October 15, 2013

Bioconductors:

We are pleased to announce Bioconductor 2.13, consisting of 749 software packages, 179 experiment data packages, and more than 690 up-to-date annotation packages.

There are 84 new software packages, and many updates and improvements to existing packages; Bioconductor 2.13 is compatible with R 3.0.2, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release includes an updated Bioconductor Amazon Machine Image.

Visit http://bioconductor.org for details and downloads.

Contents

Getting Started with Bioconductor 2.13

To update to or install Bioconductor 2.13:

  1. Install R 3.0.2. Bioconductor 2.13 has been designed expressly for this version of R.

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

New Software Packages

There are 84 new packages in this release of Bioconductor.

AllelicImbalance: Provides a framework for allelic specific expression investigation using RNA-seq data

ampliQueso: The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq

ArrayTV: Wave correction for genotyping and copy number arrays

ASSET: An R package for subset-based analysis of heterogeneous traits and subtypes

BADER: For RNA sequencing count data, BADER fits a Bayesian hierarchical model. The algorithm returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.

BAGS: R package providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest.

BiGGR: This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package aids in performing flux balance analysis (FBA). Metabolic networks and estimated fluxes can be visualized using hypergraphs.

bioassayR: bioassayR provides tools for statistical analysis of small molecule bioactivity data

BiocParallel: This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

BiocStyle: Provides standard formatting styles for Bioconductor documents. The vignette illustrates use and functionality.

BiRewire: Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes function for the analysis of the introduced randomness across the switching and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks (not bipartite) is also provided.

CexoR: Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package ‘skellam’) is used to detect significant normalized count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package ‘idr’.

ChAMP: The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number aberrations.

ChemmineOB: ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and mor. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.

chipenrich: ChIP-Enrich performs gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.

cleanUpdTSeq: This package uses the Naive Bayes classifier (from e1071) to assign probability values to putative polyadenylation sites (pA sites) based on training data from zebrafish. This will allow the user to separate true, biologically relevant pA sites from false, oligodT primed pA sites.

cleaver: In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

clonotypeR: High throughput analysis of T cell antigen receptor sequences The genes encoding T cell receptors are created by somatic recombination, generating an immense combination of V, (D) and J segments. Additional processes during the recombination create extra sequence diversity between the V an J segments. Collectively, this hyper-variable region is called the CDR3 loop.

The purpose of this package is to process and quantitatively analyse millions of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.

CNVrd2: CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, identify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

cobindR: Finding and analysing co-occuring motifs of transcription factor binding sites in groups of genes

CSSP: Power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process.

customProDB: Generate customized protein sequence database from RNA-Seq data for proteomics search

dagLogo: Visualize significant conserved amino acid sequence pattern in groups based on probability theory

DNaseR: Strand-specific digital genomic footprinting in DNase-seq data. The cumulative Skellam distribution function (package ‘skellam’) is used to detect significant normalized count differences of opposed sign at each DNA strand. This is done in order to determine the protein-binding footprint flanks. Preprocessing of the mapped reads is recommended before running DNaseR (e.g., quality checking and removal of sequence-specific bias).

EBSeq: Differential Expression analysis at both gene and isoform level using RNA-seq data

epivizr: This package provides Websocket communication to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and SummarizedExperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as well.

exomePeak: The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package (Meng, Jia, et al. “Exome-based analysis for RNA epigenome sequencing data.” Bioinformatics 29.12 (2013): 1565-1567.) with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. The package is still under active development, and we welcome all biology and computation scientist for all kinds of collaborations and communications. Please feel free to contact Dr. Jia Meng jia.meng@hotmail.com if you have any questions.

FGNet: Build and visualize functional gene networks from clustering of enrichment analyses in multiple annotation spaces. The package includes an interface to perform the analysis through David and GeneTerm Linker.

flipflop: Flipflop discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.

flowBeads: This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.

flowFit: This package estimate the proliferation of a cell population in cell-tracking dye studies. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.

flowMap: This package provides an algorithm to compare and match cell populations across multiple flow cytometry samples. The method is based on the Friedman-Rafsky test, a nonparametric multivariate statistical test, where two cell distributions match if they occupy a similar feature space. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process.

GOSim: This package implements several functions useful for computing similarities between GO terms and gene products based on their GO annotation. Moreover it allows for computing a GO enrichment analysis

h5vc: This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files. For detail see the webpage at http://www.ebi.ac.uk/~pyl/h5vc.

intansv: This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package.

interactiveDisplay: The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects.

maPredictDSC: This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.

metaSeq: The probabilities by one-sided NOISeq are combined by Fisher’s method or Stouffer’s method

methylMnM: To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.

mitoODE: The package contains the methods to fit a cell-cycle model on cell count data and the code to reproduce the results shown in the paper “Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay” (submitted).

msmsEDA: Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.

msmsTests: Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.

MSstats: A set of tools for protein significance analysis in label-free or LC-MS, SRM and DIA experiments.

mzID: A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less ‘pretty’ output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quick.

neaGUI: neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko et al. (2012). The NEA method extends the overlap statistics in GSEA to network links between genes in the experimental set and those in the functional categories by exploiting biological information in terms of gene interaction network. The neaGUI requires the following R packages: tcltk, KEGG.db, GO.db, reactome.db, org.Hs.eg.db, AnnotationDbi, and hwriter.

NetSAM: The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt (http://www.netgestalt.org) or other network analysis.

omicade4: Multiple co-inertia analysis of omics datasets

OmicCircos: OmicCircos is an R application and package for generating high-quality circular maps for omic data

openCyto: This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.

paircompviz: This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.

pathifier: Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.

plethy: This package provides the infrastructure and tools to import, query and perform basic analysis of whole body plethysmography and metabolism data. Currently support is limited to data derived from Buxco respirometry instruments as exported by their FinePointe software.

ProCoNA: Protein co-expression network construction using peptide level data, with statisical analysis. (Journal of Clinical Bioinformatics 2013, 3:11 doi:10.1186/2043-9113-3-11)

prot2D: The purpose of this package is to analyze (i.e. Normalize and select significant spots) data issued from 2D GEl experiments

PSICQUIC: PSICQUIC is a project within the HUPO Proteomics Standard Initiative (HUPO-PSI). It standardises programmatic access to molecular interaction databases.

qcmetrics: The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.

qusage: This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. For questions, contact Chris Bolen (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu)

Rchemcpp: The Rchemcpp package implements the marginalized graph kernel and extensions, Tanimoto kernels, graph kernels, pharmacophore and 3D kernels suggested for measuring the similarity of molecules.

RDAVIDWebService: Tools for retrieving data from the Database for Annotation, Visualization and Integrated Discovery (DAVID) using Web Services into R objects. This package offers the main functionalities of DAVID website including: i) user friendly connectivity to upload gene/background list/s, change gene/background position, select current specie/s, select annotations, etc. ii) Reports of the submitted Gene List, Annotation Category Summary, Gene/Term Clusters, Functional Annotation Chart, Functional Annotation Table

rfPred: Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to be connected on the Internet or to download the TabixFile and index (approximately 3.3 Go).

Roleswitch: Infer Probabilities of MiRNA-mRNA Interaction Signature (ProMISe) using paired expression data from a single sample. Roleswitch operates in two phases by inferring the probability of mRNA (miRNA) being the targets (“targets”) of miRNA (mRNA), taking into account the expression of all of the mRNAs (miRNAs) due to their potential competition for the same miRNA (mRNA). Due to dynamic miRNA repression in the cell, Roleswitch assumes that the total transcribed mRNA levels are higher than the observed (equilibrium) mRNA levels and iteratively updates the total transcription of each mRNA targets based on the above inference.

RRHO: The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test.

RTN: This package provides classes and methods for transcriptional network inference and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies, e.g., gene set enrichment, shadow and synergy analyses.

rTRM: rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.

rTRMui: This package provides a web interface to compute transcriptional regulatory modules with rTRM.

seqCNA: Copy number analysis of high-throughput sequencing cancer data with fast summarization, extensive filtering and improved normalization

SeqVarTools: An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.

shinyTANDEM: This package provides a GUI interface for rTANDEM. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files.

SigFuge: Algorithm for testing significance of clustering in RNA-seq data.

SimBindProfiles: SimBindProfiles identifies common and unique binding regions in genome tiling array data. This package does not rely on peak calling, but directly compares binding profiles processed on the same array platform. It implements a simple threshold approach, thus allowing retrieval of commonly and differentially bound regions between datasets as well as events of compensation and increased binding.

SpacePAC: Identifies clustering of somatic mutations in proteins via a simulation approach while considering the protein’s tertiary structure.

spliceR: An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

spliceSites: Align gap positions from RNA-seq data

sRAP: This package provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.

sSeq: The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.

STRINGdb: The STRINGdb package provides a user-friendly interface to the STRING protein-protein interactions database ( http://www.string-db.org ).

supraHex: A supra-hexagonal map is a giant hexagon on a 2-dimensional grid seamlessly consisting of smaller hexagons. It is supposed to train, analyse and visualise a high-dimensional omics data. The supraHex is able to carray out gene/meta-gene clustering and sample correlation, plus intuitive visualisations to facilitate exploratory analysis. Uniquely to this package, users can simultaneously understand their own omics data in a sample-specific fashion but without loss of information on large genes.

SwimR: SwimR is an R-based suite that calculates, analyses, and plots the frequency of C. elegans swimming behavior over time. It places a particular emphasis on identifying paralysis and quantifying the kinetic elements of paralysis during swimming. Data is input to SwipR from a custom built program that fits a 5 point morphometric spine to videos of single worms swimming in a buffer called Worm Tracker.

TargetScore: Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.

TCC: This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in other sophisticated packages (especially edgeR, DESeq, and baySeq).

TFBSTools: Software package for TFBS.

tRanslatome: Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.

trio: Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.

vtpnet: variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828

XVector: Memory efficient S4 classes for storing sequences “externally” (behind an R external pointer, or on disk).

NEWS from new and existing packages

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

ADaCGH2

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ASSET

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BaseSpaceR

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bioassayR

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categoryCompare

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CellNOptR

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ChemmineOB

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cleaver

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Changes in version 2012-09-06:

clusterProfiler

Changes in version 1.9.4:

Changes in version 1.9.3:

Changes in version 1.9.1:

CNAnorm

1.7.1:

CNORfuzzy

Changes in version 1.4.0:

Changes in version 1.30.0:

DART

Changes in version 1.7.1:

deepSNV

Changes in version 1.99.3 (2013-07-25):

Updates

Bugfixes

Changes in version 1.99.2 (2013-07-11):

Updates

Bugfixes

Changes in version 1.99.1 (2013-06-25):

Updates

Bugfixes

Updates

Bugfixes

Changes in version 1.99.0 (2013-04-30):

Updates

Updates

Changes in version 1.7.4 (2013-09-28):

Updates

Updates

deltaGseg

Changes in version 1.1.3:

DESeq2

Changes in version 1.1.32:

Changes in version 1.1.31:

Changes in version 1.1.24:

Changes in version 1.1.23:

Changes in version 1.1.21:

DEXSeq

Changes in version 2013-09-12:

Changes in version 2013-02-27:

Changes in version 2012-11-28:

Changes in version 2012-06-26:

Changes in version 2012-05-21:

Changes in version 2011-10-03:

Changes in version 2011-07-12:

Changes in version 2011-07-01:

DiffBind

Changes in version 1.8.0:

DOSE

Changes in version 1.99.6:

Changes in version 1.99.5:

Changes in version 1.99.4:

Changes in version 1.99.3:

Changes in version 1.99.1:

Changes in version 1.99.0:

Changes in version 1.7.1:

DSS

Changes in version 1.7.0:

Changes in version 1.6.0:

EBImage

Changes in version 4.4.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

edgeR

Changes in version 3.3.8:

Changes in version 3.3.5:

Changes in version 3.3.4:

Changes in version 3.3.3:

Changes in version 3.3.2:

Changes in version 3.3.1:

eiR

Changes in version 1.2.0:

NEW FEATURES

NEW FEATURES

NEW FEATURES

NEW FEATURES

fabia

Changes in version 2.6.1:

NEW FEATURES

NEW FEATURES

FGNet

Changes in version 1.0.0:

NEW FEATURES

flowType

Changes in version 2.0.0:

NEW FEATURES

NEW FEATURES

fmcsR

Changes in version 1.4.0:

NEW FEATURES

NEW FEATURES

gage

Changes in version 2.11.3:

gCMAP

Changes in version 1.5.4:

Changes in version 1.5.3:

Changes in version 1.5.2:

Changes in version 1.5.1:

gCMAPWeb

Changes in version 1.1.7:

Changes in version 1.1.6:

Changes in version 1.1.2:

Changes in version 1.1.1:

geNetClassifier

Changes in version 1.1.1:

BUG FIXES

GeneticsPed

Changes in version 2007-09-12:

Changes in version 2007-04-25:

Changes in version 2007-04-19:

Changes in version 2007-04-18:

Changes in version 2007-04-06:

Changes in version 2007-04-01:

Changes in version 2007-04:

Changes in version 2007-03-02:

Changes in version 2006-03-29:

Changes in version 2006-03-16:

GenomicFeatures

Changes in version 1.14:

NEW FEATURES

BUG FIXES

GenomicRanges

Changes in version 1.14.0:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

GGtools

Changes in version 4.10:

Changes in version 4.9:

gmapR

Changes in version 1.4.0:

NEW FEATURES

USER-VISIBLE CHANGES

BUG FIXES

GOSemSim

Changes in version 1.19.3:

Changes in version 1.19.2:

Changes in version 1.19.1:

GSEABase

Changes in version 1.23:

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

GWASTools

Changes in version 1.7.8:

Changes in version 1.7.7:

Changes in version 1.7.6:

Changes in version 1.7.5:

Changes in version 1.7.4:

Changes in version 1.7.3:

hapFabia

Changes in version 1.2.2:

HiTC

Changes in version 1.5.2:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.5.1:

BUG FIXES

BUG FIXES

BUG FIXES

BUG FIXES

BUG FIXES

hpar

Changes in version 1.3.1:

Changes in version 1.3.0:

HTSeqGenie

Changes in version 3.11.10:

Changes in version 3.11.9:

Changes in version 3.11.8:

Changes in version 3.11.7:

Changes in version 3.11.6:

Changes in version 3.11.5:

Changes in version 3.11.4:

Changes in version 3.11.3:

Changes in version 3.11.2:

Changes in version 3.11.1:

Changes in version 3.11.0:

Changes in version 3.10.1:

htSeqTools

Changes in version 1.7.1:

HTSFilter

Changes in version 1.0.1:

hyperdraw

Changes in version 1.13.1:

illuminaio

Changes in version 0.3.9:

Changes in version 0.3.8:

Changes in version 0.3.6:

Changes in version 0.3.5 (2013-08-02):

imageHTS

Changes in version 1.12.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

intansv

Changes in version 0.99.3:

Notes

Notes

iPAC

Changes in version 1.5.2:

IPPD

09-29-2010:

01-12-2011:

01-17-2012:

IRanges

Changes in version 1.20.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

isobar

Changes in version 1.7.6:

Changes in version 1.7.5:

Changes in version 1.7.4:

Changes in version 1.7.3:

Changes in version 1.7.2:

Changes in version 1.7.1:

KEGGgraph

KEGGprofile

lmdme

Changes in version 1.3.1:

BUGS FIXED

Changes in version 1.3.0:

MINOR CHANGES

MANOR

Changes in version 2013-07-03 (2013-07-03):

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

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

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

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

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

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

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

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

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

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

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

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

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

metagenomeSeq

Changes in version 1.2 (2013-08-20):

Changes in version 1.1 (2013-06-25):

minfi

Changes in version 1.7:

mitoODE

Changes in version 0.99.6:

Changes in version 0.99.5:

Changes in version 0.99.2:

motifStack

Changes in version 1.5.4:

NEW FEATURES

BUG FIXES

Changes in version 1.5.3:

NEW FEATURES

BUG FIXES

Changes in version 1.5.2:

NEW FEATURES

BUG FIXES

Changes in version 1.5.1:

NEW FEATURES

BUG FIXES

MSnbase

Changes in version 1.9.12:

Changes in version 1.9.11:

Changes in version 1.9.10:

Changes in version 1.9.9:

Changes in version 1.9.8:

Changes in version 1.9.7:

Changes in version 1.9.6:

Changes in version 1.9.5:

Changes in version 1.9.4:

Changes in version 1.9.3:

Changes in version 1.9.2:

Changes in version 1.9.1:

Changes in version 1.9.0:

MSstats

Changes in version 1.99.1:

Changes in version 1.99.0:

mzID

Changes in version 0.3.1:

Changes in version 0.3.0:

NEW FEATURES AND FUNCTIONS

Changes in version 0.2.1:

NEW FEATURES AND FUNCTIONS

NEW FEATURES AND FUNCTIONS

NEW FEATURES AND FUNCTIONS

Changes in version 0.1-1:

NEW FEATURES AND FUNCTIONS

Changes in version 0.0-2:

NEW FEATURES AND FUNCTIONS

PERFORMANCE

Changes in version 0.0-1:

NEW FEATURES AND FUNCTIONS

NEW FEATURES AND FUNCTIONS

mzR

Changes in version 1.7.4:

Changes in version 1.7.3:

Changes in version 1.7.2:

Changes in version 1.7.1:

NOISeq

Changes in version 2.2.0 (2013-10-14):

OSAT

Changes in version 1.8.1:

BUG FIXES

NEW FUNCTION

pathview

Changes in version 1.1.7:

Changes in version 1.1.6:

Changes in version 1.1.5:

Changes in version 1.1.3:

phyloseq

piano

Changes in version 1.2.0:

NEW FEATURES

USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.0.7:

USER-VISIBLE CHANGES

Changes in version 1.0.6:

USER-VISIBLE CHANGES

Changes in version 1.0.5:

BUG FIXES

USER-VISIBLE CHANGES

Changes in version 1.0.4:

BUG FIXES

Changes in version 1.0.3:

USER-VISIBLE CHANGES

Changes in version 1.0.2:

USER-VISIBLE CHANGES

Changes in version 1.0.1:

USER-VISIBLE CHANGES

BUG FIXES

plethy

Changes in version 0.99.4:

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

plgem

Changes in version 1.33.1:

ProCoNA

Changes in version 0.99.2:

Changes in version 0.99.1:

pRoloc

Changes in version 1.1.8:

Changes in version 1.1.7:

Changes in version 1.1.6:

Changes in version 1.1.5:

Changes in version 1.1.4:

Changes in version 1.1.3:

Changes in version 1.1.2:

Changes in version 1.1.1:

Changes in version 1.1.0:

PWMEnrich

Changes in version 2.4.4:

Changes in version 2.4.2:

Changes in version 2.4.0:

Changes in version 2.3.2:

Changes in version 2.3.1:

qcmetrics

Changes in version 0.99.3:

Changes in version 0.99.2:

Changes in version 0.99.1:

Changes in version 0.99.0:

qpgraph

Changes in version 1.18:

USER VISIBLE CHANGES

NEW FEATURES

BUG FIXES

QuasR

Changes in version 1.2.0:

NEW FEATURES

NEW FEATURES

NEW FEATURES

Rbowtie

Changes in version 1.1.1:

NEW FEATURES

RchyOptimyx

2.0:

RDAVIDWebService

Changes in version 0.99.1:

MINOR CHANGES

Changes in version 0.99.0:

DOCUMENTATION

ReactomePA

Changes in version 1.5.3:

Changes in version 1.5.2:

Changes in version 1.5.1:

RedeR

Changes in version 2.0.0:

ReportingTools

Changes in version 2013-4-1:

Rgraphviz

Changes in version 2.5:

rhdf5

Changes in version 2.6.0:

NEW FEATURES

USER VISIBLE CHANGES

Risa

1.3.3: 1. Fixed definitions of assay.filenames.per.sample and factors. 2. Fixed regulession of investigation file (i_) to be considered at the beginning of the string. 3. Added CITATION file.

RNASeqPower

Changes in version 1.0.1:

rols

Changes in version 1.3.2:

Changes in version 1.3.1:

Changes in version 1.3.0:

ROntoTools

Changes in version 1.2.0:

rqubic

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

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

Rsamtools

Changes in version 1.14.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

rSFFreader

Rsubread

Changes in version 1.12.0:

NEW FEATURES

NEW FEATURES

NEW FEATURES

NEW FEATURES

NEW FEATURES

NEW FEATURES

NEW FEATURES

NEW FEATURES

NEW FEATURES

rTANDEM

Changes in version 1.1.6:

NEW FEATURES

Changes in version 1.1.5:

BUG FIXES

NEW FEATURES

Changes in version 1.1.4:

NEW FEATURES

BUG FIXES

RTCA

Changes in version 2009-07-13:

RTN

Changes in version 1.0.0:

rtracklayer

Changes in version 1.22:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

rTRM

Changes in version 1.0:

rTRMui

Changes in version 1.0:

SBMLR

Changes in version 1.57.1:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

Notes

SCAN.UPC

Changes in version 2.2.8:

NEW FEATURES

OTHER

SeqArray

Changes in version 1.1.5:

Changes in version 1.1.4:

Changes in version 1.1.3:

Changes in version 1.1.2:

Changes in version 1.1.1:

SeqGSEA

Changes in version 1.1.5 (2013-09-01):

Changes in version 1.1.4 (2013-08-10):

Changes in version 1.1.3 (2013-06-13):

Changes in version 1.1.2 (2013-05-01):

Changes in version 1.1.1 (2013-04-23):

shinyTANDEM

Changes in version 0.99.1:

NEW FEATURES

Changes in version 0.99.0:

ShortRead

Changes in version 1.19:

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

BUG FIXES

SpacePAC

Changes in version 0.99.0:

spliceR

Changes in version 1.0.0:

supraHex

Changes in version 1.0.0:

NEW FEATURES

NEW FEATURES

NEW FEATURES

synapter

Changes in version 1.3.4:

Changes in version 1.3.3:

Changes in version 1.3.2:

Changes in version 1.3.1:

Changes in version 1.3.0:

TargetSearch

Changes in version 1.18.0:

NEW FEATURES

NEW FEATURES

NEW FEATURES

TCC

Changes in version 1.2.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.1.3:

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.0.0:

SIGNIFICANT USER-VISIBLE CHANGES

TEQC

Changes in version 3.0.0:

Changes in version 2.9.2:

tigre

Changes in version 1.14.1:

BUG FIXES

TransView

Changes in version 1.5.9:

BUG FIXES

Changes in version 1.5.8:

BUG FIXES

Changes in version 1.5.7:

BUG FIXES

Changes in version 1.5.6:

BUG FIXES

Changes in version 1.5.5:

BUG FIXES

Changes in version 1.5.4:

NEW FEATURES

BUG FIXES

Changes in version 1.5.3:

NEW FEATURES

Changes in version 1.5.2:

BUG FIXES

Changes in version 1.5.1:

BUG FIXES

triplex

Changes in version 1.2.0:

NEW FEATURES

NEW FEATURES

NEW FEATURES

NEW FEATURES

VariantAnnotation

Changes in version 1.8.0:

NEW FEATURES

MODIFICATIONS

DEPRECATED and DEFUNCT

BUG FIXES

VariantTools

Changes in version 1.4:

NEW FEATURES

USER-VISIBLE CHANGES

BUG FIXES

xcms

Changes in version 1.37.6:

NEW FEATURE

USER VISIBLE CHANGES

BUG FIXES

Changes in version 1.37.5:

BUG FIXES

Changes in version 1.37.4:

BUG FIXES

Changes in version 1.37.3:

BUG FIXES

Changes in version 1.37.1:

BUG FIXES

NEW FEATURES

xps

Changes in version 3.00:

VERSION xps-1.21.5

VERSION xps-1.21.4

VERSION xps-1.21.3

VERSION xps-1.21.2

VERSION xps-1.21.1

VERSION xps-1.19.10

VERSION xps-1.19.9

VERSION xps-1.19.8

VERSION xps-1.19.7

VERSION xps-1.19.2 - 6

VERSION xps-1.19.1

Changes in version 2.15:

VERSION xps-1.17.2

VERSION xps-1.17.1

VERSION xps-1.15.2

VERSION xps-1.15.1

Changes in version 2.14.0:

VERSION xps-1.13.10

VERSION xps-1.13.9

VERSION xps-1.13.8

VERSION xps-1.13.7

VERSION xps-1.13.6

VERSION xps-1.13.5

VERSION xps-1.13.4

VERSION xps-1.13.3

VERSION xps-1.13.2

VERSION xps-1.13.1

Changes in version 2.13.0:

VERSION xps-1.11.12

VERSION xps-1.11.11

VERSION xps-1.11.10

VERSION xps-1.11.9

VERSION xps-1.11.8

VERSION xps-1.11.7

VERSION xps-1.11.6

VERSION xps-1.11.5

VERSION xps-1.11.4

VERSION xps-1.11.3

VERSION xps-1.11.1

Changes in version 2.12.0:

VERSION xps-1.9.9

VERSION xps-1.9.8

VERSION xps-1.9.7

VERSION xps-1.9.6

VERSION xps-1.9.5

VERSION xps-1.9.4

VERSION xps-1.9.3

VERSION xps-1.9.2

VERSION xps-1.9.1

Changes in version 2.11.0:

VERSION xps-1.7.9

VERSION xps-1.7.8

VERSION xps-1.7.7

VERSION xps-1.7.6

VERSION xps-1.7.4

VERSION xps-1.7.3

VERSION xps-1.7.2

VERSION xps-1.7.1

Changes in version 2.10.0:

VERSION xps-1.5.19

VERSION xps-1.5.18

VERSION xps-1.5.17

VERSION xps-1.5.16

VERSION xps-1.5.15

VERSION xps-1.5.14

VERSION xps-1.5.13

VERSION xps-1.5.12

VERSION xps-1.5.9

VERSION xps-1.5.8

VERSION xps-1.5.7

VERSION xps-1.5.4

VERSION xps-1.5.3

VERSION xps-1.5.1

Changes in version 2.9.0:

VERSION xps-1.3.13

VERSION xps-1.3.12

VERSION xps-1.3.11

VERSION xps-1.3.8

VERSION xps-1.3.6

VERSION xps-1.3.5

VERSION xps-1.3.4

VERSION xps-1.3.3

VERSION xps-1.3.1

Changes in version 2.8.0:

VERSION xps-1.1.9

VERSION xps-1.1.8

VERSION xps-1.1.7

VERSION xps-1.1.6

VERSION xps-1.1.5

VERSION xps-1.1.4

VERSION xps-1.1.3

VERSION xps-1.1.2

VERSION xps-1.1.1

Changes in version 2.7.0:

VERSION xps-0.99.11

VERSION xps-0.99.10

VERSION xps-0.99.9

VERSION xps-0.99.8

VERSION xps-0.99.3

VERSION xps-0.4.3

VERSION xps-0.4.2

VERSION xps-0.4.1

VERSION xps-0.4.0

Packages removed from the release

The following packages are no longer in the release:

dualKS, externalVector, GeneGroupAnalysis, iFlow, KEGGSOAP, xmapcore