October 3, 2012

Bioconductors:

We are pleased to announce Bioconductor 2.11, consisting of 610 software packages and more than 650 up-to-date annotation packages. There are 58 new software packages, and many updates and improvements to existing packages; Bioconductor 2.11 is compatible with R 2.15.1, and is supported on Linux, 32- and 64-bit Windows, and Mac OS. This release includes an updated Bioconductor Amazon Machine Image. Visit http://bioconductor.org for details and downloads.

Contents

• Getting Started with Bioconductor 2.11
• New Software Packages
• NEWS from new and existing packages
• Packages removed from the release

Getting Started with Bioconductor 2.11

To install Bioconductor 2.11:

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

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

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

   source(“http://bioconductor.org/biocLite.R”)

   biocLite(“BiocUpgrade”)

New Software Packages

There are 58 new packages in this release of Bioconductor.

• agilp: provides a pipeline for the low-level analysis of gene expression microarray data, primarily Agilent data

• annmap: annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl.

• AnnotationForge: Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

• bigmemoryExtras: This package defines a “BigMatrix” ReferenceClass which adds safety and convenience features to the filebacked.big.matrix class from the bigmemory package. BigMatrix protects against segfaults by monitoring and gracefully restoring the connection to on-disk data and it also protects against accidental data modification with a filesystem-based permissions system. We provide utilities for using BigMatrix-derived classes as assayData matrices within the Biobase package’s eSet family of classes. BigMatrix provides some optimizations related to attaching to, and indexing into, file-backed matrices with dimnames. Additionally, the package provides a “BigMatrixFactor” class, a file-backed matrix with factor properties.

• bsseq: Tools for analyzing and visualizing bisulfite sequencing data

• cancerclass: The classification protocol starts with a feature selection step and continues with nearest-centroid classification. The accurarcy of the predictor can be evaluated using training and test set validation, leave-one-out cross-validation or in a multiple random validation protocol. Methods for calculation and visualization of continuous prediction scores allow to balance sensitivity and specificity and define a cutoff value according to clinical requirements.

• ChIPXpress: ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.

• chroGPS: We provide intuitive maps to visualize the association between genetic elements, with emphasis on epigenetics. The approach is based on Multi-Dimensional Scaling. We provide several sensible distance metrics, and adjustment procedures to remove systematic biases typically observed when merging data obtained under different technologies or genetic backgrounds.

• CNORdt: This add-on to the package CellNOptR handles time-course data, as opposed to steady state data in CellNOptR. It scales the simulation step to allow comparison and model fitting for time-course data. Future versions will optimize delays and strengths for each edge.

• CNORfuzzy: This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL).

• CNORode: ODE add-on to CellNOptR

• CorMut: CorMut provides functions for computing kaks for individual sites or specific amino acids and detecting correlated mutations among them. Two methods are provided for detecting correlated mutations ,including conditional selection pressure and mutual information. The computation consists of two steps: First, the positive selection sites are detected; Second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.

• DBChIP: DBChIP detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples.

• ddgraph: Distinguish direct from indirect interactions in gene regulation and infer combinatorial code from highly correlated variables such as transcription factor binding profiles. The package implements the Neighbourhood Consistent PC algorithm (NCPC) and draws Direct Dependence Graphs to represent dependence structure around a target variable. The package also provides a unified interface to other Graphical Modelling (Bayesian Network) packages for distinguishing direct and indirect interactions.

• DeconRNASeq: DeconSeq is an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.

• DirichletMultinomial: Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.

• DSS: DSS is an R library performing the differential expression analysis for RNA-seq count data. DSS implements a new dispersion shrinkage method to estimate the gene-specific biological variance. Extensive simulation results showed that DSS performs favorabily compared to DESeq and edgeR when the variation of biological variances is large.

• EasyqpcR: This package is based on the qBase algorithms published by Hellemans et al. in 2007. The EasyqpcR package allows you to import easily qPCR data files as described in the vignette. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors. This package has been created for low-throughput qPCR data analysis.

• flowPeaks: A fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

• flowQB: flowQB is a fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B), and electronic noise.

• fmcsR: The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.

• FunciSNP: FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions.

• gCMAP: The gCMAP package provides a toolkit for comparing differential gene expression profiles through gene set enrichment analysis. Starting from normalized microarray or RNA-seq gene expression values (stored in lists of ExpressionSet and CountDataSet objects) the package performs differential expression analysis using the limma or DESeq packages. Supplying a simple list of gene identifiers, global differential expression profiles or data from complete experiments as input, users can use a unified set of several well-known gene set enrichment analysis methods to retrieve experiments with similar changes in gene expression. To take into account the directionality of gene expression changes, gCMAPQuery introduces the SignedGeneSet class, directly extending GeneSet from the GSEABase package. To increase performance of large queries, multiple gene sets are stored as sparse incidence matrices within CMAPCollection eSets. gCMAP offers implementations of 1. Fisher’s exact test (Fisher, J R Stat Soc, 1922) 2. The “connectivity map” method (Lamb et al, Science, 2006) 3. Parametric and non-parametric t-statistic summaries (Jiang & Gentleman, Bioinformatics, 2007) and
  1. Wilcoxon / Mann-Whitney rank sum statistics (Wilcoxon, Biometrics Bulletin, 1945) as well as wrappers for the 5. camera (Wu & Smyth, Nucleic Acid Res, 2012) 6. mroast and romer (Wu et al, Bioinformatics, 2010) functions from the limma package. All methods return CMAPResult objects, an S4 class inheriting from AnnotatedDataFrame, containing enrichment statistics as well as annotation data and providing simple high-level summary plots.

• GeneNetworkBuilder: Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.

• gmapR: GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.

• hapFabia: A package to identify rare and short haplotype clusters in large sequencing data by FABIA biclustering. Individuals that inherited a particular DNA segment from the same founder constitute a haplotype cluster by sharing minor alleles of single nucleotide variants (SNVs) that tag/mark this segment. Knowledge of haplotype clusters are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.

• HMMcopy: Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.

• hpar: A simple interface to and data from the Human Protein Atlas project.

• HTSeqGenie: A software package to analyse high-throughput sequencing experiments

• iPAC: iPAC is a novel tool to identify somatic amino acid mutation clustering within proteins while taking into account protein structure.

• KEGGprofile: KEGGprofile is an annotation and visualization tool which integrated the expression profiles and the function annotation in KEGG pathway maps. The multi-types and multi-groups expression data can be visualized in one pathway map. KEGGprofile facilitated more detailed analysis about the specific function changes inner pathway or temporal correlations in different genes and samples.

• lmdme: linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i) Flexible formula type interface, ii) Fast limma based implementation, iii) p and F values over deflacted coefficients and iv) ploting functions for PCA and PLS

• matchBox: The matchBox package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing statistical significance.

• methyAnalysis: The methyAnalysis package aims for the DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focus on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data.

• MiRaGE: The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile.

• MotifDb: More than 2000 annotated position frequency matrices from five public source, for multiple organisms

• motifStack: motifStack is a package that is able to draw amino acid sequence as easy as to draw DNA/RNA sequence. motifStack provides the flexibility for users to select the font type and symbol colors. motifStack is designed for graphical representation of multiple motifs.

• networkBMA: An extension of Bayesian Model Averaging (BMA) for network construction using time series gene expression data. Includes assessment functions and sample test data.

• NOISeq: Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions.

• OrganismDbi: The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

• OSAT: A sizable genomics study such as microarray often involves the use of multiple batches (groups) of experiment due to practical complication. To minimize batch effects, a careful experiment design should ensure the even distribution of biological groups and confounding factors across batches. OSAT (Optimal Sample Assignment Tool) is developed to facilitate the allocation of collected samples to different batches. With minimum steps, it produces setup that optimizes the even distribution of samples in groups of biological interest into different batches, reducing the confounding or correlation between batches and the biological variables of interest. It can also optimize the even distribution of confounding factors across batches. Our tool can handle challenging instances where incomplete and unbalanced sample collections are involved as well as ideal balanced RCBD. OSAT provides a number of predefined layout for some of the most commonly used genomics platform.

• PADOG: This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package.

• PWMEnrich: Asses the enrichment of already known PWMs (e.g. from JASPAR) in DNA sequences. Motif hits in a sequence or DNA region are considered together and P-values derived for their joint pattern. The package implements multiple algorithms, including fixed-threshold (Z-score) and threshold-free (Lognormal normalization and Clover) methods. The main goal is to identify a set of transcription factors that most likely bind to a single sequence, group of sequences, or show significantly different binding affinity between two sets of sequences.

• Rcade: Rcade (which stands for “R-based analysis of ChIP-seq And Differential Expression”) is a tool for integrating ChIP-seq data with differential expression summary data, through a Bayesian framework. A key application is in identifing the genes targeted by a transcription factor of interest - that is, we collect genes that are associated with a ChIP-seq peak, and differential expression under some perturbation related to that TF.

• ReportingTools: The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser.

• RGalaxy: Given an R function and its manual page, make the documented function available in Galaxy.

• Risa: The Investigation / Study / Assay (ISA) tab-delimited format is a general purpose framework with which to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) from experiments employing a combination of technologies, spanning from traditional approaches to high-throughput techniques. Risa allows to access metadata/data in ISA-Tab format and build Bioconductor data structures. Currently, data generated from microarray, flow cytometry and metabolomics-based (i.e. mass spectrometry) assays are supported. The package is extendable and efforts are undergoing to support metadata associated to proteomics assays.

• RMassBank: Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

• rols: This package allows to query EBI’s Ontology Lookup Service (OLS) using Simple Object Access Protocol (SOAP).

• rSFFreader: rSFFreader reads sequence, qualities and clip point values from sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers. The plan is to also write out sff files and to read in flowgrams with some utils

• SCAN.UPC: SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. (The Universal Probability of expression Codes (UPC) method is an extension of SCAN and will be added to this package soon.)

• staRank: Detecting all relevant variables from a data set is challenging, especially when only few samples are available and data is noisy. Stability ranking provides improved variable rankings of increased robustness using resampling or subsampling.

• synapter: The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.

• TransView: This package provides efficient tools to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.

• triform: The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.

• VariantTools: Tools for Tools for detecting, filtering, calling, comparing and plotting variants.

• waveTiling: This package is designed to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.

NEWS from new and existing packages

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

a4Base

Changes in version 1.4.1:

• plot1gene now coerces the ‘groups’ variable to a factor in plot1gene

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 1.29.13 (2012-09-26):

• Added argument ‘cdf=FALSE’ to createCel(). Note, the previous implementation corresponded to cdf=TRUE.

• ROBUSTNESS: Now createCel() validates/sets CEL header field ‘total’ based on ‘cols’ and ‘rows’.

• ROBUSTNESS: Added a system test for validating that the package can write and read a CEL. The test is spawning of another R process so that the test is robust against core dumps.

• Bumped up package dependencies.

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

• DOCUMENTATION: Updated one Rd link.

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

• Added argument ‘aliases’ to arrangeCelFilesByChipType(), e.g. arrangeCelFilesByChipType(…, aliases=c(“Focus”=”HG-Focus”)).

• BUG FIX: arrangeCelFilesByChipType(pathnames) assumed ‘pathnames’ were files in the current directory.

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

• Updated some internal files used solely for maintainance.

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

• BUG FIX: The move to Fusion SDK 1.1.2 caused the package to not compile on Windows.

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

• Upgraded to Fusion SDK 1.1.2.

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

• Rearranged patchdir.

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

• Same updates as in v1.28.1.

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

• Added arrangeCelFilesByChipType() for moving CEL files to subdirectories named according to their chip types, which can be useful when for instance downloading GEO data sets.

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

• readPgfEnv(…, indices=NULL) no longer gives a warning.

• Updated the error messages for the CLF and PGF parsers.

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

• Now system test tests/testWriteAndReadEmptyCdf.R generates an error that is detected and reported by R CMD check.

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

• GENERALIZATION: Now system tests that launch another R process no longer assumes R is on the OS’s search path.

• ROBUSTNESS/CRAN POLICY: readCel() and readCelUnits() are no longer calling .Internal(qsort(…)).

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

• Replaced several throw() with stop(), because the former assumes that R.methodsS3 is loaded, which it may not be.

• ROBUSTNESS: Added a system test for validating that the package can write and read a CDF. The test is spawning of another R process so that the test is robust against core dumps.

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

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

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

• COMPATIBILITY: Now package compile also with gcc/g++ 4.7. Thanks Dan Tenenbaum at the Bioconductor Core Team), Fred Hutchinson Cancer Research Center, USA for this.

affyPara

Changes in version 1.17.1:

• bugfix for cdfname object in read.affypara, see BioC Mailinglist, thanks Tobias

annmap

Changes in version 0.99.3:

• BUG ANNMAP-110 XXXInRange( NULL ) used to throw an error. It now returns NULL.

• BUG ANNMAP-111 Fix crash when translation data is incorrect and causes us to fall off the translation exon when finding the UTR/Coding range.

Changes in version 0.99.2:

• BUG ANNMAP-109 geneToSymbol when passed a vector of gene IDs, returned the symbols in the order of the genes start location rather than the order the function was called with.

Changes in version 0.99.1:

• BUG ANNMAP-101 ngsBridgePlot called with no genes in range had a huge border.

• BUG ANNMAP-106 Empty ngsBridgePlot trace should draw line at 0.

• BUG ANNMAP-107 transcriptToCodingRange was very slow.

Changes in version 0.99.0:

• NEW Initial Release to Bioconductor

• BUG ANNMAP-98 A call to transcriptToTranslatedprobes for transcripts in HPRT1 caused a crash

Changes in version 0.9.16:

• BUG ANNMAP-97 geneToExonProbeset threw an error when as.vector=TRUE

Changes in version 0.9.15:

• NEW ANNMAP-94 Added annmapAddConnection method for setting up databases.

Changes in version 0.9.14:

• NEW ANNMAP-90 Added generateBridgeData method for helping with BAM file imports.

• IMPROVED ANNMAP-93 Refactored out some NCBI->Ensembl seqname mapping functions.

• IMPROVED ANNMAP-84 Added ngsBridgePlot examples to the cookbook.

Changes in version 0.9.13:

• IMPROVED ANNMAP-78 Cookbook now appears when vignette( package=’annmap’ ) is called.

Changes in version 0.9.12:

• IMPROVED ANNMAP-74, ANNMAP-75, ANNMAP-76; Fixed warnings and notes when using R-2.15

Changes in version 0.9.11:

• IMPROVED ANNMAP-73 Methods generalisedNameToNCBI, generalisedNameToEnsembl, seqnameMapping, seqnamesToNCBI and seqnamesToEnsembl added to allow easy renaming of the seqnames column of GRanges data.

Changes in version 0.9.10:

• IMPROVED ANNMAP-71 Bug in geneToSymbol fixed

Changes in version 0.9.9:

• IMPROVED ANNMAP-63 We now use GenomicRanges instead of IRanges

Changes in version 0.9.8:

• IMPROVED ANNMAP-58 Added 4 pos translation documentation to cookbook

• BUG ANNMAP-60 Webservice tests were failing

• BUG ANNMAP-54 geneToExonProbeset didn’t support as.vector

Changes in version 0.9.7:

• BUG ANNMAP-48 Error in proteinCoordsToGenome in annmap

• BUG ANNMAP-47 annmapGenePlot fails to show individual transcripts

• IMPROVED ANNMAP-45 Added a NEWS.Rd file to inst

Changes in version 0.9.6:

• BUG Fixed ANNMAP-44; genomicPlot crashes when called with very small overlapped areas

Changes in version 0.9.5:

• IMPROVED ANNMAP-41; All InRange methods are now S3 methods which work with character, data.frame or RangedData (see ?annmap.range).

• IMPROVED ANNMAP-42; genomicPlot highlights ‘colour’ column is now ‘col’ as with all other methods.

• BUG ANNMAP-40; genomicPlot crashes if highlights data.frame has unexpected columns.

AnnotationForge

Changes in version 1.9.5:

NEW FEATURES

• An organism package has been added for Streptomyces coelicolor

• extensive overhaul of inparanoid packages means that inparanoid packages now match to 100 different organisms

• Extended support for ensembl mappings to yeast and flies.

NOTEWORTHY CHANGES BETWEEN THIS version and 1.3.11

• All chip packages now depend on org packages. This simplifies the schema and also allows for more convenient updating of these packages and smaller downloads for users.

• chip package mappings that contain probes which map to multiple targets are now hidden by default, with the ability to be exposed when required. See the use of the new toggleProbes() method. * * * 1.3.11 SERIES NEWS * * *

aroma.light

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

• ROBUSTNESS: Replaced an .Internal(psort(…)) call in medianPolish() with a call to matrixStats:::.psortKM().

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

• CLEANUP: Removed weightedMedian(), which has been moved to the matrixStats package.

• BACKWARD COMPATIBILITY: Now package depends on the matrixStats (>= 0.5.2) package, so that weightedMedian() is still available when loading this package. In future releases, matrixStats will be downgraded to only be a suggested package.

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

• BUG FIX: robustSmoothSpline() would not work with most recent R devel versions.

• Updated the package dependencies.

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

• Changed the license of aroma.light to GPL (>= 2) from LGPL (>= 2), because some of the implementation was adopted from GPL (>= 2) code, i.e. robustSmoothSpline() uses code from stats::smooth.spline().

• R CMD check no longer warns about some examples depending on the R.basic package.

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

• WORKAROUND: Now robustSmoothSpline() robustly locates the proper native R fit function for smooth splines, which vary with different releases of R.

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

• Package no longer depends on R.methodsS3, only imports.

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

• ‘R CMD check’ no longer complaints about .Internal() calls.

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

• Added support for fitNaiveGenotypes(…, flavor=”fixed”).

• GENERALIZATION: Now fitNaiveGenotypes() returns also ‘flavor’ and ‘tau’. The latter are the genotype threshholds used by the caller.

• CLEANUP: Dropped argument ‘flavor’ of callNaiveGenotypes(); it is instead passed to fitNaiveGenotypes() via ‘…’.

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

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

arrayQualityMetrics

Changes in version 3.13.2:

USER VISIBLE CHANGES

• Using NEWS.Rd

• Added the arguments maxNumArrays and nrColumns to the functions aqm.maplot and aqm.spatial.

bigmemoryExtras

Version Date Category Text 0.1.8 <NA> <NA>

Biobase

Changes in version 2.17:

USER VISIBLE CHANGES

• l2e(), previously deprecated, has been made defunct.

• All objects made defunct in previous release cycles have been removed. This includes geneNames, getExpData, eList, reporterNames, getBiocRepos, read.exprSet, updateOldMiame, df2pD, read.pD, read.phenoData, exprData, exprList, and phenoData.

BitSeq

Version: 1.2.0 (27.9.2012)

• IMPORTANT change: the way samples-files are passed to getDE, estimateHyperPar, estimateDE changed. -> instead of providing 2 vectors of filenames for each condition, the files are passed as a list of vectors, each vector containing filenames for one condition (allowing use of more than 2 conditions)

• new internal structure (not visible to user)

• estimateExpression has a new convergence criterion which should result in producing fewer samples (faster and dropping the use of MCMC_scaleReduction and MCMC_samplesNmax flags) -> estimateExpressionLegacy uses the original convergence criterion

• library normalization option for getDE, estimateDE, estimateHyperPar, getMeanVariance (in form of providing the normalization constants, for getting the constants please use edgeR or similar)

CAMERA

Changes in version 2012-06-12:

• Bugfix in findIsotopes, clears ‘vec’ must be sorted non-decreasingly error

Changes in version 2012-06-11:

• Version 1.13.4

• Add ByteCompile: TRUE

• Bugfix for findIsotopes, clears subscript out of bound error

Changes in version 2012-05-25:

• Version 1.13.2

• First changes for improved isotope detection

Changes in version 2012-04-12:

• Version 1.13.1

• Bugfix for findIsotopes to fix not consecutive isotope label like [M]+,[M+2]+ without [M+1]+

ChemmineR

Changes in version 2.10.0:

NEW FEATURES

• Streaming functionality for SDFs enables processing of millions of molecules on a laptop

• Fast and memory efficient fingerprint searches with atom pair fingerprints or PubChem fingerprints

• Flexible maximum common substructure (MCS) search support provided by new fmcs.R add-on package

clusterProfiler

Changes in version 1.5.1:

• import ggtitle from ggplot2 <2012-09-07, Fri>

• update codes of plot functions accompaning with ggplot2 (version 0.9.2) <2012-09-06, Thu>

• bug fixed of buildGOmap due to the empty GO annotation query from biomaRt <2012-07-18, Wed>

Changes in version 1.5.0:

• bump up version to 1.5.0 for BioC 2.11 devel

• add URL in DESCRIPTION

• update citation and add biocView GeneSetEnrichment <2012-05-09, Wed>

• support zebrafish <2012-05-18, Mon>

cqn

Changes in version 1.3:

• Bugfix to the vignette; the two-panel (color) plot on page 6 used CQN corrected data as blue points in both panels. Now the left plot shows standard RPKM in blue. Thanks to Maria Keays <email: mkeays@ebi.ac.uk>.

• Small fix to the vignette in the edgeR example, caused by changes to edgeR.

• Updated the citations in the vignette and the CITATION file.

• cqn.fixedlength has been removed, using cqn(lengthMethod = “fixed”) instead.

• A call slot has been added to cqn objects.

• cqn() now accepts count matrices with 1 column or vectors (although it makes little sense to use the function on such data).

• Added Questions and Answers to the vignette and moved vignette to vignettes dir.

cummeRbund

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

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

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

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

v1.99.2 Bugfixes: - Fixed bug in replicate table that did not apply make.db.names to match samples table. - Fixed bug for missing values in *.count_tracking files. - Now correctly applying make.db.names to *.read_group_tracking files. - Now correctly allows for empty *.count_tracking and *.read_group_tracking files v1.99.1

• This represents a major set of improvements and feature additions to cummeRbund.
• cummeRbund now incorporates additional information emitted from cuffdiff 2.0 including:
  • run parameters and information.
  • sample-level information such as mass and scaling factors.
  • individual replicate fpkms and associated statistics for all features.
  • raw and normalized count tables and associated statistics all features.

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

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

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

Version Date Category Text 1.3.1 <NA> Dependency changed from igraph to igraph0

ddgraph

Changes in version 1.0.3:

• Fixed bugs with multiple testing correction. Show actual multiple-corrected P-values on edges.

Changes in version 1.0.2:

• Change default representation of conditional independence in DDGraphs from arrows to dots

Changes in version 1.0.1:

• Add the toyExample dataset and extend the method introduction in vignette

Changes in version 1.0.0:

• Initial release of the package

deepSNV

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

Updates

• Changed CITATION
• Updated documentation
• Updated biocViews
• Using roxygen2 for generating man pages

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

Updates

• New devel version, identical to release 1.2.3

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

Bugfixes

• Fixed Vignette
• Jumped a few numbers due to automated bioc version numbering

DESeq

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

• added function newCountDataSetFromHTSeqCount

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

• fixed handling of rank-deficient observations now also in estimateDispersions

Changes in version 1.9.6:

• fixed that varianceStabilizingTransformation was missing in exports

Changes in version 1.9.5:

• added function plotDispEsts

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

• fixed handling of rank-deficient observations

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

• fixed bug in pooled-CR dispersion estimation

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

• Added a new function ‘varianceStabilizingTransformation’

DEXSeq

Changes in version 2012-06-26:

• Now any function relies on the order of the levels of the factors.

Changes in version 2012-05-21:

• More options and flexibilty added to “estimatelog2FoldChanges”

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 1.4.0:

• Plotting

  • dba.plotMA

  • Smooth plots now default

  • Added fold parameter in addition to th (threshold)

  • dba.plotHeatmap

  • Side colorbars added

  • Add support for specifying sample mask to include any subset of samples in a contrast plot, including samples that were not in the original contrast

  • dba.plotVenn

  • Changed plotter from limma to T. Girke’s overLapper

  • Added support for 4-way Venns (also in dba/overlap)

  • dba.plotPCA

  • Add support for specifying sample mask to include any subset of samples in a contrast plot, including samples that were not in the original contrast

• Peaksets (dba and dba.peakset)

  • Peakset formats

  • narrowPeaks format supported

  • Can override file format, score column, and score orientation defaults for supported peak callers

  • Consensus peaksets

  • Added ability to generate sets of consensus peaksets based on metadata attributes: for example create consensus peaksets for each tissue type and/or condition, or for all unique samples by taking the consensus of their replicate peaksets

• Read counting (dba.count)

  • Compute Signal-to-Noise ratio when counting

  • Added bScaleControl to down-scale control reads by default

  • Add option to specify a mask in peak parameter to limit which peaksets are used to for a consensus by overlap. Works with new consensus peakset options in dba.peakset

  • Remove references to support for SAM files

• Analysis (dba.analyze)

  • edgeR: updated calls to math change sin edgeR; updated vignette and references

  • DESeq: updated to work with current DESeq; use pooled-CR dispersion estimation method for blocking analysis; update vignette

• Various bug fixes; more informative warnings; update documentation including vignette, new examples and cross-referencing in man pages

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

• more informative warnings and minor bug fixes.

DOSE

Changes in version 1.3.2:

• update codes of plot functions accompaning with ggplot2 (version 0.9.2) <2012-09-06, Thu>

• update cnetplot corresponding to igraph version 0.6 <2012-07-11, Wed>

• parameter showCategory now support term ID vector <2012-07-11, Wed>

• import termSim and combineScores from GOSemSim. <2012-06,14, Thu>

• optimize setReadable <2012-05-09, Wed>

• bug fixed of setReadable method. For those unmapped genes, return the original gene ID. <2012-05-15, Tue>

• fill color in barplot for Ontology classification. <2012-05-22, Tue>

• update color scale of cnetplot <2012-06-18, Mon>

Changes in version 1.3.1:

• update color scheme of cnetplot <2012-04-10, Tue>

• add simplot for plotting semantic similarity matrix <2012-04-20, Fri>

• bug fixed of combineScore function for DO semantic similarity matrix which containing NA rows of NA coloumns <2012-04-20, Fri>

• export doSim and geneSim functions <2012-04-20, Fri>

DSS

Changes in version 0.99-1:

• Fixed a bug in newSeqCountSet in dealing with the input experimental designs.

• Fixed a bug in computing local FDR.

• Add options to model the relationship between dispersion and mean expression.

Changes in version 0.99:

NEW FEATURES

• Initial release.

EasyqpcR

Changes in version 1.0.0:

• First version of this package.

easyRNASeq

Changes in version 1.3.14:

NEW FEATURES

• easyRNASeq now returns a SummarizedExperiment in an effort to consolidate the objects used for Next Generation Sequencing in Bioconductor. This is the new default of the count function. The count function is a new function to supersed easyRNASeq in the coming development version (1.5.x) to consolidate the parameters and output of the easyRNASeq function.

BUG FIXES

• corrected a validity check that went permissive.

• changed the print method to display the read length range when dealing with variable read lengths rather than every single value.

Changes in version 1.3.13:

BUG FIXES

• Same correction as in the stable version 1.2.5, but for those already corrected in version 1.3.3.

Changes in version 1.3.12:

• Providing the ‘outputFormat’ argument is not necessary anymore, it defaults to matrix (i.e. count table).

• Relaxed the gtf file checking. If the gene_name is absent, the gene_id is used instead.

• Improved some reporting and remove a bottle-neck occuring when there are many sequences in the reference. BUG FIXES

• Ensure that only the matched ranges are returned when reading gapped alignments.

• The library size is more exactly calculated and is the number of aligned reads.

• Corrected a bug in the validity checking that prevented bam files created by different aligners using the same reference to be processed as the reference sequences were not ordered in the same fashion.

Changes in version 1.3.11:

BUG FIXES

• Fixed a bug in the gtf file handling reported by Mark Robinson.

Changes in version 1.3.10:

• Some vignette discrepancies have been corrected. Thanks to Richard Friedman for spotting them.

• Providing the ‘filesDirectory’ argument is not necessary anymore, if the files to proceed are present in the current directory. Indeed, this parameter now defaults to the current directory as can be found out using ‘getwd()’. BUG FIXES

• Fixed a bug introduced by a change in the IRanges coverage function return value.

Changes in version 1.3.9:

• Added the manuscript citation.

• Updated the package version dependencies. BUG FIXES

• Improved the support for reads of different lengths.

• A cosmetic change to report read lengths as well when read files with variable read length are processed.

• Corrected a bug and enhanced the loading of gtf annotation files. Thanks to Tomasz Kulinski for spotting the issue and providing the dataset to reproduce it.

Changes in version 1.3.8:

NEW FEATURES

• Now bam files can be processed in parallel (long time request from Wade Davis). If the easyRNASeq argument ‘nbCore’ is greater than 1 (1 being the default), then that many core will be used to process the read files in parallel. Pay attention not to use too many cores and have enough memory available. The memory load scales up linearly with the number of files processed.

Changes in version 1.3.7:

NEW FEATURES

• easyRNASeq now supports read of different lenghts. Thanks to Mark Robinson for the toy dataset.

• Added a function that lists existing organism conversion when applying the validity checks.

• Added a bp.coverage to the fetchCoverage function that defaults to FALSE. To allow for variable length reads, it now returns read coverage proportion per bp by default.

• Added additional checks in the .checkArguments internal function.

BUG FIXES

• Not a real bug, but more a consolidation. When an organism is unknown and no custom.map is provided, then the validity checks are turned off and a warning is emitted.

• Providing the chr.sizes as as list has been deprecated. Only named numeric vector are supported.

• Removed a now useless warning in the .readGffGtf function.

• Modified the RPKM function generic to avoid using a ‘protected’ word as argument: i.e. ‘unique’ was replaced by ‘simplify’

Changes in version 1.3.6:

NEW FEATURES

• It is now possible to pass arguments to list files through the three dots. I.e. setting recursive=TRUE is now possible.

BUG FIXES

• Corrected a bug in the .getArguments internal function.

Changes in version 1.3.5:

NEW FEATURES

• bam is now the default format for the easyRNASeq method.

• chromosome sizes are now extracted from the BAM header when the ‘chr.sizes’ argument is set to “auto”. Thanks to Simon Anders for pushing that off my TODO list and the nice implementation.

BUG FIXES

• Adapted to an API change of the edgeR package for estimating the tagwise dispersion.

Changes in version 1.3.4:

NEW FEATURES

• Added an additional validity check for chromosome names Thanks to Simon Anders for generating a reproducible use-case for that. Same change as in the stable version 1.2.3

• Ensure that gtf with non Ensembl ID are correctly parsed as well.

Changes in version 1.3.3:

• Converted the package to use Roxygen2, a Doxygen like in-source documentation system for generating the RD and NAMESPACE. The original man page were converted using the Rd2roxygen package and the resulting in-source documentation manually edited. NEW FEATURES

• Added a type accessor for Genome_intervals object

• Added a coercion to GRangesList from Genome_intervals object BUG FIXES

• Adapted to the new arguments of the edgeR estimateTagwiseDisp function

• Removed the dispersion.method argument from the plotMeanVar edgeR method call as this argument is defunct.

Changes in version 1.3.2:

BUG FIXES

• Corrected a bug that was considering a GTF file as a GFF file. Thanks to Simon Anders for spotting this.

Changes in version 1.3.1:

NEW FEATURES

• Added an enhanced read length check (same as stable 1.2.1 change)

Changes in version 1.3.0:

• New development version for Bioconductor 2.11

Changes in version 1.2.5:

BUG FIXES

• Corrected a bug in the condition file name checking.

• When using edgeR, it was not possible to de-activate the drawing of the quality assessment plots.

• Some edgeR changes to the API have been ported to the stable R version, should not have occured… The following are changes that adapt to that new API, changes ported from version the easyRNASeq development version 1.3.3…

• Adapted to the new arguments of the edgeR estimateTagwiseDisp function

• Removed the dispersion.method argument from the plotMeanVar edgeR method call as this argument is defunct.

Changes in version 1.2.4:

• Added the manuscript citation.

• Updated the package version dependencies.

Changes in version 1.2.3:

NEW FEATURES

• Added an additional validity check for chromosome names Thanks to Simon Anders for generating a reproducible use-case for that.

• Ensure that gtf with non Ensembl ID are correctly parsed as well.

Changes in version 1.2.2:

BUG FIXES

• Corrected a bug that was considering a GTF file as a GFF file. Thanks to Simon Anders for spotting this.

Changes in version 1.2.1:

NEW FEATURES

• Added an enhanced read length check

EBImage

Changes in version 4.0.0:

NEW FEATURES

• ‘transpose’ function for transposing an image by swapping its spatial dimensions

• greyscale functions for computation of the self-complementary top-hat (I. Kats)

• a median filter based on Perreault’s constant time median filter (J. Barry)

SIGNIFICANT USER-VISIBLE CHANGES

• removed all dependencies towards GTK+ and ImageMagick

• replaced the former GTK+ based ‘display’ function by a new one displaying images using either a JavaScript image viewer, or R’s built-in raster graphics

• ‘readImage’ and ‘writeImage’ now rely on ‘jpeg’, ‘png’ and ‘tiff’ packages and do not depend on ImageMagick any more

• added support for images containing an alpha channel; both greyscale and color images with an alpha channel are stored as a ‘colormode = Color’ Image

• refactored the functions, not using ImageMagick any longer: ‘translate’, ‘affine’, ‘rotate’, ‘resize’

• deprecated: ‘blur’, ‘equalize’

• deprecated: ‘drawtext’, ‘drawfont’

• deprecated: ‘getFeatures’, ‘hullFeatures’, ‘zernikeMoments’, ‘edgeProfile’, ‘edgeFeatures’

• deprecated: ‘haralickFeatures’, ‘haralickMatrix’

• deprecated: ‘moments’, ‘smoments’, ‘rmoments’, ‘cmoments’

• removed ‘animate’

• improved ‘getFrame’: better performance by reassigning array dimension only when needed

• modified ‘as.raster’

• ‘inst/images/lena.gif’ is now ‘inst/images/lena.png’

• overhauled the testing procedure in ‘tests/test.R’

• added ‘NEWS.Rd’

BUG FIXES

• ‘erode’ and ‘dilate’: incorrect range of loop indices caused memory reads from outside the kernel vector

EDASeq

Changes in version 1.3:

• Fixed a bug in biasPlot relative to the lwd, xlab and ylab arguments.

• Added a color_code option and changed the behavior of col in biasPlot.

• Updated CITATION file.

• Added an option to withinLaneNormalization and betweenLaneNormalization to return unrounded values.

• A new way to deal with zero counts by adding a small positive constant.

edgeR

Changes in version 3.0.0:

• New chapter in the User’s Guide covering a number of common types of experimental designs, including multiple groups, multiple factors and additive models. Many other updates to the User’s Guide and to the help pages.

• New function edgeRUsersGuide() to open the User’s Guide in a pdf viewer.

• Many functions have made faster by rewriting the core computations in C++. This includes adjustedProfileLik(), mglmLevenberg(), maximizeInterpolant() and goodTuring().

• New argument verbose for estimateCommonDisp() and estimateGLMCommonDisp().

• The trended dispersion methods based on binning and interpolation have been rewritten to give more stable results when the number of genes is not large.

• The amount by which the tagwise dispersion estimates are squeezed towards the global value is now specified in estimateTagwiseDisp(), estimateGLMTagwiseDisp() and dispCoxReidInterpolateTagwise() by specifying the prior degrees of freedom prior.df instead of the prior number of samples prior.n.

• The weighted likelihood empirical Bayes code has been simplified or developed in a number of ways. The old functions weightedComLik() and weightedComLikMA() are now removed as no longer required.

• The functions estimateSmoothing() and approx.expected.info() have been removed as no longer recommended.

• The span used by estimateGLMTagwiseDisp() is now chosen by default as a decreasing function of the number of tags in the dataset.

• New method “loess” for the trend argument of estimateTagwiseDisp, with “tricube” now treated as a synonym.

• New functions loessByCol() and locfitByCol() for smoothing columns of matrix by non-robust loess curves. These functions are used in the weighted likelihood empirical Bayes procedures to compute local common likelihood.

• glmFit now shrinks the estimated fold-changes towards zero. The default shrinkage is as for exactTest().

• predFC output is now on the natural log scale instead of log2.

• mglmLevenberg() is now the default glm fitting algorithm, avoiding the occasional errors that occurred previously with mglmLS().

• The arguments of glmLRT() and glmQLFTest() have been simplified so that the argument y, previously the first argument of glmLRT, is no longer required.

• glmQLFTest() now ensures that no p-value is smaller than what would be obtained by treating the likelihood ratio test statistic as chisquare.

• glmQLFTest() now treats tags with all zero counts in replicate arrays as having zero residual df.

• gof() now optionally produces a qq-plot of the genewise goodness of fit statistics.

• Argument null.hypothesis removed from equalizeLibSizes().

• DGEList now longer outputs a component called all.zeros.

• goodTuring() now longer produces a plot. Instead there is a new function goodTuringPlot() for plotting log-probability versus log-frequency. goodTuring() has a new argument ‘conf’ giving the confidence factor for the linear regression approximation.

• Added plot.it argument to maPlot().

ExiMiR

Changes in version 1.99.1:

• NAMESPACE: removing the load of limma and affy that are in dependencies

Changes in version 1.99.0:

• inst/doc/fig0.png: new figure

• man/bg.correct.miR.Rd: new help file

• man/createAB.Rd: new help file

• man/NormiR.methods.Rd: new help file

• R/createAB.R: new feature implementation

• R/NormiR.methods: new file for giving availables methods

• All the others files have been updated according new features implementation

fabia

Changes in version 2.3.1:

NEW FEATURES

• Getters and setters for class Factorization

flowCore

• add new classes “filters”, “filtersList” to allow flowViz to plot multiple filters/gates for one flowFrame
• add argument “emptyValue” to read.FCS API so that parser can still work correctly when either cases below occurs :
  1. there is double-delimiter in keyword values (sometime like\n\\c:\\path\\…)
  2. there is empty keyword value\n(\\keyword1\\value1\\keyword2\\\\keyword3)
• fix the bug that malformed spillover matrix in write.FCS

flowViz

CHANGES IN VERSION 1.21.1

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

fmcsR

Changes in version 0.99.0:

• fmcsR submitted to Bioconductor

FunciSNP

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

• Updated package to address issues and comments by BioC curator.

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

• Initial Bioconductor release. New citation included.

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

• Created. Initial build and release of FunciSNP.

GeneAnswers

Changes in version 1.14:

NEW FEATURES

• Multigroup concept-gene analysis html report supports interactive network with cytoscape web support as well as original fixed images

• caBIO pathway and REACTOME pathway are included with xml queries, therefore, internet access is required.

• The total number of pooled genes in Hypergeometric test can be set by the amount of genes in annotation library or the total annoted genes in the given species.

• Add gene annotation summarization functions. Please check geneFunctionSummarize.pdf for more details.

GeneNetworkBuilder

Changes in version 1.0.0:

NEW FEATURES

• buildNetwork() to build the network by binding list and interaction map

• filterNetwork() to filter the network by expression data

• polishNetwork() to generate graphNEL object for visualization

BUG FIXES

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

GenomicFeatures

Changes in version 1.10:

NEW FEATURES

• Add makeTranscriptDbFromGFF(). Users can now use GFF files to make TranscriptDb resources.

• Add restricted “seqinfo<-“ method for TranscriptDb objects. It only supports replacement of the sequence names (for now), i.e., except for their sequence names, Seqinfo objects ‘value’ (supplied) and ‘seqinfo(x)’ (current) must be identical.

• Add promoters() and getPromoterSeq().

• Add ‘reassign.ids’ arg (FALSE by default) to makeTranscriptDb().

SIGNIFICANT USER-VISIBLE CHANGES

• Updated vignette.

• Improve how makeTranscriptDbFromUCSC() and makeTranscriptDbFromBiomart() assign internal ids (see commit 65144 for the details).

• 2.5x speedup of fiveUTRsByTranscript() and threeUTRsByTranscript().

DEPRECATED AND DEFUNCT

• Are now defunct: transcripts_deprecated(), exons_deprecated(), and introns_deprecated().

• Deprecate loadFeatures() and saveFeatures() in favor of loadDb() and saveDb(), respectively.

BUG FIXES

• Better handling of BioMart data anomalies.

GenomicRanges

Changes in version 1.10.0:

NEW FEATURES

• SummarizedExperiment gains direct GRanges / GRangesList interface to rowData.

• Add “distanceToNearest” method for GenomicRanges objects.

• SummarizedExperiment class can now be subset by row when there are no ‘columns’, and by column when there are no ‘rows’.

• Add ‘drop.D.ranges’ argument to coverage,GappedAlignments and coverage,GappedAlignmentPairs methods.

• findOverlaps() now supports ‘select=”last”’ and ‘select=”arbitrary”’ (in addition to ‘select=”all”’ and ‘select=”first”’) on GenomicRanges objects.

• summarizeOverlaps(…, mode=”IntersectionStrict”) now handles circular chromosomes. A warning is issued and circular chromosomes in ‘reads’ are omitted from counting.

• Add disjoin,GRangesList method.

• Add findSpliceOverlaps() for identifyng ranges (reads) that are compatible with a specific transcript isoform (the non-compatible ranges are analyzed for the presence of novel splice events).

• Add ngap,GappedAlignmentPairs method.

• Add introns() generic with methods for GappedAlignments and GappedAlignmentPairs objects.

• No more arbitrary max of 3 gaps per read in isCompatibleWithSplicing() and isCompatibleWithSkippedExons().

• Add findCompatibleOverlaps() and countCompatibleOverlaps().

• Passing ‘…’ down through as.data.frame(GRanges, …) so user can tweak stringsAsFactors default for metadata columns.

• Add extractSteppedExonRanks(), extractSpannedExonRanks() and extractQueryStartInTranscript() utilities (work with single- and paired-end reads).

• Add ‘flip.query.if.wrong.strand’ arg (FALSE by default) to “encodeOverlaps” method for GRangesList objects.

• Add makeSeqnameIds() low-level utility.

SIGNIFICANT USER-LEVEL CHANGES

• SummarizedExperiment rowData and assays operations have significant performance improvements.

• mcols() is now the preferred way (over elementMetadata() or values()) to access the metadata columns of a GenomicRanges, GRangesList, GappedAlignments, GappedAlignmentPairs, SummarizedExperiment object, or any Vector object. elementMetadata() and values() might go away at some point in the (not so close) future.

• Add “$” and “$<-“ methods for GenomicRanges only. Provided as a convenience and as the result of strong popular demand. Note that those methods are not consistent with the other “$” and “$<-“ methods in the IRanges/GenomicRanges infrastructure, and might confuse some users by making them believe that a GenomicRanges object can be manipulated as a data.frame-like object. It is therefore recommended to use them only interactively, and their use in scripts or packages is discouraged. For the latter, use ‘mcols(x)$name’ instead of ‘x$name’.

• No more warning when doing as(x, “GRanges”) on a RangedData object with no “strand” column.

• Refactor “[” method for GenomicRanges objects. The new implementation always preserves the names of the selected elements instead of trying to return a GenomicRanges object with unique names. This new behavior is consistent with subsetting of ordinary vectors and other Vector objects defined in IRanges/GenomicRanges. Also modify “seqselect” method for GenomicRanges objects so it also preserves the names of the selected elements (and thus remains consistent with new behavior of “[” method for GenomicRanges objects).

• No more names on the integer vector returned by “ngap” method for GappedAlignments objects.

• Many improvements to the “Overlap encodings” vignette.

• Remove ‘param’ argument from summarizeOverlaps() generic.

DEPRECATED AND DEFUNCT

• Defunct previously deprecated grg() function.

• Defunct previously deprecated countGenomicOverlaps() generic and methods.

BUG FIXES

• Fix several issues with “precede”, “follow”, “nearest”, and “distance” methods for GenomicRanges objects.

• Fix bug in summarizeOverlaps(…, ignore.strand=TRUE).

• 6x speedup (and a 6x memory footprint reduction) or more when using encodeOverlaps() on big GRangesList objects.

• Fix bug in renameSeqlevels() wrt order of rename vector.

• Fix bug in selectEncodingWithCompatibleStrand().

genoset

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

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

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

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

GGBase

Changes in version 3.20.0:

• MAFfilter now treats lower, upper as a left-open interval, i.e., retains x if lower < x <= upper; previously was closed at both ends

ggbio

Changes in version 1.5.16:

NEW FEATURES

• ggplot generic method added.

• mold generic method added for molding object to data.frame.

• support ggplot(data) + stat_* style, original data being kept.

• tracks function updated, API is enhenced, utilities could control attributes of plots and trakcs.

• autoplot now support: VCF, SummarizedExperiments, matrix, where when genomic position is provided, options to visualize a heatmap sitting on the genomic position.

• theme could define track based themes.

• ideogram: support + xlim method, when embeded with tracks, automatically update zoomed region.

• pheno.plot added to SuumarizedExperiemnts and ExpressionSet.

SIGNIFICANT USER-LEVEL CHANGES

• align.plots is deprecated, alignPlots created

Notes

• updated website for ggbio: http://tengfei.github.com/ggbio manuals and vignettes and paper added

GGtools

Changes in version 4.6:

• The primary tools for one-population analyses are best.cis.eQTLs and transScores. Multipopulation analyses are handled with meta.best.cis.eQTLs and meta.transScores.

• High volume genotype data has been addressed by packaging ExpressionSet and chromosome-specific SnpMatrix instances; requests for expression plus genotype data are directed to packages mediated through GGBase::getSS.

• Two species of data filtering parameters that may be used jointly in the primary tools are exFilter, which operates on expression component prior to any analyses, and smFilter, which operates on the entire smlSet. exFilter may be used to isolate samples of interest early in the workflow, for example when an expression plus genotype package includes samples from distinct tissues on the same individuals.

• june 2012: exFilter facility properly handled in best.cis.eQTLs.mchr

• may 2012: best.cis.eQTLs has getDFFITS option

GOSemSim

Changes in version 1.15.3:

• remove all the S4 classes and methods <2012-09-12, Wed>

• add progress bar for mgeneSim <2012-09-12, Wed>

• re-implement calculating semantic values in Wang’s method <2012-09-12, Wed>

• update IC data for next release <2012-09-12, Wed>

• bug fixed in getSV <2012-09-13, Thu>

Changes in version 1.15.2:

• re-implement gene2GO <2012-09-7, Fri>

• information content based methods implemented in c++ <2012-09-5, Wed>

Changes in version 1.15.1:

• export termSim, which can be used in other ontological semantic similarity measurement <2012-06-14, Thu>

• update vignette. <2012-06-14, Thu>

GSEABase

Changes in version 1.19:

NEW FEATURES

• Added UniprotIdentifier class

Gviz

Changes in version 1.2.0:

NEW FEATURES

• A SequenceTrack class has been added to draw genomic sequence information on a Gviz plot. Possible inputs for the track are DNAStringSet objects or directly from BSgenome packages.

• GeneRegionTracks can now deal with coding and non-coding regions by means of the feature property in combination with the thinBoxFeature display parameter.

• StackedTracks now have a new display parameter ‘reverseStacking’ which reverts the horizontal ordering of stacked items. If set to TRUE, the lowest items are moved to the top of the stack, and vice versa.

SIGNIFICANT USER-VISIBLE CHANGES

• Updated the show methods for most tracks to give more meaningful and more compact information about the track’s content. Availablability of data on other chromosomes than the currently active one should now be indicated.

• IdeogramTracks can now be constructed from a cytoband table via the new bands argument in the constructor.

• AnnotationTrack objects now by default draw connecting lines in a light gray color. This feature can be controlled via the col.line display parameter.

• Sliding window summarization can now deal with NA values.

• Exporting drawGD from the name space now to allow for sub-classing of GdObjects in other packages.

• When building GeneRegionTracks from TrasncriptDb objects, the information about UTRs and coding regions is now retained.

BUG FIXES

• When zooming into the emty space between two grouped features, the connecting line will now be plotted for all classes inheriting from AnnotationTrack.

• An error in calculating ylims when drawing AlignedReadTracks has been fixed.

• Numerous other little fixes that mainly aim at improving performance.

GWASTools

Changes in version 1.3.16:

• Added convertVcfGds to extract bi-allelic SNPs from a VCF file.

• Added ncdfImputedDosage to convert output from common imputation programs to NetCDF. assocTestRegression has an additional argument dosage=TRUE to be used with these files.

• Added vignette describing GWASTools data structures.

Changes in version 1.3.15:

• Bug fix in pedigreePairwiseRelatedness related to use of character identifiers.

Changes in version 1.3.14:

• assocTestRegression returns NA for snps where cases or controls are monomorphic, added assocTestFisherExact to use in that case.

• Added snp.exclude argument to pseudoautoIntensityPlot.

• Bug fix in messages reporting file read times when creating or checking netCDF files.

Changes in version 1.3.13:

• Added vignette on converting VCF to NetCDF with annotation.

• Prevent duplicateDiscordance from checking correlation by SNP in cases of no variation.

Changes in version 1.3.12:

• Added GdsReader and GdsGenotypeReader classes with dependency on gdsfmt. GenotypeData objects can also be created with GdsGenotypeReader objects in the “data” slot.

Changes in version 1.3.11:

• Fixed bug in duplicateDiscordance when Y chromosome is not included.

Changes in version 1.3.10:

• Fixed bug in chromIntensityPlot so ideogram scales correctly if SNPs are excluded.

Changes in version 1.3.9:

• Fixed bug in assocTestCPH that could lead to false positives if additive model failed but GxE model did not.

• Allow multiple variables for stratified analysis in assocTestCPH.

Changes in version 1.3.8:

• Pedigree functions accept non-numeric identifiers and provide additional output.

Changes in version 1.3.7:

• In batchChisqTest, Yates correction cannot be bigger than the terms it corrects. Changed to match bug fix to chisq.test in R 2.15.1.

Changes in version 1.3.6:

• Removed automatic subtitle from qqPlot.

• Allow selection of theoretical boundaries to draw in ibdPlot.

Changes in version 1.3.5:

• Added function asSnpMatrix to convert a GenotypeData object to a SnpMatrix object for use with snpStats.

Changes in version 1.3.4:

• Added chromosome ideograms to chromIntensityPlot and anomStatsPlot. anomStatsPlot has an option to put multiple anomalies on the same plot.

Changes in version 1.3.3:

• Updated vignette.

Changes in version 1.3.2:

• Use lazy loading of data.

• manhattanPlot and snpCorrelationPlot accept character vectors of chromosome; chrom.labels argument no longer used.

Changes in version 1.3.1:

• close method of NcdfReader returns invisibly.

HiTC

Changes in version 1.1.3:

NEW FEATURES

• Adding CITATION file

DEPRECATED AND DEFUNCT

• Update of getExpectedCount function to use the lowess() function (stats). The ‘C’ call in stats is now deprecated

Changes in version 1.1.2:

NEW FEATURES

• New package vignette

• Add new normalization method - normPerTrans

• Add importC and exportC function, to load and import csv file

SIGNIFICANT USER-VISIBLE CHANGES

• The CQC function now returns a matrix

• Simplify getExpectedCounts help page

• Update of import.my5C function. Simplify the import for matrix data

DEPRECATED AND DEFUNCT

• The export method is now replace by exportC. The standard csv format is now exported.

• The normPerZscore method is depracted. See normPerExpected instead

• Remove Bau et al. 5C dataset

BUG FIXES

• isBinned. Fix bug for interchromosomal interactions

• extracRegion. Add a chromosome parameter, and changes for interchromosomal data

• binningC. Changes for interchromosomal maps

• Sort xgi and ygi objects when the HTCexp constructor is called

• Force the xgi and ygi objects to have some ids

Changes in version 1.1.1:

NEW FEATURES

• Include the Nora et al (Nature 2012) 5C dataset (GSE35721).Two mouse samples are included in the package ; male undifferentiated ES cells (E14, GSM873935) and male embryonic fibroblasts (MEF, GSM873924). Only the cis interaction maps chrX vs chX are provided.

hpar

Changes in version 0.99.1:

• Added collate field <2012-09-14 Fri>

• Updated to HPA version 10 <2012-09-15 Sat>

• Updated installation part in section to use biocLite <2012-09-15 Sat>

Changes in version 0.99.0:

• Added vignette <2012-09-06 Thu>

Changes in version 0.1.0:

• Initial commit <2012-09-06 Thu>

htSeqTools

Changes in version 1.3.1:

• Fixed bug in plotMeanCoverage

iPAC

Changes in version 0.3.0:

• First release of the iPAC package.

• ClusterFind method allows the use of MDS and linear mappers.

• Two beta methods available to reconcile data between the COSMIC and PDB databases.

IRanges

Changes in version 1.16.0:

NEW FEATURES

• as( , “SimpleList”), as( , “CompressedList”), and as( , “List”) now work on atomic vectors, and each element of the vector corresponds to an element of the returned List (this is consistent with as.list).

• Add as.list,Rle method.

• Add as.matrix,Views method. Each view corresponds to a row in the returned matrix. Rows corresponding to views shorter than the longest view are right-padded with NAs.

• Add FilterClosure closure class for functions placed into a FilterRules. Has methods for getting parameters and showing.

• Support ‘na.rm’ argument in “runsum”, “runwtsum”, “runq”, and “runmean” methods for Rle and RleList objects.

• Add splitAsList() and splitAsListReturnedClass().

• Improve summary,FilterRules to support serial evaluation, discarded counts (instead of passed) and percentages.

• Make rename work on ordinary vector (in addition to Vector).

• Add coercion from RangedData to CompressedIRangesList, IRangesList, or RangesList. It propagates the data columns (aka values) of the RangedData object to the inner metadata columns of the RangesList object.

• Add ‘NG’ arg to PartitioningByEnd() and PartitioningByWidth() constructors.

• Make PartitioningByEnd() work on list-like objects (like PartitioningByWidth()).

• Fast disjoin() for moderate-sized CompressedIRangesList.

• Add countQueryHits() and countSubjectHits().

• coverage() now supports method=”auto” and this is the new default.

• Add the flippedQuery(), levels(), ngap(), Lngap(), Rngap(), Lencoding(), and Rencoding() getters for OverlapEncodings objects.

• Add “encodeOverlaps” method for GRangesList objects.

• Enhance “[” methods for IRanges, XVector, XVectorList, and MaskCollection objects, as well as “[<-“ method for IRanges objects, by supporting the following subscript types: NULL, Rle, numeric, logical, character, and factor. (All the methods listed above already supported some of those types but no method supported them all).

• Add remapHits() for remapping the query and subject hits of a Hits object.

• Add match,Hits method.

• Add %in%,Vector method.

• Add “compare”, “==”, “!=”, “<=”, “>=”, “<”, “>”, “is.unsorted”, “order”, “rank”, “match”, and “duplicated” methods for XRawList objects. unique() and sort() also work on these objects via the “unique” and “sort” methods for Vector objects.

• Add expand() for expanding a DataFrame based on the contents of one or more designated columms.

• After being deprecated (in BioC 2.9) and defunct (in BioC 2.10), the “as.vector” method for AtomicList objects is back, but now it mimics what as.vector() does on an ordinary list i.e. it’s equivalent to ‘as.vector(as.list(x), mode=mode)’. Also coercions from AtomicList to logical/integer/numeric/double/complex/character/raw are back and based on the “as.vector” method for AtomicList objects i.e. they work only on objects with top-level elements of length <= 1.

• DataFrame constructor now supports ‘check.names’ argument.

• Add revElements() generic with methods for List and CompressedList objects.

SIGNIFICANT USER-VISIBLE CHANGES

• Splitting / relisting a Hits object now returns a HitsList instead of an ordinary list.

• Operations in the Ops group between a List and an atomic vector operand now coerce the atomic vector to List (SimpleList or CompressedList) before performing the operation. Also, operands are recycled and a better job is done returning zero length results of the correct type.

• Change the warning for ‘Integer overflow …’ thrown by sum() on integer-Rle’s

• DataFrame now coerces List/list value to DataFrame in [<-.

• Fix as.matrix,DataFrame for zero column DataFrames. Returns an nrow()x0 logical matrix.

• union,Hits method now sorts the returned hits first by query hit, then by subject hit.

• Add mcols() accessor as the preferred way (over elementMetadata() and values()) to access the metadata columns of a Vector object.

• By default, mcols(x) and elementMetadata(x) do NOT propagate the names of x as the row names of the returned DataTable anymore. However the user can still get the old behavior by doing mcols(x, use.names=TRUE).

• [<-,XVectorList now preserves the original names instead of propagating the names of the replacement value, which is consistent with how [<- operates on an ordinary vector/list.

• coverage() now returns a numeric-Rle when passed numeric weights.

• When called on a List object with use.names=TRUE, unlist() no longer tries to mimic the kind of non-sense name mangling that base::unlist() does (e.g. on list(a=1:3)) in a pointless effort to return a vector with unique names.

• Remove ‘hits’ argument from signature of encodeOverlaps() generic function.

• unique,Vector now drops the names for consistency with base::unique().

• Remove make.names() coercion in colnames<-,DataFrame for consistency with data.frame.

DEPRECATED AND DEFUNCT

• Deprecated tofactor().

• Remove RangesMatching, RangesMatchingList, and Binning classes.

• Change from deprecated to defunct: matchMatrix(), “dim” method for Hits objects, and RangesMatchingList().

BUG FIXES

• Fix bug in pintersect,IRanges,IRanges when input had empty ranges (broken since 2010-03-04).

• Avoid integer overflow in mean,Rle method by coercing integer-Rle to numeric-Rle internally.

• Change evaluation frame of with,List to parent.frame(), and get the enclosure correct in eval,List.

• Many fixes and improvements to coercion from RangesList to RangedData (see commit 68195 for the details).

• Fix “runValue” and “ranges” methods for CompressedRleList objects (broken for a very long time).

• shift,Ranges method now fails in case of integer overflow instead of returning an invalid Ranges object.

• mstack() now works on Vector objects with NULL metadata columns.

• In case of integer overflow, coverage() now puts NAs in the returned Rle and issues a warning.

• Fix bug in xvcopy,XRawList objects that prevented sequences from being removed from the cache of a BSgenome object. See commit 67171 for the details.

• Fix issues related to duplicate column names in DataFrame (see commit 67163 for the details).

• Fix a bunch of subsetting methods that were not subsetting the metadata columns: “[”, “subseq”, and “seqselect” methods for XVector objects, “seqselect” and “window” methods for XVectorList objects, and “[” method for MaskCollection objects.

• Fix empty replacement with [<-,Vector

• Make %in% robust on an empty ‘table’ argument when operating on Hits objects.

iSeq

Changes in version 1.9.0:

• Previously, peakreg fails when only one posterior probability is greater than ppcut or fdrcut, although this condition is really rare. This bug has been fixed.

• A tutorial of ChIP-seq data analysis using iSeq and an R script called iSeq.R that can be used as a command line program have been posted at https://sites.google.com/site/quincymobio/teaching-materials

• The document for iSeq has been updated.

isobar

• Rockerbox import (just define the XXX.dat.peptides.csv as identifications)
• possibility to define columns for XLS report in properties.R. e.g. xls.report.columns <- c(“ratio”,”is.significant”, “ratio.minus.sd”,”ratio.plus.sd”, “p.value.ratio”,”p.value.sample”, “log2.ratio”,”log2.variance”)

KEGGprofile

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

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

limma

Changes in version 3.14.0:

• limma license upgraded to GPL (>=2) instead of LGPL to match R itself.

• Many updates to the User’s Guide. Sections have been added on reading single channel Agilent and Illumina data. The chapter on experimental designs has been split into three chapters on single-channel, common reference and two-color designs respectively. The material on the fixed effect approach to technical replication has been deleted. There are new sections on nested interactions for factorial designs and on multi-level designs.

• The links to the Apoa1, Weaver and Bob1 datasets in the User’s Guide have been updated to help users download the data themselves if they wish to repeat the case study analyses.

• The help page for camera() now cites published paper Wu and Smyth (NAR, 2012). In view of the results of this paper, the claim is no longer made on help page for geneSetTest() that genes might be treated as independent when the experimental units are genetically identical mice.

• Minor edits to CITATION file.

• New function propTrueNull() for fast estimation of the proportion of true null hypotheses from a vector of p-values.

• New function zscore() to compute z-score equivalents for deviates from any continuous distribution. Includes the functionality of the older functions zscoreGamma() and zscoreT() as special cases.

• roast() now accepts observation level weights, through a new argument ‘weights’.

• loessFit() now applies minimum and maximum bounds by default to avoid zero or infinite weights. Equal weights are now treated as if the weights were NULL, even all zero weights, so that the lowess code is called instead of the loess code.

• When there are no weights, loessFit() now extracts residuals directly from the C code output instead of computing in R.

• fitFDist() now permits missing values for x or zero values for df1 even when there is a covariate. This means that squeezeVar() and eBayes() now work with trends even when not all the data values are informative.

• New argument ‘file’ for convest(), implementing edits contributed by Marcus Davy. Arguments doplot and dereport renamed to ‘plot’ and ‘report’.

• Two improvements for plotMDS(). It now coerces labels to be character, and now makes extra room on the plot when the text labels are wide.

• plotMDS() no longer gives an error when the requested number of top genes is greater than the total number of rows of data.

• Code speed-up for alias2SymbolTable()

• any(duplicated()) replaced by anyDuplicated() in several functions.

• Fix to voom() so that it computes weights correctly even when the design matrix is not of full rank.

• Bug fix for roast() when the fitted model has only one coefficient.

lmdme

Changes in version 0.99.1:

MINOR CHANGES

• Getters now accept a character vector in term parameter, in order to specify one than one term if required. In addition, design and model were added, and pvalues like Fvalues were changed to match slot names. (Thanks to Valerie Obenchain)

• lmdme now works with NA presence in data matrix. This bug is related to lmFit intercept coefficient behavior, which breaks the data structure using drop (to numeric instead of keeping a matrix with one column) only if NA are present.

• lmdme is now the only constructor. Method initialize was erased due to different reasons as described in https://stat.ethz.ch/pipermail/bioc­devel/2012­August/003554.html

• decomposition example sections using subset parameter for simplicity (not all the data has to be decomposed in the example).

• Enhance of biplot and screeplot functions with term and mfcol to simplify the graphic output specification.

DOCUMENTATION

• NEWS file was added.

minfi

Changes in version 1.3:

• Updated preprocessSwan to fix a bug when mSet was not set to the default value of NULL. Specifically, now the “counts” tables is used to construct “subset”.

• Changed the function manifestNew() to IlluminaMethylationManifest().

• Added IlluminaMethylationAnnotation().

• Added placeholders for unit testing based on RUnit.

• Introduced a new show method for MethylSet and RGChannelSet, derived from the eSet method in Biobase.

• The annotation slot of a MethylSet/RGChannelSet is now intended to not be a scalar, but instead have length 2 with components ‘array’ and ‘annotation’. This foreshadows introdution of annotation packages for use with minfi.

• Reorganization of R files; rewriting of the man pages for MethylSet, RGChannelSet.

• getMeth, getUnmeth, getBeta, getM are now methods.

• bug fix to qcReport thanks to Tao Shi.

• Changes to getBeta / getM, both in terms of which arguments the methods take and how the values are computed.

• Changes to the manifest structure; it now has separate slots for genotype probes and these probes are no longer part of a MethylSet (using eg. preprocessRaw). They can be accessed using getProbeInfo(rgSet, type) with type equal to “SnpI” or “SnpII”.

• Introduction of mapToGenome, getLocations and the new class GenomicMethylSet. man pages are reasonably complete, still need to add examples to the vignette. This will be a standard part of an extended pipeline.

• Introduction of IlluminaHumanMethylation450lannotation.ilmn.v1.2 which contains some new annotation needed for mapToGenome/getLocations. This package will be split into several packages moving forward, in an attempt to harmonize efforts by us and Tim Triche. getLocations/mapToGenome will stay the same.

• getControlTypes added (returns the different types of control probes).

• GenomicMethylSet now inherits a number of methods including granges(), start(), end() etc. from SummarizedExperiemnt. They have therefore been deleted from minfi.

• Bugfix to getLocations(…, mergeManifest = TRUE). It now longer throws an error.

• mapToGenome now returns a GenomicMethylSet ordered according to the chromosome name ordering chr1,..,chr22,chrX,chrY,unmapped, the last one not present if drop=TRUE (default).

MLInterfaces

Changes in version 1.37.1:

• added NEWS file (lgatto) <2012-04-02 Mon>

• renamed ‘predScores’ to ‘predScore’ and new ‘predScores’ method that returns the full prediction score matrix (lgatto) <2012-04-02 Mon>

• remove ununsed t argument for predScore (lgatto) <2012-04-02 Mon>

• changed maxit to maxiter in RAB4es and decr to decreasing in fs.absT (partial argument matching note during checking) (lgatto) <2012-04-02 Mon>

• fixed predScores <2012-04-03 Tue>

MLP

Changes in version 1.5.2:

• remove require(mouse4302mmentrezg.db) calls to keep R CMD check from giving inappropriate warnings

Changes in version 1.5.0:

• update exampleGeneSet.rda using GO.db for BioC 2.11

Changes in version 1.4.2:

• further improvements in getGeneSets and addGeneSetDescription

Changes in version 1.4.1:

• better checks on geneSetSource in getGeneSets

mosaics

Changes in version 1.5.3:

BUG FIXES

• mosaicsRunAll(): Bug fix when byChr = TRUE.

Changes in version 1.5.2:

SIGNIFICANT USER-VISIBLE CHANGES

• constructBins(): Supports aligned read file formats for PET data (eland results and SAM formats).

• mosaicsRunAll(): Supports aligned read file formats for PET data.

• Add generateWig(): Constructs wiggle files for PET and SET data.

• Use tab separator instead of whitespaces for generateWig() and constructBins().

• Improve the vignette (case studies, example lines for input files, generateWig()).

BUG FIXES

• constructBins(): Bug fix for capping and excludeChr. Fix incorrect summary when byChr = TRUE.

• mosaicsRunAll(): Bug fix for excludeChr & handling the full path for chipFile and controlFile.

Changes in version 1.5.1:

SIGNIFICANT USER-VISIBLE CHANGES

• constructBins(): Chromosome information can now be specified.

• mosaicsRunAll(): Chromosome information can now be specified.

Changes in version 1.4.1:

BUG FIXES

• constructBins(): Bug fix for the “outfileLoc” argument.

• mosaicsFit(): Minor changes in two-signal-component model fitting.

• mosaicsPeak(): No warning with the updated IRanges package.

motifStack

Changes in version 1.0.0:

NEW FEATURES

• draw DNA/RNA sequence logo

• draw Amino Acid sequence logo

• draw aligned motif logo stacks with phylogenetic tree

BUG FIXES

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

MSnbase

Changes in version 1.5.25:

• fixed bug when quantifying exp of length 1 (reported by Colin Archer), added test <2012-09-26 Wed>

• fixed parallel default to FALSE <2012-09-26 Wed>

Changes in version 1.5.24:

• updated clean, removePeaks, combineFeatures, purityCorrect, trimMz, plot, MSnSet-class examples to not use readMSData <2012-09-25 Tue>

• fixed clean,MSnExp-method <2012-09-25 Tue>

• space in log message in extractPrecSpectra <2012-09-25 Tue>

Changes in version 1.5.23:

• updated quantify documentation <2012-09-24 Mon>

• changed all foo.class functions to foo_class <2012-09-24 Mon>

Changes in version 1.5.22:

• setting parallel default to FALSE <2012-09-22 Sat>

• enhanced parallel in DESCRIPTION and detectCores() passed to registerDoMC <2012-09-23 Sun>

Changes in version 1.5.21:

• removed registerDoMC no visible global function NOTE <2012-09-21 Fri>

• fixed NOTE about xvarname which was a bug <2012-09-21 Fri>

Changes in version 1.5.20:

• an immediate warning is thrown is any(centroided(object)) in quantify.MSnExp <2012-09-15 Sat>

• mzTab file and loading time is now recorded in processingData <2012-09-15 Sat>

• temporarily dontrun’ing’ the mzTab read/write examples as OLS is down (and breaks rols) (note: modifed Rd files, not roxygen template) <2012-09-15 Sat>

Changes in version 1.5.19:

• updated all ReporterIons rda data <2012-09-13 Thu>

• Using && in testing parallel, require(foreach and doMC) <2012-09-14 Fri>

Changes in version 1.5.18:

• new log method for MSnSet instances <2012-09-13 Thu>

• new MAplot methods using generic and ma.plot/mva.pairs from affy <2012-09-13 Thu>

Changes in version 1.5.17:

• changed TMT7[7] mass from 229.26 to 230.17 and ReporterIons descriptions <2012-09-12 Wed>

Changes in version 1.5.16:

• parallel quantify is now always set to FALSE on Windows, fixing example checking issues <2012-09-11 Tue>

• fixed types in plotMzDelta man <2012-09-11 Tue>

Changes in version 1.5.15:

• updating code to ggplot2 v0.9.2 <2012-09-07 Fri>

Changes in version 1.5.14:

• added platform test to use doMC (d.tenenbaum) <2012-08-31 Fri>

Changes in version 1.5.13:

• updated fillUp function <2012-08-15 Wed>

• added tikzDevice to suggests <2012-08-16 Thu>

• tikzDevice no longer on CRAN - removing from Suggests and using pdf as device in vignette <2012-08-16 Thu>

Changes in version 1.5.12:

• using knitr instead of pgfSweave and misc vignette updated<2012-08-13 Mon>

• spectrum2 reporter plotting params updates <2012-08-14 Tue>

• added reporterNames to NAMESPACE <2012-08-14 Tue>

Changes in version 1.5.11:

• type in filterNA log messaging and also rounding pNA <2012-06-07 Thu>

• typo in demo vignette - Gb instead of Mb <2012-07-15 Sun>

Changes in version 1.5.10:

• Fixed readMSData instrumentInfo handling (reported by Gopuraja Dharmalingam) <2012-06-05 Tue>

• new multiple file loading test in test_io <2012-06-05 Tue>

Changes in version 1.5.9:

• topN now properly updates processingData <2012-06-01 Fri>

• combineFeatures updates featureNames based on the groupBy argument - updated demo vignette and man accordinlgy <2012-06-01 Fri>

• additional parameters were not passed when normalise using vsn <2012-06-01 Fri>

Changes in version 1.5.8:

• added aa data in environment data.frame <2012-05-22 Tue>

• fixed MSnbase:::subsetBy (used by topN) when ncol(object) == 1 <2012-05-25 Fri>

• new nQuants function <2012-05-31 Thu>

• minor vignettes updates <2012-05-31 Thu>

• nQuants now return a matrix with col names, taken form sampleNames(object) <2012-05-31 Thu>

Changes in version 1.5.7:

• changed title method to exptitle to avoid conflict/confusion with graphics::title and consitency with expinfo method <2012-05-15 Tue>

• changed email to expemail <2012-05-15 Tue>

• Added rols to Suggests <2012-05-15 Tue>

Changes in version 1.5.6:

• new ionSource, analyser, detectorType, title accessor methods for MIAPE, pSet and MSnSet classes <2012-05-06 Sun>

• updated quantify example to use data(itraqdata) instead of reading dummyiTRAQ.mzXML <2012-05-09 Wed>

• initial mzTab write support <2012-05-10 Thu>

• mzTab read support <2012-05-10 Thu>

• updated demo and io vignettes with mzTab info <2012-05-10 Thu>

Changes in version 1.5.5:

• added email slot in MIAPE and accessor <2012-05-04 Fri>

• added expinfo methods to pSet and MSnSet <2012-05-04 Fri>

• updated itraqdata <2012-05-04 Fri>

• misc man typos fixed <2012-05-04 Fri>

• quantify now properly propagates processingData <2012-05-04 Fri>

Changes in version 1.5.4:

• automatically populating experiment data instrument info while reading data <2012-04-30 Mon>

• msInfo fixed and exported <2012-04-30 Mon>

• update demo vignette with 14 fractions analysis paragraph <2012-05-01 Tue>

Changes in version 1.5.3:

• extractSpectra is now defunct <2012-04-20 Fri>

• caching full header in level 1; this is required when and MSnExp instance with many spectra (created from many raw files) is quantified - calling header(object) is a too big overhead compared to actual reporter quantification. <2012-04-20 Fri>

• The header() method now uses the cached dataframe if level >= 1; the (unexported) .header function can be used to generate the dataframe using the assayData slot data. <2012-04-20 Fri>

• Setting processingData in MSnSet initialisation. <2012-04-20 Fri>

• Dropping index column from header. <2012-04-20 Fri>

• new Spectrum class v0.2.0 has tic slot. <2012-04-21 Sat>

• tic method (data stored as a Spectrum slot) now returns total ion current (as commonly used) and total ion count is obtain using ionCount. <2012-04-21 Sat>

• fixed normalisation boxplot titles and other tic/ionCount changes in demo vignette. <2012-04-21 Sat>

• removed qual subetting in MSnSet’s “[” method <2012-04-24 Tue>

Changes in version 1.5.2:

• transposing and MSnSet does silently drop the protocolData now <2012-04-03 Tue>

• fixed MSnExp pData creation for multiple files, feature names have a .fileNumber extension now. <2012-04-19 Thu>

• testing for uniqueness of files (filenames) in readMSData <2012-04-19 Thu>

• updated itraqdata.RData <2012-04-19 Thu>

• added a paralle argument to quantify and using paralle = FALSE in vignette, to avoid duplicated display of the command <2012-04-19 Thu>

• defined “reporterNames<-“ generics <2012-04-19 Thu>

• fixed warning in readMSData where all not used for comparison of verctors of length > 1 <2012-04-20 Fri>

Changes in version 1.5.1:

• updated NA warning message in readIspyData <2012-03-05 Mon>

• fixed combineFeatures/combineMatrixFeatures for 1 sample <2012-03-20 Tue>

• image method for MSnSet instances <2012-03-20 Tue>

• fixed bug in plotNA (first t was wring) <2012-03-21 Wed>

• import plot from stats4 <2012-03-21 Wed>

• using reshape2 <2012-03-30 Fri>

Changes in version 1.5.0:

• new devel version bump

ncdfFlow

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

netresponse

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

• added remove.negative.edges function

• added positive.edges argument to detect.responses

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

• igraph dependency moved to igraph0

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

• dmt added to dependencies

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

USER-VISIBLE CHANGES

• added PlotMixtureMultivariate function

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

USER-VISIBLE CHANGES

• added parallelization on update.model.pair step

BUG FIXES

• removed merge updates for potential subnet merges that would exceed max size

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

SIGNIFICANT USER-VISIBLE CHANGES

• added bic.threshold option in detect responses and downstream functions

• latent.class.analysis function replaced with mixture.model

BUG FIXES

• Rd conflicts resolved

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

SIGNIFICANT USER-VISIBLE CHANGES

• changed all documentation into Roxygen

• added bic.mixture.univariate function

• added argument mixture.method in detect.responses and to consecutive downstream functions

BUG FIXES

• added information.criterion option to edge.delta costind.ab calculation

• “c.max <- max.responses - 1”–> “c.max <- max.responses” in vdp.mixt

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

• added the plot.mode = “pca” in plot.responses function

• added tests/mclust-mixture.R example

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

• removed the redundant network.nodes parameter from independent.models input

oligo

Changes in version 1.22:

USER VISIBLE CHANGES

• Improved results by getProbeInfo();

• fitPLM, coefs and resids are now Defunct. Use fitProbeLevelModel, coef and residuals respectively. ‘coef’ and ‘residuals’ follow the standards used elsewhere in R;

BUG FIXES

• Fixed problem caused by the fact that oligoClasses had its own annotation() method when BiocGenerics added a new one;

• Several fixes to probe selector, allowing ‘target’ to be used;

• PA Calls didn’t know about target;

phyloseq

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

phyloseq 1.1.50

• Fixed several compatibility issues to support latest version of ggplot2 (0.9.2).
• Also changes plot_richness_estimates() to plot_richness().

phyloseq 1.1.45

• Backward compatibility for import_qiime_sampleData, now superseded by import_qiime_sample_data
• Added a functioning example based on the GlobalPatterns example sample-map file included in the package extdata.

phyloseq 1.1.44

• Fixed minor bug in tax_glom function. Thanks to Katie Shelef for the bug report. Bug only affected tax_glom behavior when the right-most rank was specified as the position for merging.

phyloseq 1.1.43

• fixed distance() issue from species/taxa replacement for type argument.

phyloseq 1.1.42

• fixed make_network/plot_network issue from species/taxa replacement for type argument.

phyloseq 1.1.41

• Fixed documentation for prune_taxa and prune_samples
• Updated prune_samples method to allow for logical vectors.
• Fixed prune_taxa so that it properly fails with a message if the taxa argument is a logical of wrong length. There was some potential (and no warning) for unpredictable vector-recycling with short vectors in the old implementation.

phyloseq 1.1.40

Huge Update and Renaming Event.

• Made all functions use an underscore for English word delimiter, if they were using an abbreviation.
• Replaced “species” in all function names with “taxa”.
• These changes are all backward compatible, for now, so your old code should work. Let me know if it doesn’t and I will quickly make the adjustment. This will remain true through the next official release, but functional references to “species” will not be supported afterward, except in the occasions where you actually mean taxonomic species, like tax_glom(x, "species").

phyloseq 1.1.33

• Revise taxglom() such that it handles phyloseq and taxonomyTable classes, throws warning otherwise. It should not take a manually-produced character vector, as this is roughly equivalent to functionality supported in other method, especially prune_species()/merge_species().
• Also added unit-tests and executable examples for taxglom().
• Got rid of taxglom.internal, incorporated directly into taxglom(). taxglom() is no longer an S4-method, and doesn’t need to be now that the character-vector argument option is omitted, with S4-class handling delegated to merge_species().
• Updated “taxTab<-“ to be S4 assignment, clearer handling of taxonomy Table assignments, especially useful for taxglom.

phyloseq 1.1.29

• Add unit tests and example files for import_biom (as well as import(“biom”,…) ).

phyloseq 1.1.28

• Added rarefy_even_depth() function for random subsampling of microbiome samples to the same number of reads. Default uses the minimum total reads among the samples in the dataset. This is based on the core “sample” function, which can have its random number generator fixed by set.seed for reproducibility.

phyloseq 1.1.27

• Fix bug in plot_ordination that caused an error rather than produce unannotated plots when sampleData absent in the input.

phyloseq 1.1.23-26

• Added unit tests and bugfixes

phyloseq 1.1.19-22

• Improving import_qiime() importer to handle large datasets, like the HMPv35 dataset, for example, while also providing useful status messages during non-trivial imports that might take 10 minutes or more to complete.

phyloseq 1.1.18

• Added replicate labels as a “Sample” factor in the soilrep dataset.

phyloseq 1.1.17

• Fix possible bug that results from the latest version (0.6+) of igraph not being backward compatible. A stable igraph0 package is available on CRAN as a stop-gap, and so all igraph dependencies were migrated to “igraph0” until the phyloseq-source can be updated to match the igraph latest.

phyloseq 1.1.15

• plot_heatmap: Added default (but adjustable) threshold to omit taxa/sample labels

phyloseq 1.1.14

• Update import_qiime() function to import latest non-BIOM qiime output files. Also added check for presence of taxonomy information (consensus lineage).

phyloseq 1.1.10

• Add plot_heatmap() function, for easy flexible heat maps built with ggplot2

phyloseq 1.1.8-9

• Fix bug for some variants of new BIOM format
• Add import_RDP_otu() import function for new RDP pipeline export format

phyloseq 1.1.7

• Removed the old plot_tree_phyloseq() function, in favor of the new ggplot2-based plot_tree()
• Uncommented / tested formal examples in documentation of plot-functions
• Updated variable names and doc for the plot_taxa_bar() function

phyloseq 1.1.6

• Update vignette with plot_tree() example, replacing the old base-graphics function, plot_tree_phyloseq().
• Fix bug in legend for trees with size mapped to abundance

phyloseq 1.1.5

• Add initial version of tree_plot(), built with ggplot2
• Adds several internal functions borrowed from devel version of ggphylo

phyloseq 1.1.4

• Add errorIfNULL option to auxiliary accessors (e.g. sample.variables(), rank.names())

phyloseq 1.1.1-3

• R version updated to match Bioconductor, R-2.15.0+
• ape-package version updated to 3.0+
• ape-package now import dependency
• ggplot2-package version updated to 0.9.0+
• ggplot2-package now import dependency

PWMEnrich

Changes in version 1.0.2:

• Use core package parallel instead of doMC

Changes in version 1.0.1:

• Fix a typo in test cases and remove doMC as build dependency

Changes in version 1.0.0:

• Initial release of the package

qpgraph

Changes in version 1.14:

NEW FEATURES

• new qpPlotMap() function to show associations between genetic markers and gene expression profiles using their positions along the genome

• conditional independence tests and non-rejection rate estimation with missing data via complete-case analysis and the EM algorithm

• new qpAllCItests() function to perform multiple conditional independence tests with a fixed conditioning set.

• new arguments fix.Q and restrict.Q for functions estimating the non-rejection rate in order to restrict and fix variables in the conditioning subsets of the independence tests.

R453Plus1Toolbox

Changes in version 1.7.4:

• Added ability to read in data from Roche’s latest Amplicon Variant Analyzer (v2.7).

• New method ava2vcf to write the variants in an AVA-Set to a file in VCF format.

• Multiple bugfixes.

ReactomePA

Changes in version 1.1.1:

• remove geneID2Name, instead import EXTID2NAME from DOSE. <2012-03-12, Mon>

• remove most of the codes in enrichPathway, instead import enrich.internal in DOSE. implement some S3 method for mapping. pathID2Name was rename to TERM2NAME, which will called by enrich.internal. <2012-03-12, Tue>

RedeR

Version Date Category Text 2011-03-23 <NA> <NA>

ReQON

Changes in version 1.3.4:

NEW FEATURES

• An additional option has been added to ReadPosErrorPlot.R. The option “startpos” now allows users to designate the starting read position to be plotted. The default start position is 1.

BUG FIXES

• The required version of R has increased to 2.15. Major changes to the ReQON package were made in version 1.2.0, and older versions of R would download ReQON v. 1.0.0, which is incompatible with the current documentation.

• There were minor inconsistencies between the FWSE reported in the output plots and FWSE calculated from the recalibrated BAM file, which has now been fixed.

Changes in version 1.3.2:

NEW FEATURES

• ReQON no longer recalibrates ‘N’ bases. It returns the original quality score for these bases in the output BAM file.

• Minor modifications have been made to FWSEplot.R. Points are now shaded according to the relative frequency of bases assigned that quality score. See the reference manual for more details.

Rgraphviz

Changes in version 2.1:

• Rgraphviz now requires Graphviz >= 2.16.

• Added graphvizCapabilities() that reports the capabilities of Graphviz. This requires Graphviz >= 2.28 and returns NULL if the Rgraphviz installation does not support it.

• Rgraphviz now comes bundled with Graphviz 2.28, greatly simplifying installation.

• Numerous bugfixes for bugs introduced in the 2.x.x versions.

Risa

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

rols

Changes in version 0.99.12:

• updated README.md (for github) and .Rbuildignore <2012-09-19 Wed>

Changes in version 0.99.11:

• updated biocViews <2012-09-18 Tue>

Changes in version 0.99.10:

• using knitr instead of pgfSweave <2012-08-13 Mon>

Changes in version 0.99.9:

• fixed olsQuery issued warning when missing(ontologyNames) irrespective of extact <2012-05-22 Tue>

Changes in version 0.99.8:

• really using pdfSweave <2012-05-18 Fri>

Changes in version 0.99.7:

• using pdfSweave <2012-05-16 Wed>

• changed VignetteIndexEntry <2012-05-16 Wed>

• removed roxygen2 from Suggests <2012-05-16 Wed>

• added README file describinh Rd generation with roxygen2 <2012-05-16 Wed>

Changes in version 0.99.6:

• implementing Mark Carlson’s suggestions

• (Temporarily) removing pgf <2012-05-15 Tue>

• added Collate field <2012-05-15 Tue>

• moving generics and class definitions to AllGenerics.R and AllClasses.R <2012-05-15 Tue>

• olsQuery now repeats query ‘n’ times if reply is empty - see man page for a brief discussion <2012-05-15 Tue>

• updated vignette to discuss off/on-line data access <2012-05-15 Tue>

Changes in version 0.99.5:

• downgraded SSOAP dependency to (>= 0.8.0), as later SSOAP versions are not available through biocLite (due to check errors). rols works with SSOAP 0.8.0 and XMLSchema 0.7.2. <2012-05-11 Fri>

Changes in version 0.99.4:

• added url to DESCRIPTION <2012-05-11 Fri>

• released CVParam validity contrains: now CVParam name must match term or any synonym <2012-05-11 Fri>

• new CVParam constructor <2012-05-11 Fri>

Changes in version 0.99.3:

• minor vignette update <2012-05-04 Fri>

• new CVParam class <2012-05-08 Tue>

• More verbose CVParam validity error msg <2012-05-08 Tue>

• new ‘rep’ method for CVParam <2012-05-09 Wed>

Changes in version 0.99.2:

• olsQuery has a new ‘exact’ parameter <2012-05-04 Fri>

Changes in version 0.99.1:

• import(XMLSchema) to remove warning at startup <2012-05-04 Fri>

Changes in version 0.99.0:

• vignette update <2012-04-30 Mon>

• added GO.db to Suggests for vignette <2012-04-30 Mon>

• bumped version to 0.99 for Bioc submission <2012-04-30 Mon>

Changes in version 0.2.2:

• added a vignette <2011-12-18 Sun>

• added xtable in suggests for vignette <2011-12-18 Sun>

• added parents() and childrenRelations() query functions <2011-12-18 Sun>

Changes in version 0.2.1:

• added specific SSOAP and XMLSchema version requirements <2011-12-18 Sun>

• fixed a couple of typos <2011-12-18 Sun>

Changes in version 0.2.0:

• initial release

RPA

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

• affinity estimates storing option added to rpa.online

• moved sigma2 -> tau2 to make notation compatible with publications

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

NEW FEATURES

• added arguments in rpa.online function: save.batches.dir, keep.batch.files, unique.run.identifier

• changed the default for save.batches option in rpa.online into TRUE

BUG FIXES

• fixed load.batches bug in summarize.batches

Rsamtools

Changes in version 1.10.0:

NEW FEATURES

• BamFile and TabixFile accept argument yieldSize; repeated calls to scanBam and scanTabix return successive yieldSize chunks of the file. readBamGappedAlignments, VariantAnnotation::readVcf automatically gain support for yield’ing through files.

• Add getDumpedAlignments(), countDumpedAlignments(), and flushDumpedAlignments() low-level utilities for manipulating alignments dumped by findMateAlignment().

• Add quickBamCounts() utility for classifying the records in a BAM file according to a set of predefined groups (based on the flag bits) and for counting the nb of records in each group.

SIGNIFICANT USER-VISIBLE CHANGES

• scanBamFlag isValidVendorRead deprecated in favor of isNotPassingQualityControls

• Rename makeGappedAlignmentPairs() arg ‘keep.colnames’ -> ‘use.mcols’.

BUG FIXES

• close razip, bgzip files when done

• bamReverseComplement<- failed to return the updated object

• scanBcfHeader works on remote files

• allow asBam to work without warnings on header-only SAM files

• some bug fixes and and small performance improvements to findMateAlignment()

• fix bug in readBamGappedAlignmentPairs() where fields and tags specified by the user were not propagated to the returned GappedAlignmentPairs object

Rsubread

Changes in version 1.8.0:

NEW FEATURES

• Fine-tuning of read alignment function (align) and exon-exon junction detection function (subjunc).

• Major update to SNP calling algorithm (now use Fisher’ exact tests to call SNPs).

• More efficient implementation for removing duplicated reads (eg. supporting multi-threads and using less memory).

ShortRead

SIGNIFICANT USER-VISIBLE CHANGES

• as(ShortReadQ, “matrix”) now accepts ShortReadQ instances with heterogenous widths, returning a matrix x[i, j] with NA values in when j > width()[i].

NEW FEATURES

• FastqStreamer accepts IRanges for selecting input records

BUG FIXES

• readAligned, type=”BAM” correctly adds requried ‘what’ elements

• FastqSampler would only randomize first read; introduced 1.13.9 2011-12-02, fixed 1.15.4 2012-04-25

• report(qa, …) no longer produces obviously confused base calls per cycle

• FastqFileList would fail to initialize correctly from a character vector

synapter

Changes in version 0.99.15:

• updated ref in package man (2) <2012-09-14 Fri>

• updated Synapter show method to display short log <2012-09-14 Fri>

Changes in version 0.99.14:

• updated ref in package man <2012-09-11 Tue>

Changes in version 0.99.13:

• bumping version number to take all previous changes into account <2012-08-29 Wed>

Changes in version 0.99.12:

• fixed build problem on windows <2012-08-27 Mon>

• updated refs in vignette <2012-08-28 Tue>

Changes in version 0.99.11:

• using dev=’pdf’ in vignette and removing tikzDevice (not on CRAN anymore) from Suggests<2012-08-16 Thu>

Changes in version 0.99.10:

• added tikzDevice suggestion for vignette <2012-08-15 Wed>

Changes in version 0.99.9:

• using knitr instead of pgfSweave <2012-08-13 Mon>

• new verbose arg to loadIdentOnly taken into account by estimateMasterFdr and makeMaster <2012-08-13 Mon>

Changes in version 0.99.8:

• vignette update with summary table <2012-07-17 Tue>

• vignette update with additional PLGS slides <2012-07-17 Tue>

Changes in version 0.99.7:

• updated vignette <2012-07-12 Thu>

• removed README.org file <2012-07-12 Thu>

• added github page in DESCRIPTION <2012-07-12 Thu>

Changes in version 0.99.6:

• Masterpeptides has new fdr and method slots <2012-07-10 Tue>

• added method arg to makeMaster <2012-07-10 Tue>

• fixed non-match precuror.leIDs when using master <2012-07-11 Wed>

Changes in version 0.99.5:

• removed ‘precursor.Mobility’ columns from light merged and matched csv output, as these are not available when a MSe master is used <2012-07-09 Mon>

Changes in version 0.99.4:

• use log2 for t.test <2012-07-05 Thu>

• updates to vignette <2012-07-06 Fri>

Changes in version 0.99.3:

• git/svn integration messing up and testing <2012-07-03 Tue>

• late night testing <2012-07-03 Tue>

Changes in version 0.99.2:

• changed merged to total FDR in MasterFdrResults plot x label, as in manuscript <2012-06-13 Wed>

• mention multtest in vignette <2012-06-13 Wed>

• qvalue refs <2012-06-14 Thu>

• Synapter.Rd updates, to match manuscript nomenclature <2012-06-14 Thu>

• Added ‘Getting help’ section in vignette and package man page <2012-06-14 Thu>

• Changed HDMSe to ident in plotGrid plot legend <2012-06-25 Mon>

Changes in version 0.99.1:

• Latex typo in vignette <2012-06-11 Mon>

• Dan’s suggestions for <2012-06-13 Wed>

Changes in version 0.99.0:

• bump version for Bioconductor submission <2012-06-08 Fri>

TargetSearch

Changes in version 1.14.0:

NEW FEATURES

• New function ‘fixRI’. This function can be used to correct RI markers or to manually force their location to specific retention times if, for example, the RI markers were not co-injected with the biological samples. Replaces the now deprecated ‘fixRIcorrection’.

• New function ‘riMatrix’. This function searches RI markers in RI files instead of CDF files.

• Improvements in CDF import functions: - Automatic detection of m/z range. - Detection and correction of CDF files with non-integer m/z values. These values are converted to nominal mass.

• ImportLibrary: - New parameter ‘file.opt’. A list containing arguments to be passed to ‘read.delim’. - It can take a data frame instead of a file to create a library object.

SIGNIFICANT USER-VISIBLE CHANGES

• Function ‘fixRIcorrection’ is deprecated. Use ‘fixRI’.

BUG FIXES

• The .Call function in FindPeaks.R would incorrectly coerce RI limits to integers instead of double.

• ImportLibrary: - Fixed bug when reading one-metabolite libraries. - Check for unexpected quotation mark characters in input file or input data.frame. They will be removed.

• Profile: check for at least three top masses to calculate spectra similarity scores.

• quantMatrix: use character indeces instead of numeric indeces.

tigre

Changes in version 1.12.0:

• Minor speed optimisation

• Minor documentation reorganisation and updates

TransView

Changes in version 0.99.3:

NEW FEATURES

• Renamed all C files. Registering now takes place in a separate file.

• plotTV can now alternatively take a character vector of IDs matching ‘transcript_id’ in the gtf instead of a GRanges object. This is useful to plot RNA-Seq data matching without regions.

BUG FIXES

• Added PACKAGE argument to .call

• readthrough_pairs argument to parseReads declared experimental.

• Removed the matching RNA-Seq data set and added pasillaBamSubset as an example for RNA-Seq visualisation.

Changes in version 0.99.2:

NEW FEATURES

• Added getter methods for all slots of DensityContainer and inherited classes for individual access. Added setter methods for spliced and ex_name

• removed dc.size() and added the slot ‘size’ instead. Also added env and data_pointer slots to class DensityContainer

• improved documentation of S4 methods with usage section

• gtf2df and macs2df renamed to gtf2gr and macs2gr respectively. They are now returning a GRanges object.

• annotatePeaks takes and returns only GRanges objects.

• id2tss renamed to peak2tss and now returning an updated GRanges object

• plotTV accepts GRanges objects rather than data.frames for gtf and peaks input

BUG FIXES

• Removed all direct slot accessions

• Removed unnecessary call to dyn.load and dyn.unload in parseReads()

Changes in version 0.99.1:

NEW FEATURES

• plotTV returns ordering to reproduce kmeans clustering

BUG FIXES

• sliceNT did not flip the exons on the negative strand

• Argument rowv to plotTV did not work with expression threshold remove_lowex

• Installation on 32bit Windows was not possible

xcms

CHANGES IN VERSION 1.33.16

USER VISIBLE CHANGES

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

CHANGES IN VERSION 1.33.16

UPDATED FEATURES:

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

CHANGES IN VERSION 1.33.15

BUG FIXES

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

CHANGES IN VERSION 1.33.14

BUG FIXES

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

CHANGES IN VERSION 1.33.13

BUG FIXES

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

CHANGES IN VERSION 1.33.12

BUG FIXES

o write.mzData adds Polarity to the file if available

CHANGES IN VERSION 1.33.11

USER VISIBLE CHANGES

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

NEW FEATURES

o placeholder

BUG FIXES

o group.mzClust was failing when result had one peak

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

CHANGED BEHAVIOUR since Version 1.32:

Other Changes since Version 1.32:

• improved mzData writing, now includes MSn spectra and less verbose.
• improved netCDF writing, but not yet good enough for AMDIS

yaqcaffy

Changes in version 1.17.2:

• fixed NOTE about no visible binding for global variable ‘latex’ <2012-09-21 Fri>

• ‘Warning: found methods to import for function ‘as.list’ but not the generic itself’ comes from upstreams. <2012-09-22 Sat>

Changes in version 1.17.1:

• fixed boxplot alignment <2012-05-30 Wed>

• deleted vignette Makefile <2012-05-30 Wed>

Packages removed from the release

No packages have been removed from the release.