add S4 method of plot, which accept parameter type = “cnet”, and call cnetplot.enrichResult method. <2012-02-23, Thu>
add S3 method cnetplot.enrichResult for plotting enrichResult object. <2012-02-23, Thu>
define cnetplot function for category-gene network visualization. <2012-02-23, Thu>
remove generic definition of show and summary, import show from methods and summary from stats4 <2012-02-23, Thu>
redefine functions as S3 methods for mapping ID among gene and Term. this will make enrich.internal which calling these mapping function more robust <2012-02-23, Thu>

Changes in version 1.1.4:

add Enrichment Analysis session in vignette. <2012-02-22, Wed>
optimize enrichDO, ten time faster. <2012-02-22, Wed>
separate code of enrichDO to enrich.internal, make it more general, and can be applied to other ontology. <2012-02-22, Wed>
rename enrichDOResult class to enrichResult and add slot geneInCategory. <2012-02-22, Wed>
export infoContentMethod and wangMethod. <2012-02-22, Wed>

Changes in version 1.1.3:

update infoContentMethod to make it consistent between DOSE and GOSemSim. <2011-12-31, Sat>

Changes in version 1.1.2:

change to using roxygen for generating Rd docs

Changes in version 1.1.1:

add function rebuildAnnoData
update Disease-Gene Mapping data

easyRNASeq

Changes in version 1.1.10:

NEW FEATURES

Added a naPositionFilter extending ShortRead srFilters

BUG FIXES

Worked on Wade Davis case with 3 different sets of chromosome names in the three different input (reads, annotation, chromosome sizes)
Worked on smoother error handling when not using bam files. Again through Wade Davis example
Ensured that chromosome names conversion occurs whether provided with a factor or a character vector
extended the NAMESPACE

Changes in version 1.1.9:

BUG FIXES

Added an \alias{RNAseq} to ease the class documentation access; an H.Pages suggestion
Changed the DESCRIPTION file to make sure that the latest ShortRead (1.13.13) and BiocGenerics (0.1.11) package are required

Changes in version 1.1.8:

BUG FIXES

Corrected the last occurence of the deprecated matchMatrix call
Corrected an issue on windows raised by the parallel package. Thanks to Wade Davis for pointing that one out.

Changes in version 1.1.7:

BUG FIXES

Fixed the NAMESPACE and the vignette generation

Changes in version 1.1.6:

BUG FIXES

Thanks to Francesco Lescai, a bug was fixed. Namely I was not expecting the chromosome names in the bam files and in the chromosome name lists to be two different set with a common intersect. I always consider that one would be the subset of the other one. Now, when such situation occurs only the common set is kept and used for the calculations.
Herve Pages changed the findOverlaps value. It is now an object of the Hits class that does not support the matchMatrix accessor anymore. The code was adapted to the new accessor queryHits.
Corrected the package structure to add a vignettes sub-directory. Moved the relevant files there

Changes in version 1.1.5:

BUG FIXES

Removed the fitInfo method extension to the DESeq package as it as been implemented in that package
Reworked the plotDispersionEstimates and .normalizationDispatcher function to deal with the new fitInfo function (the information is stored in an environment rather than in a list)

Changes in version 1.1.4:

Package introduced in Bioconductor

EDASeq

Changes in version 1.2.0:

Fixed a bug in methods plotQuality and plotNtFrequency that now allow the strand information to be missing in the SAM/BAM file.
Fixed a bug in method biasPlot. It doesn’t require anymore that one of the column of pData is called “conditions”.
biasPlot method of SeqExpressionSet has now the argument “col” to specify the column of pData to use for color coding.

edgeR

Changes in version 2.6.0:

edgeR now depends on limma.
Considerable work on the User’s Guide. New case study added on Pathogen inoculated arabidopsis illustrating a two group comparison with batch effects. All the other case studies have been updated and streamlined. New section explaining why adjustments for GC content and mappability are not necessary in a differential expression context.
New and more intuitive column headings for topTags() output. ‘logFC’ is now the first column. Log-concentration is now replaced by log-counts-per-million (‘logCPM’). ‘PValue’ replaces ‘P.Value’. These column headings are now inserted in the table of results by exactTest() and glmLRT() instead of being modified by the show method for the TopTags object generated by topTags(). This means that the column names will be correct even when users access the fitted model objects directing instead of using the show method.
plotSmear() and plotMeanVar() now use logCPM instead of logConc.
New function glmQLFTest() provides quasi-likelihood hypothesis testing using F-tests, as an alternative to likelihood ratio tests using the chisquare distribution.
New functions normalizeChIPtoInput() and calcNormOffsetsforChIP() for normalization of ChIP-Seq counts relative to input control.
New capabilities for formal shrinkage of the logFC. exactTest() now incorporates formal shrinkage of the logFC, controlled by argument ‘prior.count.total’. predFC() provides similar shrinkage capability for glms.
estimateCommonDisp() and estimateGLMCommonDisp() now set the dispersion to NA when there is no replication, instead of setting the dispersion to zero. This means that users will need to set a dispersion value explicitly to use functions further down the analysis pipeline.
New function estimateTrendedDisp() analogous to estimateGLMTrendedDisp() but for classic edgeR.
The algorithms implemented in estimateTagwiseDisp() now uses fewer grid points but interpolates, similar to estimateGLMTagwiseDisp().
The power trend fitted by dispCoxReidPowerTrend() now includes a positive asymptote. This greatly improves the fit on real data sets. This now becomes the default method for estimateGLMTrendedDisp() when the number of genes is less than 200.
New user-friendly function plotBCV() displays estimated dispersions.
New argument target.size for thinCounts().
New utility functions getDispersion() and zscoreNBinom().
dimnames() methods for DGEExact, DGELRT and TopTags classes.
Function pooledVar() removed as no longer necessary.
Minor fixes to various functions to ensure correct results in special cases.

ExiMiR

Changes in version 1.3.1:

NEWS: add NEWS file for tracking changes.
inst/doc/ExiMiR-vignette.Rnw: Fix vignette generation issue

exomeCopy

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

support for multisample projects: distribute sample segmentation across workstations, compile results and plot CNVs across samples (see vignette for a reworked example)
log odds ratios for CNV segments using the fitted distribution of counts for the predicted and normal state
strand-aware read starts and duplicate read removal for counting reads from a BAM file in genomic ranges
functions for generating background read depth and calculating GC content

flowCore

Changes in version 1.21.5:

SIGNIFICANT USER-VISIBLE CHANGES

add .readFCSdataRaw routine to read FCS containing bit-packed integer data (with odd-bitwidth like 9,11 instead of 8,16,32,64)
Currently the bit-wise manipulation is done within R,it can be moved to C if speed issue becomes a problem in the future.

Changes in version 1.21.1:

SIGNIFICANT USER-VISIBLE CHANGES

add TEXT segment parser in readFCStext function for FCS3 when the delimiter characters existing inside of keyword values. Note this parser require all keywords and their values to be non-empty, which conforms to FCS3 standard

GeneGroupAnalysis

Changes in version 1.1:

Considering on having more flexibility on the linear models that can be fitted by the Gibb’s sampler.

GeneticsPed

Changes in version 2007-09-12:

Added prune function for pruning/trimming the pedigree. It does not work on pedigree, but assumes a data.frame with defined structure. Adaption needed.
We depend on genetics package since gpLong2Wide and hwp assume that input is of genotype class.
Added two utility functions (gpLong2Wide and hwp) for work with gpi(). There is also a separate help page for them.
Internal fixes in gpi - no need to transpose inputs for Fortran call anymore - check that there are no NA values in gp and hwp

Changes in version 2007-04-25:

Version bump to follow BioC releases. # 0.1.4

Changes in version 2007-04-19:

Added internal .get* functions for retrieving slot values and use of it.

Changes in version 2007-04-18:

R CMD check should now fail also when R error (usually call to stop()) occurs in unit testing.
Added unit tests for sort, examples in help page and clarified sort help page.

Changes in version 2007-04-06:

New small dataset Falconer5.1.
Added sex(), sex<-(), ascendantSex() and ascendantSex<-() functions.
Added some more tests for relationshipAdditive, inverseAdditive and inbreeding. # 0.1.2

Changes in version 2007-04-01:

Now we are more rigorous for value of ascendantSex argument in Pedigree(). It must accord to values in sex column, if that one is passed of course.
MASS added to depends due to use of fractions() in many places in documnetation.
Added vignette on quantitative genetic (animal) model and model.matrix.Pedigree() functions for educational purposes.
Created data directory and added pedigree example Mrode2.1 and Mrode3.1.
Added unit tests for genetic relationship matrices that should test all related functions - mainly against Mrode’s book examples - runit.genRelMatrix.R.
Added arguments sort and names to inverseAdditive(), relationshipAdditive() and inbreeding().
Reworked core for relationshipAdditive() into vectorized form.
Added geneFlowT(), geneFlowTinv(), geneFlowM() and mendelianSamplingD() functions.

Changes in version 2007-04:

Implemented sort by pedigree information only. # 0.1.3

Changes in version 2007-03-02:

Registration of native routines - src/register.cc.
Added gpi() function. # 0.1.1
Temporarily removed unknown funcs, due to planned move to BioC and change to S4.
All depends are now in gdata –> removing ggmisc.

Changes in version 2006-03-29:

codeUnit to get internal codes for subject and ascendants if factors are used.
Handled unused levels in nlevels.pedigree and summary.pedigree now produces a simple summary
Started to implement checks in check.pedigree and friends
Proper factor handling

Changes in version 2006-03-16:

Playing around with NA/unknown representation - it is very likely that I messed up some things with factors –> subject to changes. # Version 0.1
Initial version # NEWS ends here

GenomicFeatures

Changes in version 1.8:

NEW FEATURES

Added asBED and asGFF methods to convert a TranscriptDb to a GRanges that describes transcript structures according to either the BED or GFF format. This enables passing a TranscriptDb object to rtracklayer::export directly, when targeting GFF/BED.

GenomicRanges

Changes in version 1.8.0:

NEW FEATURES

Add GappedAlignmentPairs class (with accessors first(), last(), left(), right(), seqnames(), strand(), isProperPair()), and readGappedAlignmentPairs() for dealing with paired-end reads. Most of the GappedAlignments functionalities (e.g. coercion to GRangesList, “findOverlaps” and related methods, “coverage”, etc…) work on a GappedAlignmentPairs object.
Add encodeOverlaps,GRangesList,GRangesList,missing and related utilities flipQuery(), selectEncodingWithCompatibleStrand(), isCompatibleWithSplicing(), isCompatibleWithSkippedExons() and extractSkippedExonRanks().
Add ‘order.as.in.query’ arg to grglist() and rglist().
SummarizedExperiment gains direct access to colData columns with $, $<-, [[, and [[<- methods
Add map,GenomicRanges,GRangesList and map,GenomicRanges,GappedAlignments methods. These allow mapping from genome space to transcript space, and genome space to read space, respectively.
Add seqinfo methods (and friends) for RangedData, RangesList, and other IRanges data structures. These use metadata(x)$seqinfo.
Add disjointBins,GenomicRanges.
Add score,GRangesList and score,GenomicRanges (gets the score column like for RangedData).
Add RangedDataList -> GenomicRangesList coercion.
Add RleViewsList -> GRanges coercion.
Add pintersect,GRangesList,GRangesList
Add stack,GenomicRangesList
ignore.strand argument now more uniformly supported on set operations.
Add Ops,GenomicRanges (from rtracklayer).
Add strand,Rle (only logical-Rle is supported).
Add compare,GenomicRanges
Add ‘drop.empty.ranges’ arg (FALSE by default) to low-level cigar utilities cigarToIRanges(), cigarToIRangesListByAlignment(), and cigarToIRangesListByRName().
Add ‘reduce.ranges’ arg to cigarToIRangesListByAlignment().

SIGNIFICANT USER-LEVEL CHANGES

grglist,GappedAlignments now carries over element metadata.
Names are no longer forced to be unique when unlisting a GRangesList with use.names=TRUE.
seqnames() is now preferred over rname() on a GappedAlignments object.
cigarToIRangesListByAlignment() now returns a CompressedIRangesList instead of CompressedNormalIRangesList.
Low-level CIGAR utilities now ignore CIGAR operation P (instead of trowing an error).
The ‘weight’ arg in “coverage” method for GenomicRanges objects now can also be a single string naming a column in elementMetadata(x).
Ranges outside the sequences bounds of the underlying sequences are now accepted (with a warning) in GenomicRanges/GRangesList/GappedAlignments objects.
When called with ‘ignore.strand=TRUE’, the “range” and “disjoin” methods for GenomicRanges objects now behave like if they set the strand of the input to “*” before they do any computation.
When called with ‘ignore.strand=TRUE’, “reduce” method for GenomicRanges objects, and “union”, “intersect” and “setdiff” methods for GRanges objects now set the strand of their arguments to “*” prior to any computation.
No more mangling of the names when combining GRanges objects (“c” method for GRanges objects was trying to return unique names).
Remove isCircularWithKnownLength() generic and methods (nobody knows, uses, or needs this).

BUG FIXES

flank,GRangesList no longer forces ‘use.names’ to TRUE and ‘both’ to FALSE.
range,GenomicRanges was broken when object had no ranges
Fix integer overflow issue that can occur in cigarQNarrow() or cigarQNarrow() when the cigar vector is very long.

genoset

Changes in version 1.4.19:

SIGNIFICANT USER-VISIBLE CHANGES

Minor API change Rarely used (by me) method, orderedChrs, gone. It’s just chrOrder(chrNames(x)) anyway. ‘names’ on GenoSet depricated. chrNames gives universal way to get chromosome names (i.e. names, seqlevels) for GenoSet, RangedData, GRanges.

Changes in version 1.4.10:

SIGNIFICANT USER-VISIBLE CHANGES

segTable for Rle now optionally takes chrIndices table, start and stop from locData for speed. segTable for DataFrame uses this trick. Much faster. About 95% time reduction for a large dataset on a large chip.

Changes in version 1.4.9:

** API Changes ** segTable on a DataFrame of Rle now has a “stack” argument to rbind the resulting list of data.frames of per-sample segments into on giant data.frame. A “Sample” column will be added to separate samples. The list of individual data.frames no longer has an “ID” column. Also, some refactoring to speed up this method.

ggbio

Changes in version 1.1.8:

NEW FEATURES

create lower level API and rewrite higher level API
new geom: geom_alignment, geom_chevron, geom_arch, geom_arrow, geom_arrowrect
redefined geom: geom_rect, geom_segment
new stat: stat_aggregate, stat_coverage, stat_mismatch, stat_gene, stat_table, stat_stepping
redefined stat: stat_identity
new layout: layout_circle, layout_karyogram
tracks function are more smart and with more accessors.
themes provided.
More supported object for autoplot: VCF, ExpressionSet, GenomicRangesList.

SIGNIFICANT USER-LEVEL CHANGES

qplot changed to generic autoplot function.
argument use only “facets”, no alias “facet_gr” or “facet” accepted.
plotMismatchSum will be replaced by stat_mismatch, or autoplot, BamFile.

Notes

new website for ggbio: http://tengfei.github.com/ggbio hosting docs, tutorials and case study
pdf version vignette will not longer supported or just provide a short form.

GOSemSim

Changes in version 1.13.6:

remove dependency of organism annotation packages. <2012-03-09, Fri> User not need to install all these annotation packages for using GOSemSim. User only need to install the specific organism annotation package they want to calculate.
update IC data sets for 1.14 release. <2012-03-30, Fri>

Changes in version 1.13.5:

fixed BibTeX database file .bib. month = , must be month = someMonth, leave it blank will cause texi2dvi failed. <2012-03-01, Thu>

Changes in version 1.13.4:

update vignette. <2012-02-28, Tue>

Changes in version 1.13.3:

bug fixed for multiple annotation. <2012-02-01, Fri>

Changes in version 1.13.2:

update infoContentMethod to make it consistent between DOSE and GOSemSim. <2011-12-31, Sat>

Changes in version 1.13.1:

remove dependency of DOSE
remove Streptomyces coelicolor support, as the genome wide annotation package contributor no longer supports it.

gprege

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

Fixed error that exhaustivePlot gave on profiles with zero data variance. Now it simply ignores such profiles.

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

Initial version in Bioconductor.

GRENITS

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

Corrected ggplot2 (0.9.0) problems

GSVA

Changes in version 1.4:

USER VISIBLE CHANGES

removed the system-requirement dependency from the GNU Scientific Library
added two additional gene-set expression summarization methods: single-sample GSEA from Barbie et al. (Nature, 2009) and a combined Z-score method similar to the one used by Lee et al. (PLos Comp Biol, 2008) via a new ‘method’ argument in the ‘gsva()’ function
added handling of RNA-seq expression data matrices by the GSVA method with a new ‘rnaseq’ argument in the ‘gsva()’ function
added a method with signature(expr=”matrix”, gset.idx.list=”GeneSetCollection”, annotation=”character”) which did not exist before. Now gsva() accepts the following pairs of data structures storing expression data and gene sets: ExpressionSet-GeneSetCollection, ExpressionSet-list, matrix-GeneSetCollection and matrix-list

BUG FIXES

matching of gene IDs from ExpressionSet objects to GeneSetCollection objects now also works with Entrez-based gene IDs in ExpressionSet objects (e.g., when annotation(eset) == “org.Hs.eg.db”) by using GSEABase >= 1.17.4

GWASTools

Changes in version 1.1.9:

anomSegStats checks for SNPs in centromere gaps.
anomStatsPlot has option to plot LRR/BAF individually (for greater flexibility in layout).
Updates to arguments for plot titles in chromIntensityPlot, anomStatsPlot, and pseudoautoIntensityPlot for consistency.
plinkCheck has map.alt argument to override default GenotypeData -> PLINK annotation conversion.

Changes in version 1.1.8:

Updated positions of pseudoautosomal regions.
Added plinkToNcdf to convert PLINK files to NetCDF for use in GWASTools.

Changes in version 1.1.7:

chromIntensityPlot and pseudoautoIntensityPlot have cex=0.5 by default.
chromIntensityPlot colors now match anomStatsPlot colors.
plinkCheck has options to skip checking parents and sex.
plinkCheck sorts alleles by character to avoid phase mismatches.
plinkWrite and plinkCheck print progress messages if verbose=TRUE.

Changes in version 1.1.6:

duplicateDiscordance and duplicateDiscordanceAcrossDatasets use only one pair of scans per subject by default.
duplicateDiscordanceProbability sets small negative values to 0.

Changes in version 1.1.5:

duplicateDiscordance has an option to compute correlation by SNP.
Added scan.exclude argument to plinkCheck.

Changes in version 1.1.4:

Added ncdfSetMissingGenotypes function.
plinkCheck now writes a log file with all mismatches found.
duplicateDiscordance excludes Y chrom SNPs for females.
duplicateDiscordance has an option to consider only pairs involving the minor allele.

Changes in version 1.1.3:

batchChisqTest and batchFisherTest now return n results for n batches even if n=2.
batchFisherTest has return.by.snp=FALSE as default.

Changes in version 1.1.2:

Added LR tests to assocTestRegression.
Bug fix in calculation of mean odds ratio in batchFisherTest.
Bug fix in missingGenotypeByScanChrom for data sets with only one female.

Changes in version 1.1.1:

Added functions plinkWrite and plinkCheck for writing and checking PLINK ped and map files.
Added pcaSnpFilters data set for identifying regions with high PC-SNP correlation.

HTqPCR

Changes in version 1.9:

SIGNIFICANT USER-VISIBLE CHANGES

Altered plotCtCor to plot 1-correlation instead of correlation.
Altered qPCRset object to inherit from eSet. This extends the range of (meta) data that can be included.

NEW FEATURES

qPCRset now contains slots for phenoData, featureData, protocol experiment etc. inherited from eSet.
readCtData has been expanded to include file formats from multiple qPCR detection systems and vendors.

BUG FIXES

htSeqTools

Changes in version 1.1.5:

Added missing documentation

Changes in version 1.1.4:

Fixed bug in cmds for method with empty chromosomes

Changes in version 1.1.3:

Fixed bug in alignPeaks (no longer directly accessing matchMatrix slot of RangesMatchingList object)
Added plotMeanCoverage
Fixed bug in gini for method with no chromosome lengths

Changes in version 1.1.2:

Add methods for objects of class GRanges and GRangesList.
Add set.seed to vignette.
Use pvec instead of mclapply in tabDuplReads and filterDuplReads.
Correct rpkm form enrichedRegions and remove it from enrichedPeaks
Fixed giniCoverage for ranges with low numbers of reads

Changes in version 1.1.1:

Adjusted parallel computing in enrichedPeaks so that it no longer spans an uncontrolled number of child processes when mc.cores>1
Added arguments “labels” and “cex.text” to the plot method for cmdsFit objects.
Added monotonicity contraint to filterDuplReads and fdrEnrichedCounts to ensure that the estimated FDR decreases with the number of repeats
Fixed overflow problem in enrichedChrRegions which occurred for long genomes (e.g. human)
Adjusted behavior of stdPeakLocation so that it is consistent with PeakLocation
Fixed bug in RPKM calculation by enrichedRegions
Added option to compute Spearman correlations in cmds

IRanges

Changes in version 1.14.0:

NEW FEATURES

The map generic and RangesMapping class for mapping ranges between sequences according to some alignment. Some useful methods are implemented in GenomicRanges.
The Hits class has experimental support for basic set operations, including setdiff, union and intersect.
Added a number of data manipulation functions and methods, including mstack, multisplit, rename, unsplit for Vector.
Added compare() generic for generalized range-wise comparison of 2 range-based objects.
Added OverlapEncodings class and encodeOverlaps() generic for dealing with “overlap encodings”.
subsetByOverlaps() should now work again on an RleViews object.
DataFrame now supports storing an array (like a matrix) in a column.
Added as.matrix,DataFrame method.
Added merge,DataTable,DataTable method.
Added disjointBins,RangesList method.
Added ranges,Rle and ranges,RleList methods.
Added which.max,Rle method.
Added drop,AtomicList method.
Added tofactor() wrapper around togroup().
Added coercions from vector to any AtomicList subtype (compressed and uncompressed).
Added AtomicList to Character/Numeric/Logical/Integer/Raw/ComplexList coercions.
Added revElements() for reversing individual elements of a List object.

SIGNIFICANT USER-VISIBLE CHANGES

RangesMatching has been renamed to Hits and extends Vector, so that it supports element metadata and other features.
RangesMatchingList has been renamed to HitsList.
The 2 columns of the matrix returned by the “as.matrix” method for Hits objects are now named queryHits/subjectHits instead of query/subject, for consistency with the queryHits() and subjectHits() getters.
queryLength()/subjectLength() are recommended alternatives to dim,Hits.
breakInChunks() returns a PartitioningByWidth object.
The ‘weight’ arg in “coverage” methods for IRanges, Views and MaskCollection objects now can also be a single string naming a column in elementMetadata(x).
“countOverlaps” methods now propagate the names of the query.

DEPRECATED AND DEFUNCT

matchMatrix,Hits is deprecated.
Moved the following deprecated features to defunct status: - use of as.data.frame() or as( , “data.frame”) on an AtomicList object; - all coercion methods from AtomicList to atomic vectors; - subsetting an IRanges by Ranges; - subsetting a RangesList or RangedData by RangesList.

BUG FIXES

within,RangedData/List now support replacing columns
aggregate() override no longer breaks on . ~ x formulas
”[”, “c”, “rep.int” and “seqselect” methods for Rle objects are now safer and will raise an error if the object to be returned has a length > .Machine$integer.max
Avoid blowing up memory by not expanding ‘logical’ Rle’s into logical vectors internally in “slice” method for RleList objects.

isobar

Changes in version 1.1.3:

better matching of file patterns of peaklist and id in report
tab2xls improvements:
fix when there are cells with preceeding colons - would think they are cell properties
fix row limitation of 65536 - add new worksheet with remaining lines
re-added ibspiked_set2 dataset as the xz requirement allows for additional data

Changes in version 1.1.2:

fixed handling of divergent identifications in one search engine
fixed number of spectra in isobar-analysis report
fixed recently introduced error when reading mgf file
identifications tab in XLS report is now in concise format
shared peptides are colored in gray
added xls report format = wide

Changes in version 1.1.1:

NEW FEATURES

normalization can now be performed on individual channels (and channel pairs)
added semi-quantitative Quantitation with emPAI, dNSAF and spectral count
proteinInfo can now be gathered from Uniprot directly
added reporter intensity plot shpwing effect of normalization
added linear regression as ratio estimator
improved MA plot: added ‘Infinity’ on the axis

KEGGgraph

Changes in version 1.11.1:

SIGNIFICANT USER-VISIBLE CHANGES

The colorectalcancerSPIA dataset has been compressed with R CMD build –resave-data

limma

Changes in version 3.12.0:

read.maimages() with source=”agilent” now reads median foreground estimates instead of mean foreground. New option source= “agilent.mean” preserves earlier meaning of source=”agilent”.
Agilent single-channel case study added to User’s Guide.
removeBatchEffect() now corrects for continuous covariates as well as qualitative factors.
new function camera() performs competitive gene set tests while adjusting for inter-gene correlation.
new function interGeneCorrelation() estimates the average intergene correlation for a set of genes.
columns in output from roast() have been re-ordered.
arguments ‘selected’ and ‘selected2’ renamed to ‘index’ and ‘index2’ in functions barcodeplot(), geneSetTest() and wilcoxGST().
default labels for barcodeplot() are now somewhat more explicit.
new function rankSumTestWithCorrelation extends the Wilcoxon-Mann-Whitney test to allow for correlation between cases in one of the groups. geneSetTest() now calls this function instead of wilcox.test, with a consequence improvement in speed.
The lfc (log-fold-change) cutoff argument of topTable() is now applied to the minimum absolute logFC when ranking by F-statistic. Previously lfc was only used when ranking by t-statistic.
new methods “fast” and “affy” for normalizeCyclicLoess(), with “fast” becoming the default method. New argument ‘cyclic.method’ for normalizeBetweenArrays() gives access to the different cyclic loess methods.
There were problems with using the argument gene.weights in mroast(). This argument is now permitted to be of the same length as the number of probes in the data set. It is then automatically subsetted for each gene set.
mroast() now uses mid-p-values by default when adjusting for multiple testing.
neqc(), nec() and normexp.fit.control() now give user-friendly error messages when no negative control probes or no regular probes are found.

MANOR

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

Updated calls to ‘GLAD:::daglad’ in the vignette to fix an error caused by changes in the defaults of ‘daglad’.

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

Cleaned ‘data/flags.RData” which contained objects from an old ‘globalenv’.
Updated maintainer’s email address.

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

Added (back) ‘intensity.flag’ to ‘data/flags.RData’ (had been removed since v 1.12.0 for an unknown reason).

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

misplaced alignment tab in man/spatial.Rd.

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

updated references in .Rd files.
fixed warnings due to incorrect use of \item in .Rd files.

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

‘norm’ and ‘sort’ are now S3 methods as well

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

(almost) one file per function in R/
removed empty section \details in man/qscore.Rd
added a NAMESPACE
removed inst/doc/Makefile (not needed anymore because no html output required)

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

removed another non-standard keyword

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

only one keyword per \keyword entry…

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

now use standard “keyword”s
changed \link{\code{stuff}} into \code{\link{stuff}}

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

filled in “keyword” sections in .Rd files.
removed empty “examples” sections from .Rd files.
initialized a few variables upon declaration in C code to prevent warnings in R CMD CHECK.

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

modification de la fonction cv pour retourner NA lorsque toutes la valeurs du vecteur sont <e0> NA
modification de la function getChromosomeArm pour que cytoband ne soit pas positionn<e9>e <e0> NULL

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

added a CHANGELOG
updated outdated reference in the .bib file
changed the definition of flag “rep.flag” to avoid the error now caused by sd(NA, na.rm=TRUE)

minfi

Changes in version 1.1:

Changed NAMESPACE file
Defined constructors for MethylSet, RGChannelSet, RGChannelSetExtended.
Included a version number in the class definition for MethylSet and RGChannelSet. Old objects can be updated by calls of the form updateObject(Mset).
read.manifest (not exported) updated to include nCpGs.
preprocessSwan was added. Still work in progress.
Changed background calculation in preprocessSwan.
Added a section to the vignette describing preprocessSwan.
Bug fix: ilogit2 is now in base (it used to be base e). Thanks to Time Triche, Jr tim.triche@gmail.com.
Added and dcoumented the IlluminaMethylationAnnotation class; still work in progess.
Moved package vignette from inst/doc to vignettes.

MinimumDistance

Changes in version 1.0:

USER VISIBLE CHANGES

Using NEWS.Rd

MLP

Changes in version 1.3.0:

update using new annotation packages
move to roxygen2

Changes in version 1.2.1:

also export addGeneSetDescription

mosaics

Changes in version 1.3.4:

SIGNIFICANT USER-VISIBLE CHANGES

Improve help documents for all classes and functions.

BUG FIXES

mosaicsPeak(): Correct bin size calculation when binsize=NA.

Changes in version 1.3.2:

SIGNIFICANT USER-VISIBLE CHANGES

Simplify arguments of mosaicsRunAll(), constructBind(), and export().
Add parallel argument in mosaicsFit().
Extensive use of parallel processing/computing.
Overall speed improvements in the package.
Update the vignette.
Use parallel package instead of multicore package.

Changes in version 1.2.5:

Correct version number in DESCRIPTION and package?mosaics.

Changes in version 1.2.4:

SIGNIFICANT USER-VISIBLE CHANGES

Add parallel argument in readBins().
Add parallel argument in mosaicsRunAll().

BUG FIXES

DESCRIPTION: ‘multicore’ package in ‘Enhances’ instead of ‘Suggests’.

Changes in version 1.2.3:

NEW FEATURES

New model for deeply sequenced ChIP-seq data.
Genome-wide analysis of ChIP-seq data is now available.
Supports more aligned read file formats: eland_result, eland_extended, eland_export, bowtie, SAM, BED, CSEM.
Preprocessing of aligned read files can be done within the R environment using constructBins().
Easier model fitting for the two sample analysis using mosaicsRunAll().
Preprocessing and model fitting become much faster (Rcpp).
Parallel processing/computing is now supported (multicore).

SIGNIFICANT USER-VISIBLE CHANGES

Add constructBins(): Preprocess aligned read files to bin-level files.
Add mosaicsRunAll(): Convenient two sample analysis.
Add bgEst argument in mosaicsFit(): Choose background estimation approach.
Add nCore argument in readBins(): Parallel processing.
Vignettes is now extensively updated.
Rcpp package is required and multicore package is suggested.

DEPRECATED AND DEFUNCT

Drop chrID argument in export().

BUG FIXES

Fix mosaicsPeak() for the case that no peak is called.
Fix export() by removing unnecessary spaces in output text files.

MSnbase

Changes in version 1.3.15:

new updateFeatureNames function <2012-02-17 Fri>
updated vignettes to illustrate vertical/horizontal combine <2012-02-17 Fri>
typo in normalised.Rd <2012-02-19 Sun>
TODO combine unit tests

Changes in version 1.3.14:

new is.na.MSnSet <2012-02-16 Thu>
updated vignette and NA related man pages with cross-links <2012-02-16 Thu>

Changes in version 1.3.13:

new plotNA method + doc <2012-02-15 Wed>
new filterNA method + doc + tests <2012-02-15 Wed>
added a check on ‘n’ in topN <2012-02-16 Thu>
created a .Rinstignore <2012-02-16 Thu>
Update package Rd <2012-02-16 Thu>

Changes in version 1.3.12:

new topN methods + doc + tests <2012-02-14 Tue>

Changes in version 1.3.11:

changed explicit close(file) in writeMgf methods to on.exit(close(file)) <2012-02-12 Sun>
typo in vignette <2012-02-13 Mon>

Changes in version 1.3.10:

type in writeMgfData man <2012-02-07 Tue>
updated TITLE in writeMgfData <2012-02-08 Wed>

Changes in version 1.3.9:

updated demo vignette <2012-02-03 Fri>
sorting numeric subsets in “[” pSet, as unsorted numerical indexes fails <2012-02-03 Fri>
Added match.arg in combineFeatures so that a unique default value (the first) is used when no fun is specified <2012-02-03 Fri>

Changes in version 1.3.8:

Modified trimMz warning to report acquisition number <2012-02-01 Wed>
add ‘experimentData(object, value) <- ‘ method for signature eSet and MIAPE <2012-02-02 Thu>
combine methods for MIAPE instances <2012-02-02 Thu>
combine methods for MSnProcess instances <2012-02-02 Thu>
changed qual drop warning into message in combineFeatures, updated test_MSnSet accordingly <2012-02-02 Thu>
new updateFvarLabels and updateSampleNames function <2012-02-03 Fri>
combine method for MSnSets <2012-02-03 Fri>
Updated demo vignette figure 8 <2012-02-03 Fri>

Changes in version 1.3.7:

Speeded up writeMgfData <2012-01-28 Sat>
fixes for ggplot2 0.9.0
added import(grid) and import(reshape) <2012-01-30 Mon>
importFrom(plyr, …) instead of only llply <2012-01-31 Tue>
loading reshape and grid in vignette <2012-01-31 Tue>
fixed chunk 21 (label = quantitation-plot) <2012-01-31 Tue>

Changes in version 1.3.6:

Updated NoteAboutSpeedAndMemory since parallel processing has been added. <2011-12-18 Sun>
Added CITATION <2012-01-27 Fri>
Added information to header output: acquisition number and precursor intensity <2012-01-27 Fri>
Added a test in plot.Spectrum2 for empty dataframe <2012-01-27 Fri>
moved foreach, doMC to enhances <2012-01-27 Fri>

Changes in version 1.3.5:

added a gc() before mzR::close(msdata)… seems to help with Rcpp and ref classes issue. <2011-12-09 Fri>
added a show parameter to getCacheEnv to define .cache should be printed out before being returned. <2011-12-09 Fri>
added cache unit test <2011-12-09 Fri>
readMzXMLData is now defunct and remove xcms from Imports <2011-12-16 Fri>

Changes in version 1.3.4:

fixed bug in show MSnExp method for MS1 experiments. When loading MS1 spectra, cache is set to 0. Bug reported by Jesse Meyer. <2011-12-06 Tue>
fixed another bug/typo in readMSData <2011-12-06 Tue>
now running extractSprectum example again <2011-12-06 Tue>
setting default cache to 0, as cache=1 introduces unstabel behavious… will investigate that <2011-12-06 Tue>

Changes in version 1.3.3:

added parallel computation for MSnExp quantitation using foreach with llply(…, .parallel=TRUE) <2011-12-03 Sat>
TODO document above in quantify-methods.Rd
added foreach and doMC in Suggests <2011-12-03 Sat>
added Spectrum removePeaks and clean’ing in readMSData <2011-12-05 Mon>

Changes in version 1.3.2:

\dontrun{} extractSpectrum example, as this seems to be a major offender producing the intermittent check ‘Error in function (x) : attempt to apply non-function’ error <2011-11-07 Mon>
typo in Author@R <2011-11-14 Mon>
modified utils.removePeaks and utils.clean to call sapply instead of IRanges:sapply <2011-12-01 Thu>

Changes in version 1.3.1:

Herve added BioGenerics as a dependency and import statement in NAMESPACE <2011-11-29 Tue>

Changes in version 1.3.0:

Version bump for Bioc 2.10 devel

ncdfFlow

Changes in version 1.1.2:

SIGNIFICANT USER-VISIBLE CHANGES

Using temporary directory instead of working directory to store cdf file in creating ncdfFlowSet from flowSet
allow for user specified path in ncdfFlowSet_sync method to save the cdf in different location other than original one
clone.ncdfFlowSet function: - change argument name to avoid confusion:sNewNcFile–>isNew ;newNcFile–>fileName -avoid copying the entire cdf repository when clone subsetted ncdfFlowSet -fix the bug of inconsistent dimensions (sample*colnames) when create the new cdf file
check whether source file exist in read.ncdfFlowSet
.writeSlice: -allow for either flowFrame or matrix to be added by -add sample name to the error message to help troubleshoot the problematic FCS file especially for loading large datasets
add isNew=FALSE to split method to allow for splitting into multipe cdf files for the sake of parallel computing
set compress=FALSE to disable compression mode of CDF

Changes in version 1.1.1:

SIGNIFICANT USER-VISIBLE CHANGES

netCDF support for large data sets.
centralized storage of flow data in 3-D matrix (samplechannelevent)
fast data accessing,subsetting and splitting
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 1.7.38 (2012-03-28):

SIGNIFICANT USER-VISIBLE CHANGES

added the option to ignore network in detect.responses (netw=NULL); then the methods assumes fully connected network. Without speedups the performance may be very slow.
added (optional) initial mutual information based filtering of the network edges also in the first stage where pairwise similarities are calculated for all node pairs This can give considerable speedups with large networks
merged netresponse.visualization package in the netresponse main package
added mode = hard in sample2response function
plot.associations -> plotAssociations
plot.pca -> plotPCA
get.gofz -> getqofz

BUG FIXES

changed dependency RBGL into RColorBrewer
changed dependencies multicore and doMC into parallel
Modified mk.hp.posterior so as to accommodate ‘max number of responses’ (c.max) option. Validations in tests/vdpmixture.R ok
now allowing max.subnet.size = 1 in detect.responses
order.responses: fixed minor bug which occurs when no enrichments are detected

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

changed dependency RBGL into RColorBrewer

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

Modified mk.hp.posterior so as to accommodate ‘max number of responses’ (c.max) option. Validations in tests/vdpmixture.R ok

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

added the option to ignore network in detect.responses (netw=NULL); then the methods assumes fully connected network. Without speedups the performance may be very slow.

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

merged netresponse.visualization package in the netresponse main package

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

switched to R-2.14.1
now allowing max.subnet.size = 1 in detect.responses
order.responses: fixed minor bug which occurs when no enrichments are detected
added mode = hard in sample2response function
added (optional) initial mutual information based filtering of the network edges also in the first stage where pairwise similarities are calculated for all node pairs This can give considerable speedups with large networks
plot.associations -> plotAssociations
plot.pca -> plotPCA
get.gofz -> getqofz

oligo

Changes in version 1.20:

USER VISIBLE CHANGES

New getProbeInfo() function added, to simplify probe selection without using SQL.
New fitProbeLevelModel() function added. It allows probe-level models (‘plm’ and ‘medianpolish’), which can be used for QC.
fitPLM, coefs and resids are now Deprecated. Use fitProbeLevelModel, coef and residuals respectively. ‘coef’ and ‘residuals’ follow the standards used elsewhere in R.
Now using foreach for parallelization.

BUG FIXES

Addressed issue in which probes without chr info would be removed from pmChr, leading to results whose dimensions did not match PM matrix (on TilingFeatureSet).

oneChannelGUI

Changes in version 1.21.11:

SIGNIFICANT USER-VISIBLE CHANGES

adding interface to EDASeq package

pdInfoBuilder

Changes in version 1.20:

USER VISIBLE CHANGES

The annotation packages for Affymetrix Tiling arrays now contain strand information (suggestion and implementation: Kristof De Beuf)

phyloseq

Changes in version 0.99:

Bioconductor development release updates.
BIOM format import: import_biom() function
Parallel Fast UniFrac
distance() wrapper for ecological distance calculations
ordinate() wrapper, calculates many different ordination methods.
plot_ordination() powerful, flexible ordination plotting using ggplot2
make_sample_network(), plot_sample_network() - microbiome network visualization
plot_richness_estimates() for easy, flexible summary of species richness
Support for Double Principle Coordinate Analysis (DPCoA)
Several published exampled datasets included
General importer for all supported data formats: import()
Lots of documentation updates.
Lots and lots of fixes and improvements.

pint

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

fixed missing documentations

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

added remove.duplicates option to pint.match

procoil

Changes in version 1.5.1:

made arguments xlab and ylab accessible to users

qpgraph

Changes in version 1.12:

NEW FEATURES

Results of conditional independence tests with qpCItest() are now returned using the R standard htest class
qpCItest() allows one to test mixed interactions involving phenotypic data variables and expression profiles in ExpressionSet objects, and phenotypic/genetic variables and expression profiles in smlSet objects
qpEdgeNrr() estimates the non-rejection rate involving phenotypic data variables and expression profiles in ExpressionSet objects, and phenotypic/genetic variables and expression profiles in smlSet objects

QUALIFIER

Changes in version 1.0.0:

FEATURES

outlier detection for different population stats(counts,proportion,MFI,Spike) of gated/ungated flow data
xyplot and boxplot on different dimensions
scatter plot for gated population
HTML report with svg support
fuzzy match of population name to select the same population from the different gating path

KNOWN ISSUES

extracting populations stats needs further optimization on speed
extend the formula parser to allow more functions to be applied by formula

R453Plus1Toolbox

Changes in version 1.5.2:

Added new graphical components, options and annotations to the plotVariants function.

RCytoscape

Changes in version 1.6.0:

NEW FEATURES

setNodeOpacityRule, controlling node fill color, border and/or label; interpolate & lookup modes both supported
getNodeSize
saveImage now supports pdf as well as png and svg formats
setDefaultEdgeFontSize
getAdjacentEdgeNames

SIGNIFICANT USER-VISIBLE CHANGES

changed method names: layout -> layoutNetwork, version -> pluginVersion, get/setPosition -> get/setNodePosition
NAMESPACE now imports four more methods from the graph package, helpful for package developers using RCytoscape: edgemode, addNode, addEdge, requested by Robert Flight.

BUG FIXES

Changed getNodePosition node.name.delimiter to eliminate regex token, from ‘:.:’ to ‘:-:’ saveLayout now has optional 3rd parameter, ‘timestamp.in.filename’
Fixed bug in setNodeLabelDirect. Multiple nodes, one label now works.
setCenter now casts x,y to numeric before sending out to CyRPC

ReactomePA

Changes in version 0.99.0:

change package name to ReactomePA, for there is already an RPA package. <2012-03-02, Fri>
Vignette issues: <2012-03-02, Fri> change image format from .eps to .pdf, make it easier to build. remove the tolatex tag of sessionInfo(), make the output more readble.
re-implement geneID2Name using select method. <2012-03-02, Fri>
add examples in man pages. <2012-03-02, Fri>
remove man pages of internal functions. <2012-03-02, Fri>
import plot summary from stats4, for BiocGenerics (version 0.1.10) removed them <2012-03-03, Sat>

Changes in version 0.2.3:

@exportMethod plot <2012-02-15 Wed>
fix bug when calling summary method from plot, for summary defined in base is S3 method, instead import summary generic from stats4 <2012-02-15 Wed>

Changes in version 0.2.2:

remove generic definition of show, summary and plot, add NAMESPACE import show from methods and plot from graphics. summary need not to import, for is defined in the base package <2012-02-10 Fri>

Changes in version 0.2.1:

update vignette <2012-02-09 Thu>
add sample data (an example list of genes from ProfCom: http://webclu.bio.wzw.tum.de/profcom/gene_Lists/example1.txt the gene symbols were converted to entrezgene) <2012-02-09 Thu>

Changes in version 0.2.0:

separate codes of mapping pathway ID to pathway Name to a new function pathID2Name <2012-02-09 Thu>
implement geneID2Name function for mapping gene ID to gene Symbol <2012-02-09 Thu>
add parameter readable in function enrichPathway <2012-02-09 Thu>
implement cnetplot for plotting category net <2012-02-09 Thu>
modify plot function for class enrichPathwayResult to use cnetplot <2012-02-09 Thu>

Changes in version 0.1.1:

add vignette <2012-02-08 Wed>
bug fixed for multiple mapping of pathway ID to pathway Name such as pathway 162906 can mapping to 1629061 and 1629062 when getting pathway name, remain the first one. <2012-02-08 Wed>

Changes in version 0.1.0:

implement show, summary and plot method for enrichPathwayResult class <2012-02-08 Wed>
define class enrichPathwayResult to store result of enrichPathway <2012-02-08 Wed>
implement enrichPathway function for enrichment analysis. using hypergeometric model <2012-02-08 Wed>
initial package skeleton <2012-02-08 Wed>

RedeR

Changes in version 1.1.16:

NEW FEATURES

Loading performance, xml serialization, data packing and post formats.
Server/client connection.
Control over the app main features from R.
Node-container assignment options.

BUG FIXES

Correction/fine-tune of dynamic layout function under zoom-in/zoom-out requests.
Merge out-edge function is fixed to rescale with node size.
Legend function is fixed for node/edge shape attributes.
Legend color is fixed for two-palette option.
The method ‘addGraph’ is fixed to load/convert directed graphs from igraph to RedeR.

ReQON

Changes in version 1.2.0:

NEW FEATURES

Output BAM file keeps input header and adds header line: “@CO Quality scores were recalibrated with ReQON.”
Allow threshold options (nerr and nrf) to remove positions from the training set that are likely to contain incorrect error calls. (e.g., novel variants and systematic mapping errors)
diagnostic output now outputs flagged read positions ($FlagPos) and regression coefficients ($coeff)

RPA

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

modifications to accommodate single-probe probesets without errors
sigma2.method default to “robust” in functions RPA.sigma2.update and rpa.fit
changed defaults in set.alpha function
added missing data imputation in rpa.fit

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

removed cind option from update.hyperparameters in RPA.online

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

online functions work properly

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 1.1-3 (2012-01-05):

Minor bug fix in readBiclusterResults: bicluster files without any bicluster are recognized
Minor bug fix in readBiclusterResults: bicluster files with only one bicluster and one row/column not report error anymore (previously due to matrix dropping)
Minor bug fix in readBiclusterResults: feature/condition names are written in “features”/”conditions” items in the info list
Feature improvement in readBiclusterResults: featureNames and sampleNames are written in Parameters, so as to be used by the coerce method in the eisa package, to coerce a Biclust object into an ISAModules object
Methods features and conditions now have a two-step strategy: first try the info list, if failed, then try the matrix names
length.Biclust returns 0 if the Biclust object contains no bicluster
combineBiclusts support non-empty Biclust objects with empty Biclust objects, e.g. those without valid biclusters detected.

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

Add fcFilter for feature-condition filtering

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

Generalize S4 methods for QUBICBiclusterSet to Biclust: most of the S4 methods now can be applied to a Biclust object.
Add the combineBiclusts method to combine multiple Biclust/QUBICBiclusterSet objects.
Add readBiclusterResults function to complement the writeBiclusterResults function in the biclust package.

Rsamtools

Changes in version 1.8.0:

NEW FEATURES

Add readBamGappedAlignmentPairs() (plus related utilities findMateAlignment() and makeGappedAlignmentPairs()) to read a BAM file into a GappedAlignmentPairs object.

SIGNIFICANT USER-VISIBLE CHANGES

update samtools to github commit dc27682f70713a70d4f31bca652cf78e00757da2
Add ‘bitnames’ arg to bamFlagAsBitMatrix() utility.
By default readBamGappedAlignments() and readBamGappedReads() don’t drop PCR or optical duplicates anymore.

BUG FIXES

readBamGappedAlignments handles empty ‘tag’ fields
scanTabix would omit variants overlapping range ends
scanFa would segfault on empty files or empty ids

Rsubread

Changes in version 1.6.0:

NEW FEATURES

Significant improvement on the exon-exon junction detection (subjunc function).
Calling SNPs using a simple allele fraction approach (callSNPs function) .
Removing duplicated reads (removeDupReads 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.

rtracklayer

Changes in version 1.15:

NEW FEATURES

Integrated with tabix via Rsamtools. BED and GFF export methods now generate a tabix index, if index=TRUE. Most import() methods gain a ‘which’ argument that takes advantage of tabix, when available.
Added wigToBigWig() function for efficient conversion of WIG to BigWig.
Added SeqinfoForBSGenome() and SeqinfoForUCSCGenome() for conveniently retrieving Seqinfo objects for a given genome.
Added support for FASTA import/export via Biostrings.
GTF and GVF files are now parsed as GFF.

SIGNIFICANT USER-VISIBLE CHANGES

The import/export API is now based on RTLFile objects, which wrap a file path, URL or connection. There is an RTLFile subclass for every file format. This makes it easier to extend rtracklayer (export, import) with new file types. The existing API is still supported (and even encouraged for most uses).
Handle CSV attributes in GFF3 using CharacterList columns.
BED columns thickStart/thickEnd translate to an IRanges column named “thick”. The blockStarts/Sizes/Count columns now map to a single RangesList “blocks” column.

BUG FIXES

Numerous fixes in the import/export methods, as a result of implementing a full unit test suite. If something was not working for you in the past, please try again.
Compression and connections should now work fairly uniformly across file types. (start date: 29 March, 2012)

ShortRead

Changes in version 1.13:

SIGNIFICANT USER-VISIBLE CHANGES

FastqSampler is considerably faster
FastqSampler and FastqStreamer require explicit close() to avoid warnings about closing unused connections

BUG FIXES

qa reports on very large lanes would overflow alphabetFrequency
qa report scales adapaterContamination correctly
FastqSampler would rarely sample fewer than requested reads
FastqSampler supports outputs of >2^31 - 1 total nucleotides
readFastq parses records with 0 width

TargetSearch

Changes in version 1.12.0:

SIGNIFICANT USER-VISIBLE CHANGES

New binary file format for the peak-list files, a.k.a. RI files. This speeds up metabolite searches by 5-10 fold. The old TEXT format is kept for compatibility. See method ‘fileFormat’. Also see ‘bin2text’ and ‘text2bin’ funtions.
New plot peak function ‘plotPeak’. The old function was renamed as plotPeakSimple. The function show also the regions in which the searches were performed to provide better quality controls.

BUG FIXES

Changed to check.names=TRUE in ‘read.delim’ call in functions TargetSearchGUI() and ImportLibrary(). This prevents empty column names that might produce errors in downstream functions.

VariantAnnotation

Changes in version 1.2.0:

NEW FEATURES

readVcf() has genome argument, can be subset on ranges or VCF elements with ScanVcfParam()
scanVcfHeader() returns VCFHeader class with accessors fixed, info, geno, etc.
writeVcf() writes out a VCF file from a VCF class
locateVariants() - returns GRanges instead of DataFrame - output includes txID, geneID and cdsID - has cache argument for repeated calls over multiple vcf files
predictCoding() - returns GRanges instead of DataFrame - output includes txID, geneID, cdsID, cDNA-based, cds-based and protein-based coordinates

xps

Changes in version 2.15.0:

VERSION xps-1.15.2

move to ROOT version 5.32/01, update README

VERSION xps-1.15.1

update zzz.R

Changes in version 2.14.0:

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

Changes in version 2.13.0:

VERSION xps-1.11.12

update functions: plotBoxplot(), plotAffyRNAdeg()

VERSION xps-1.11.11

update functions: plotImage(), plotAffyRNAdeg()

VERSION xps-1.11.10

add functions: plotImage(), plotBoxplot()
update methods image()

VERSION xps-1.11.9

add method: pcaplot()
update method plotAffyRNAdeg()

VERSION xps-1.11.8

add methods: corplot(), madplot()

VERSION xps-1.11.7

update method plotAffyRNAdeg()

VERSION xps-1.11.6

add methods for RNA degradation plots: xpsRNAdeg(), plotAffyRNAdeg()
add man pages

VERSION xps-1.11.5

correct minor bug in XPSProcessing.cxx: ExportExprTreeInfo()
update method image()
add man pages

VERSION xps-1.11.4

add new class QualTreeSet to add quality control features
add functions qualify() and fitQC() and derived functions
add method image() for residual plots of IVT, Gene ST, Exon ST and plate arrays
add new plots coiplot() and borderplot()
update boxplot(), callplot(), image() to be independent of slot ‘data’

VERSION xps-1.11.3

add function trma()

VERSION xps-1.11.1

update DESCRIPTION to correct SystemRequirements to root_v5.27.04
update function READ_WSTRING() to handle big endian for PPC

Changes in version 2.12.0:

VERSION xps-1.9.9

update method XExonChip::ProbesetLevel() for whole genome annotation na31 files

VERSION xps-1.9.8

revert update of Makefile.win

VERSION xps-1.9.7

update Makefile.win to clean xpsLinkDef.h
update script4schemes.R for annotation na31 (updated release)

VERSION xps-1.9.6

update information files for new ROOT Version 5.27/04 (root_v5.27/04)
update script4xps.R, script4schemes.R for annotation na31

VERSION xps-1.9.5

update import.data to use make.names(celnames) to protect against certain characters

VERSION xps-1.9.4

update root.profile.R, macroDrawProfilePlot.C to allow selecting subset of trees
in read.table() set stringsAsFactors=FALSE

VERSION xps-1.9.3

update method XPreFilter::Calculate() to handle exon arrays correctly

VERSION xps-1.9.2

update Makefile and Makefile.arch

VERSION xps-1.9.1

add support in XPSAnalysis.cxx to export exon array probeset annotations (filters)

Changes in version 2.11.0:

VERSION xps-1.7.9

update method validData() to handle slot data containing different column types
update methods seExprTreeSet(), rleplot(), mvaplot(), nuseplot()

VERSION xps-1.7.8

add method xpsFIRMA()
add functions firma(), firma.expr(), firma.score()

VERSION xps-1.7.7

update bgcorrect.R to warn from using tmpdir resulting in empty root file
update normalize.R to warn from using tmpdir resulting in empty root file

VERSION xps-1.7.6

minor change to allow computation with g++ 4.4.x

VERSION xps-1.7.4

add NEWS

VERSION xps-1.7.3

add ExprTreeSet methods validSE(), nuseplot(), rleplot()
allow to export layout trees for incomplete *.CLF files
update examples/updateAnnotation.R

VERSION xps-1.7.2

add examples/updateAnnotation.R
update script4xps.R

VERSION xps-1.7.1

allow using mas5() and mas5.call() with plate arrays w/o MMs
update script4xps.R

Changes in version 2.10.0:

VERSION xps-1.5.19

update script4xps.R

VERSION xps-1.5.18

add parameter bgcorrect.option to function mas5.call()

VERSION xps-1.5.17

update README

VERSION xps-1.5.16

allow handling of probesets w/o MMs on Citrus.CDF

VERSION xps-1.5.15

validBgrd() implement ‘which’
add vignette xpsPreprocess.pdf
add example/macro4xpsPreprocess.R

VERSION xps-1.5.14

update export() to include read.table(..,comment.char=’’)
update methods.DataTreeSet.R to allow probe-level lowess and supsmu normalization

VERSION xps-1.5.13

update express() to allow setting bufsize for tree baskets

VERSION xps-1.5.12

changes to allow import of miRNA-1_0.CDF

VERSION xps-1.5.9

update validOption() to allow ‘separate:none’

VERSION xps-1.5.8

update rma() to allow improved ties handling as option like preprocessCore

VERSION xps-1.5.7

update method validCall()
add methods validExpr() and validPVal()
update vignette APTvsXPS.pdf
update examples script4xps2apt.R and script4bestmatch.R

VERSION xps-1.5.4

update function exonLevel() to use affx=c(4,8,16,32)
update function dataDataTreeSet() to return correct ids for mask
add new internal function exonLevelIDs()

VERSION xps-1.5.3

update help file exonLevel.Rd

VERSION xps-1.5.1

update validData() to check for duplicate rownames
allow reading of genetitan plate data

Changes in version 2.9.0:

VERSION xps-1.3.13

update DESCRIPTION to mention root version
update README

VERSION xps-1.3.12

correct bug in implementation of FDR and Hochberg

VERSION xps-1.3.11

make function exonLevel public and add exonLevel.Rd

VERSION xps-1.3.8

update all initialize methods to prevent checkS3forClass warnings
update bgcorrect.rma, bgcorrect.mas5
update script4xps.R, script4exon.R

VERSION xps-1.3.6

support using genome array as exon arrays

VERSION xps-1.3.5

add code in function import.data() to replace dots, colons in celnames with underscores

VERSION xps-1.3.4

correct bug in xpsPreprocess for add.data=FALSE
correct sub(.root, .txt, x) to sub(.root, .txt, x)
update root.image() to get setname from setName()

VERSION xps-1.3.3

change intensity<- to allow using slot data for further processing

VERSION xps-1.3.1

add function root.merge.data()

Changes in version 2.8.0:

VERSION xps-1.1.9

protect class XRMABackground against defect Affy chips, e.g. zero division
protect root.data() etc against duplicate celnames or treenames

VERSION xps-1.1.8

correct bug in class XINICall resulting in buffer overflow

VERSION xps-1.1.7

add call method I/NI-call (Talloen et al)

VERSION xps-1.1.6

prevent import of CEL-files with zero max intensity
update functions returning ExprTreeSet to import results as option only
update functions returning CallTreeSet to import results as option only
update root.density etc to allow saving from R function
add root.profile to use root graphics for boxplots
add summarization method FARMS (Hochreiter et al)
add summarization method DFW (Chen et al)
update vignette xps.pdf

VERSION xps-1.1.5

correct problem in validData for CEL-files starting with numbers

VERSION xps-1.1.4

update vignette xps.pdf
add new vignette APTvsXPS.pdf
update examples script4exon.R
add examples script4xps2apt.R and script4bestmatch.R
update README

VERSION xps-1.1.3

to allow CEL-names starting with a number, update to read.table(…, check.names=FALSE)
update ExprTreeSet to set slot exprtype to correct type
add functions root.expr() and root.call()
need to change setname for dabg.call() from CallTreeSet to CallSet as for mas5.call()

VERSION xps-1.1.2

allow different exonlevels for bgrd, normalization, summarization
update replacement methods exprs, pvalData, presCall to allow subsetting
add function metaProbesets to compute metacoreList.mps for apt

VERSION xps-1.1.1

increase maximum root file size from 2GB to 2TB
decrease computation time
correct bug preventing export of exon probeset normalized data

Changes in version 2.7.0:

VERSION xps-0.99.11

correct bug resulting in empty exon probeset column

VERSION xps-0.99.10

update source code to handle tmpdir correctly on WinXP
update examples script4xps.R and script4exon.R

VERSION xps-0.99.9

update methods namePart, extenPart, validData, validBgrd to handle names with underscores

VERSION xps-0.99.8

update functions root.xxx to work with WinXP

VERSION xps-0.99.3

package can now be built for Windows XP
added possibility to add current date and/or time to root filename
added function existsROOTFile
updated vignette xps.Snw

VERSION xps-0.4.3

new method rawCELName() to get the names of the imported CEL-files

VERSION xps-0.4.2

add support to import generic (calvin) CEL-files
update method volcanoplot

VERSION xps-0.4.1

change DESCRIPTION
add method volcanoplot
correct update bug in xpsUniFilter

VERSION xps-0.4.0

import.data: import CEL-files from different directories
update DESCRIPTION, NAMESPACE
add possibility to apply non-sepcific filters and univariate filters
add S4 classes Filter, PreFilter, UniFilter
add S4 classes FilterTreeSet and AnalysisTreeSet

yaqcaffy

Changes in version 1.15.1:

remove url from DESCRIPTION <2011-12-23 Fri>

Packages removed from the release

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

Contents

Getting Started with Bioconductor 2.10

New Software Packages

NEWS from new and existing packages

a4Base

ADaCGH2

affxparser

aroma.light

ArrayExpressHTS

biovizBase

CAMERA

categoryCompare

cellGrowth

clusterProfiler

CNAnorm

codelink

cqn

cummeRbund

deepSNV

DESeq

DEXSeq

DiffBind

DOSE

easyRNASeq

EDASeq

edgeR

ExiMiR

exomeCopy

flowCore

GeneGroupAnalysis

GeneticsPed

GenomicFeatures

GenomicRanges

genoset

ggbio

GOSemSim

gprege

GRENITS

GSVA

GWASTools

HTqPCR

htSeqTools

IRanges

isobar

KEGGgraph

limma

MANOR

minfi

MinimumDistance

MLP

mosaics

MSnbase

ncdfFlow

netresponse

oligo

oneChannelGUI

pdInfoBuilder

phyloseq

pint

procoil

qpgraph

QUALIFIER

R453Plus1Toolbox

RCytoscape

ReactomePA

RedeR

ReQON

RPA

rqubic

Rsamtools

Rsubread

RTCA

rtracklayer

ShortRead

TargetSearch

VariantAnnotation

xps

yaqcaffy

Packages removed from the release