Bioconductors:

We are pleased to announce Bioconductor 2.14, consisting of 824 software packages, 200 experiment data packages, and more than 860 up-to-date annotation packages.

There are 77 new software packages, and many updates and improvements to existing packages; Bioconductor 2.14 is compatible with R 3.1.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release includes an updated Bioconductor [Amazon Machine Image] (http://bioconductor.org/help/bioconductor-cloud-ami/).

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

Contents

Getting Started with Bioconductor 2.14

To update to or install Bioconductor 2.14:

  1. Install R 3.1.0. Bioconductor 2.14 has been designed expressly for this version of R.

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

New Software Packages

There are 77 new packages in this release of Bioconductor.

ABSSeq - Inferring differential expression genes by absolute expression differences between two groups, utilizing generalized Poisson model to account for over-dispersion across samples and heterogeneity of differential expression across genes.

alsace - Alternating Least Squares (or Multivariate Curve Resolution) for analytical chemical data, in particular hyphenated data where the first direction is a retention time axis, and the second a spectral axis. Package builds on the basic als function from the ALS package and adds functionality for high-throughput analysis, including definition of time windows, clustering of profiles, retention time correction, etcetera.

asmn - Performs all sample mean normalization using raw data output from BeadStudio and MethyLumiM data.

ASSIGN - ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literatures or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.

AtlasRDF - Query the Gene Expression Atlas RDF data at the European Bioinformatics Institute using genes, experimental factors (such as disease, cell type, compound treatments), pathways and proteins. Also contains a function to perform an enrichment of your gene list across Experimental Factor Ontology (EFO) using the Atlas background set.

Basic4Cseq - Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

BEAT - Model-based analysis of single-cell methylation data

BiocCheck - Bioconductor-specific package checks

biosvd - The biosvd package contains functions to reduce the input data set from the feature x assay space to the reduced diagonalized eigenfeature x eigenassay space, with the eigenfeatures and eigenassays unique orthonormal superpositions of the features and assays, respectively. Results of SVD applied to the data can subsequently be inspected based on generated graphs, such as a heatmap of the eigenfeature x assay matrix and a bar plot with the eigenexpression fractions of all eigenfeatures. These graphs aid in deciding which eigenfeatures and eigenassays to filter out (i.e., eigenfeatures representing steady state, noise, or experimental artifacts; or when applied to the variance in the data, eigenfeatures representing steady-scale variance). After possible removal of steady state expression, steady-scale variance, noise and experimental artifacts, and after re-applying SVD to the normalized data, a summary html report of the eigensystem is generated, containing among others polar plots of the assays and features, a table with the list of features sortable according to their coordinates, radius and phase in the polar plot, and a visualization of the data sorted according to the two selected eigenfeatures and eigenassays with colored feature/assay annotation information when provided. This gives a global picture of the dynamics of expression/intensity levels, in which individual features and assays are classified in groups of similar regulation and function or similar cellular state and biological phenotype.

CAFE - Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input

ccrepe - The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets. In microbial abundance data, for example, the total abundances of all microbes sum to one; CCREPE is designed to take this constraint into account when assigning p-values to similarity measures between the microbes. The package has two functions: ccrepe: Calculates similarity measures, p-values and q-values for relative abundances of bugs in one or two body sites using bootstrap and permutation matrices of the data. nc.score: Calculates species-level co-variation and co-exclusion patterns based on an extension of the checkerboard score to ordinal data.

ChIPQC - Quality metrics for ChIPseq data

ChIPseeker - This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak. Visualization functions are implemented to summarize genomic annotation, distance to TSS, and overlap of peaks or genes.

Clomial - Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.

CNEr - Large-scale identification and advanced visualization of sets of conserved noncoding elements.

COHCAP - This package provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.

COMPASS - COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.

compcodeR - This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data and interfaces to several packages for performing the differential expression analysis.

CompGO - This package contains functions to accomplish several tasks. It is able to download full genome databases from UCSC, import .bed files easily, annotate these .bed file regions with genes (plus distance) from aforementioned database dumps, interface with DAVID to create functional annotation and gene ontology enrichment charts based on gene lists (such as those generated from input .bed files) and finally visualise and compare these enrichments using either directed acyclic graphs or scatterplots.

COPDSexualDimorphism - Sexual dimoprhic and COPD differential (SDCD) analysis contrasts regression coefficients from two stratified analysis. Stratification can be done in two ways: by COPD status or by sex. For COPD-stratified analysis, SDCD analysis contrasts sexual dimorphism between cases and controls, while sex-stratified SDCD analsysis contrasts COPD differential expression pattern between males and females. The package is meant to be used in conjunction with the package limma.

CopyNumber450k - This package contains a set of functions that allow CNV calling from Illumina 450k methylation microarrays.

CoverageView - This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome

CRISPRseek - The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. This package leverages Biostrings and BSgenome packages.

DMRcate - De novo identification and extraction of differentially methylated regions (DMRs) in the human genome using Illumina Infinium HumanMethylation450 BeadChip array data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes bedGraph and plotting functions.

DMRforPairs - DMRforPairs allows researchers to compare n>=2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishes DMRforPairs from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance.

dualKS - This package implements a Kolmogorov Smirnov rank-sum based algorithm for training (i.e. discriminant analysis--identification of genes that discriminate between classes) and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the "multiclass" problem. That is, it can discriminate between more than 2 classes.

EDDA - EDDA can aid in the design of a range of common experiments such as RNA-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance.

ELBOW - Elbow an improved fold change test that uses cluster analysis and pattern recognition to set cut off limits that are derived directly from intrareplicate variance without assuming a normal distribution for as few as 2 biological replicates. Elbow also provides the same consistency as fold testing in cross platform analysis. Elbow has lower false positive and false negative rates than standard fold testing when both are evaluated using T testing and Statistical Analysis of Microarray using 12 replicates (six replicates each for initial and final conditions). Elbow provides a null value based on initial condition replicates and gives error bounds for results to allow better evaluation of significance.

fastLiquidAssociation - This package extends the function of the LiquidAssociation package for genome-wide application. It integrates a screening method into the LA analysis to reduce the number of triplets to be examined for a high LA value and provides code for use in subsequent significance analyses.

flowBin - Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers.

flowCL - Semantic labelling of flow cytometric cell populations.

flowCyBar - A package to analyze flow cytometric data using gate information to follow population/community dynamics

flowMatch - Matching cell populations and building meta-clusters and templates from a collection of FC samples.

FRGEpistasis - A Tool for Epistasis Analysis Based on Functional Regression Model

gaucho - Use genetic algorithms to determine the relationship between clones in heterogenous populations such as cancer sequencing samples

GeneOverlap - Test two sets of gene lists and visualize the results.

geneRxCluster - Detect Differential Clustering of Genomic Sites such as gene therapy integrations. The package provides some functions for exploring genomic insertion sites originating from two different sources. Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of False Discovery Rates (FDRs) providing statistical methods for comparing retroviral vectors. A scan statistic for comparing two vectors using multiple window widths to detect clustering differentials and compute FDRs is implemented here.

GenomeInfoDb - Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

GenomicAlignments - Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

GenomicFiles - This package provides infrastructure for parallel queries distributed 'by file' or 'by range'. User defined map and reduce functions provide added flexibility for data combination and manipulation.

GOTHiC - This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.

GSCA - GSCA takes as input several lists of activated and repressed genes. GSCA then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. GSCA provides both traditional R functions and interactive, user-friendly user interface.

iClusterPlus - Integrative clustering of multiple genomic data using a joint latent variable model

INPower - An R package for computing the number of susceptibility SNPs and power of future studies

massiR - Predicts the sex of samples in gene expression microarray datasets

MeSHDbi - The package is unified implementation of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db and also is interface to construct Gene- MeSH package (org.MeSH.XXX.db). loadMeSHDbiPkg import sqlite file and generate org.MeSH.XXX.db.

meshr - A set of annotation maps describing the entire MeSH assembled using data from MeSH

messina - Messina is a collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression.

metaMS - MS-based metabolomics data processing and compound annotation pipeline.

metaseqR - Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

MIMOSA - Modeling count data using Dirichlet-multinomial and beta- binomial mixtures with applications to single-cell assays.

Mirsynergy - Detect synergistic miRNA regulatory modules by overlapping neighbourhood expansion.

MLSeq - This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART, to RNA-Seq data.

mmnet - This package gives the implementations microbiome metabolic network constructing and analyzing. It introduces a unique metagenomic systems biology approach, mapping metagenomic data to the KEGG global metabolic pathway and constructing a systems-level network. The system-level network and the next topological analysis will be of great help to analysis the various functional properties, including regulation and metabolic functionality of the metagenome.

NetPathMiner - NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.

nondetects - Methods to model and impute non-detects in the results of qPCR experiments.

npGSEA - Current gene set enrichment methods rely upon permutations for inference. These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. We are able to reduce the computational burden and granularity issues of permutation testing with our method, which is implemented in this package. npGSEA calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.

PECA - Calculates Probe-level Expression Change Averages (PECA) to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively.

PhenStat - Package contains methods for statistical analysis of phenotypic data such as Mixed Models and Fisher Exact Test.

QDNAseq - Quantitative DNA sequencing for chromosomal aberrations.

Rariant - The 'Rariant' package identifies single nucleotide variants from sequencing data based on the difference of binomially distributed mismatch rates between matched samples.

Rcpi - The Rcpi package offers an R/Bioconductor package emphasizing the comprehensive integration of bioinformatics and chemoinformatics into a molecular informatics platform for drug discovery.

RefNet - Molecular interactions with metadata, some archived, some dynamically obtained

roar - Identify preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.

rpx - This package implements an interface to proteomics data submitted to the ProteomeXchange consortium.

sangerseqR - This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms.

sapFinder - sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.

savR - Parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots.

scsR - Corrects genome-wide siRNA screens for seed mediated off-target effect. Suitable functions to identify the effective seeds/miRNAs and to visualize their effect are also provided in the package.

SomaticSignatures - The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs).

Sushi - Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures

TitanCNA - Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalenece of clonal clusters in tumour whole genome sequencing data.

trackViewer - plot ChIP-seq, RNA-seq, miRNA-seq, DNA-seq and etc NGS sequence data, especially for big files.

UNDO - UNDO is an R package for unsupervised deconvolution of tumor and stromal mixed expression data. It detects marker genes and deconvolutes the mixing expression data without any prior knowledge.

unifiedWMWqPCR - This packages implements the unified Wilcoxon-Mann- Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.

VariantFiltering - Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minimum allele frequencies across human populations, splice site strength, conservation, etc.

viper - Inference of protein activity from gene expression data, including the VIPER and msVIPER algorithms

NEWS from new and existing packages

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

ADaCGH2

Changes in version 2.3.10 (2013-12-27):

Changes in version 2.3.9 (2013-11-28):

Changes in version 2.3.8 (2013-11-26):

Changes in version 2.3.7 (2013-11-26):

Changes in version 2.3.6 (2013-11-24):

Changes in version 2.3.5 (2013-11-11):

Changes in version 2.3.4 (2013-11-09):

Changes in version 2.3.3:

Changes in version 2.3.2 (2013-10-22):

Changes in version 2.3.1 (2013-10-20):

Changes in version 2.3.0 (2013-10-20):

affxparser

Changes in version 1.36.0 (2014-04-11):

Changes in version 1.35.3 (2014-02-28):

Changes in version 1.35.2 (2014-02-28):

Changes in version 1.35.1 (2014-02-27):

Changes in version 1.35.0 (2013-10-14):

AllelicImbalance

Changes in version 1.2.0:

NEW FEATURES

BUG FIXES

alsace

Changes in version 0.2:

annmap

Changes in version 1.5.10:

Changes in version 1.5.8:

Changes in version 1.5.7:

Changes in version 1.5.6:

Changes in version 1.5.5:

Changes in version 1.5.4:

Changes in version 1.5.3:

AnnotationDbi

Changes in version 1.26:

NEW FEATURES and API changes

BUG FIXES AND CODE MAINTENANCE

AnnotationHub

Changes in version 1.4.0:

NEW FEATURES

SIGNIFICANT USER VISIBLE CHANGES

BUG FIXES

aroma.light

Changes in version 2.0.0 (2014-04-11):

Changes in version 1.99.3 (2014-03-31):

BaseSpaceR

Changes in version 1.7:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

BiGGR

Changes in version 1.1.4:

Changes in version 1.1.3:

BiocInstaller

Changes in version 1.14.0:

NEW FEATURES

BiocParallel

Changes in version 0.5.5:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 0.5.2:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BiocStyle

Changes in version 1.2.0:

USER VISIBLE CHANGES

BUG FIXES

biomvRCNS

Changes in version 1.3.3:

NEW FEATURES

BUG FIXES

Changes in version 1.3.2:

BUG FIXES

bsseq

Changes in version 0.11:

bumphunter

Changes in version 1.3.5:

Changes in version 1.3:

CAFE

Changes in version 0.99.2:

Changes in version 0.99.1:

CAMERA

CHANGES IN VERSION 1.19.1

CellNOptR

Changes in version 1.10.0 (2014-03-13):

ChemmineOB

Changes in version 1.2.0:

NEW FEATURES

ChemmineR

Changes in version 2.16.0:

NEW FEATURES

chimera

Changes in version 1.5.2:

NEW FEATURES

ChIPpeakAnno

Changes in version 2.11.4:

NEW FEATURE

Changes in version 2.11.3:

NEW FEATURE

ChIPQC

Changes in version 1.0.0:

cisPath

Changes in version 1.3.3:

Changes in version 1.3.1:

cleanUpdTSeq

Changes in version 1.1.3:

NEW FEATURES

BUG FIXES

Changes in version 1.1.2:

NEW FEATURES

BUG FIXES

Changes in version 1.1.1:

NEW FEATURES

BUG FIXES

Changes in version 1.1.0:

NEW FEATURES

BUG FIXES

cleaver

Changes in version 1.1.8 (2014-03-26):

Changes in version 1.1.7 (2014-03-25):

Changes in version 1.1.5 (2014-02-25):

Changes in version 1.1.4 (2013-12-20):

Clomial

Changes in version 0.99.0 (2014-02-11):

clonotypeR

Changes in version 1.2.0:

NEW FEATURES

BUG FIXES

clusterProfiler

Changes in version 1.11.3:

Changes in version 1.11.2:

CNAnorm

1.9.2: Added function CNAnormWorkflow Added window weighting (for segmentation) depending on dispersion. Fixed a bug that made plotGenome crash if the interval of interest had no valid values. Changed vignette to better reflect typical usage and defined basic and advanced use.

codelink

Changes in version 1.32.0:

COMPASS

Changes in version 0.9.0:

compcodeR

0.99.2: Bug fixes

0.99.1: improved documentation of the compData class

0.2.0: more examples, checks and error messages

0.2.0: more options for providing user-specified values in the data simulation

0.2.0: changed the range of the color palette in the Spearman correlation plots to [-1,1]

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

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

Updates

DESeq2

Changes in version 1.4.0:

Changes in version 1.3.58:

Changes in version 1.3.24:

Changes in version 1.3.17:

Changes in version 1.3.15:

Changes in version 1.3.12:

Changes in version 1.3.6:

Changes in version 1.3.5:

DEXSeq

Changes in version 2014-03-21:

DiffBind

Changes in version 1.10.0:

easyRNASeq

Changes in version 1.99.3:

Changes in version 1.99.2:

Changes in version 1.99.1:

Changes in version 1.99.0:

Changes in version 1.9.7:

Changes in version 1.9.6:

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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:

EBImage

Changes in version 4.6.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

EDASeq

Changes in version 1.9:

EDDA

Changes in version 0.99.2:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.99.1:

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

Changes in version 0.99.0:

SIGNIFICANT USER-VISIBLE CHANGES

edgeR

Changes in version 3.6.0:

eiR

Changes in version 1.4.0:

NEW FEATURES

UPGRADING

ensemblVEP

Changes in version 1.4.0:

NEW FEATURES

MODIFICATIONS

FGNet

Changes in version 2.0:

NEW FEATURES

BUG FIXES

Changes in version 1.3.1:

NEW FEATURES

BUG FIXES

flipflop

Changes in version 1.1.6:

NEW FEATURES

Changes in version 1.1.4:

NEW FEATURES

USER-LEVEL CHANGES

MINOR CHANGES

Changes in version 1.1.2:

BUG FIXES

fmcsR

Changes in version 1.6.0:

NEW FEATURES

FRGEpistasis

Changes in version 0.99.5:

Changes in version 0.99.4:

Changes in version 0.99.3:

Changes in version 0.99.1:

gage

Changes in version 2.12.1:

gCMAP

Changes in version 1.7.2:

Changes in version 1.7.1:

gCMAPWeb

Changes in version 1.3.2:

Changes in version 1.3.1:

geNetClassifier

Changes in version 1.3.1:

NEW FEATURES

BUG FIXES

GenomeInfoDb

Changes in version 0.99.14:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.99.7:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.99.6:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

DEPRECATED AND USED INTERNALLY(NOT EXPORTED

Changes in version 0.99.1:

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

GenomicAlignments

Changes in version 0.99:

NEW FEATURES

GenomicFiles

Changes in version 1.0.0:

NEW FEATURES

GenomicRanges

Changes in version 1.16.0:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

BUG FIXES

genoset

Changes in version 1.16.0:

NEW FEATURES

DEPRECATED AND DEFUNCT

GGBase

Changes in version 3.25.1:

GGtools

Changes in version 4.11:

gmapR

Changes in version 1.6.0:

NEW FEATURES

USER-VISIBLE CHANGES

GOSemSim

Changes in version 1.21.3:

graphite

Changes in version 1.9.4 (2014-04-04):

Gviz

Changes in version 1.8.0:

NEW FEATURES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

gwascat

Changes in version 1.7.6:

USER VISIBLE CHANGES

Changes in version 1.7.1:

USER VISIBLE CHANGES

CHANGES PRIOR TO VERSION 1.7.1

GWASTools

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:

HiTC

Changes in version 1.7.11:

NEW FEATURES

BUG FIXES

Changes in version 1.7.5:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.7.4:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.7.3:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

HTSeqGenie

Changes in version 3.13.13:

Changes in version 3.13.12:

Changes in version 3.13.11:

Changes in version 3.13.10:

Changes in version 3.13.9:

Changes in version 3.13.8:

Changes in version 3.13.7:

Changes in version 3.13.6:

Changes in version 3.13.5:

Changes in version 3.13.4:

Changes in version 3.13.3:

Changes in version 3.13.2:

Changes in version 3.13.1:

Changes in version 3.13.0:

HTSFilter

Changes in version 1.2.1:

illuminaio

Changes in version 0.6.0 (2014-04-11):

Changes in version 0.5.6 (2014-03-10):

Changes in version 0.5.5 (2014-01-19):

Changes in version 0.5.2 (2013-11-05):

Changes in version 0.5.1 (2013-11-04):

Changes in version 0.5.0:

inSilicoDb

Changes in version 2.0.0:

NEW FEATURES

OTHER

inSilicoMerging

Changes in version 1.8.0:

NEW FEATURES

BUG FIXES

OTHER

intansv

Changes in version 1.2.1:

Notes

isobar

Changes in version 1.9.3:

Changes in version 1.9.2:

KEGGgraph

Changes in version 1.21.1 (2013-10-17):

BUG FIXES

limma

Changes in version 3.20.0:

metagenomeSeq

Changes in version 1.5 (2014-04-17):

metaMS

Changes in version 0.99.8:

Changes in version 0.99.7:

Changes in version 0.99.6:

metaseqR

Changes in version 1.0.0 (2014-04-11):

NEW FEATURES

Changes in version 0.99.6 (2014-04-09):

NEW FEATURES

BUG FIXES

Changes in version 0.99.5 (2014-03-31):

NEW FEATURES

BUG FIXES

Changes in version 0.99.4 (2014-03-18):

BUG FIXES

Changes in version 0.99.3 (2014-03-17):

NEW FEATURES

BUG FIXES

Changes in version 0.99.2 (2014-03-14):

NEW FEATURES

BUG FIXES

Changes in version 0.99.1 (2014-03-12):

NEW FEATURES

BUG FIXES

Changes in version 0.99.0 (2014-02-21):

NEW FEATURES

BUG FIXES

Changes in version 0.93.0 (2014-02-12):

NEW FEATURES

BUG FIXES

Changes in version 0.92.0 (2014-01-25):

NEW FEATURES

BUG FIXES

Changes in version 0.91.0 (2014-01-03):

NEW FEATURES

BUG FIXES

Changes in version 0.9.1 (2013-11-27):

NEW FEATURES

BUG FIXES

Changes in version 0.9.0 (2013-11-21):

NEW FEATURES

MIMOSA

Changes in version 0.99.2:

Changes in version 0.9.12:

Changes in version 0.9.9:

Changes in version 0.8.0:

Changes in version 0.7.0:

minfi

Changes in version 1.9:

MotifDb

Changes in version 1.5.9:

NEW FEATURES

motifStack

Changes in version 1.7.7:

NEW FEATURES

BUG FIXES

Changes in version 1.7.6:

NEW FEATURES

BUG FIXES

Changes in version 1.7.5:

NEW FEATURES

BUG FIXES

Changes in version 1.7.3:

NEW FEATURES

BUG FIXES

Changes in version 1.7.2:

NEW FEATURES

BUG FIXES

Changes in version 1.7.1:

NEW FEATURES

BUG FIXES

MSnbase

Changes in version 1.11.14:

Changes in version 1.11.13:

Changes in version 1.11.12:

Changes in version 1.11.11:

Changes in version 1.11.10:

Changes in version 1.11.9:

Changes in version 1.11.8:

Changes in version 1.11.7:

Changes in version 1.11.6:

Changes in version 1.11.5:

Changes in version 1.11.4:

Changes in version 1.11.3:

Changes in version 1.11.2:

Changes in version 1.11.1:

Changes in version 1.11.0:

MSstats

Changes in version 2.1.3:

Changes in version 2.1.1:

mzID

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:

mzR

Changes in version 1.9.8:

Changes in version 1.9.7:

Changes in version 1.9.6:

Changes in version 1.9.3:

Changes in version 1.9.2:

Changes in version 1.9.1:

nondetects

Changes in version 0.99.2:

BUG FIXES

Changes in version 0.99.1:

BUG FIXES

Changes in version 0.99.0:

npGSEA

Changes in version 0.99.0:

pathview

Changes in version 1.3.6:

Changes in version 1.3.4:

Changes in version 1.2.4:

Changes in version 1.2.3:

Changes in version 1.2.2:

Changes in version 1.2.1:

phyloseq

Changes in version 1.7.24:

USER-VISIBLE CHANGES

Changes in version 1.7.23:

USER-VISIBLE CHANGES

Changes in version 1.7.22:

USER-VISIBLE CHANGES

Changes in version 1.7.21:

USER-VISIBLE CHANGES

Changes in version 1.7.20:

USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.7.19:

USER-VISIBLE CHANGES

Changes in version 1.7.18:

USER-VISIBLE CHANGES

Changes in version 1.7.17:

USER-VISIBLE CHANGES

Changes in version 1.7.16:

USER-VISIBLE CHANGES

Changes in version 1.7.15:

USER-VISIBLE CHANGES

Changes in version 1.7.14:

USER-VISIBLE CHANGES

Changes in version 1.7.13:

USER-VISIBLE CHANGES

Changes in version 1.7.12:

USER-VISIBLE CHANGES

Changes in version 1.7.11:

USER-VISIBLE CHANGES

Changes in version 1.7.10:

USER-VISIBLE CHANGES

Changes in version 1.7.9:

USER-VISIBLE CHANGES

Changes in version 1.7.8:

USER-VISIBLE CHANGES

Changes in version 1.7.7:

USER-VISIBLE CHANGES

Changes in version 1.7.6:

USER-VISIBLE CHANGES

Changes in version 1.7.5:

NEW FEATURES

USER-VISIBLE CHANGES

Changes in version 1.7.4:

NEW FEATURES

Changes in version 1.7.3:

NEW FEATURES

USER-VISIBLE CHANGES

Changes in version 1.7.2:

USER-VISIBLE CHANGES

Changes in version 1.7.1:

USER-VISIBLE CHANGES

piano

Changes in version 1.4.0:

NEW FEATURES

BUG FIXES

DOCUMENTATION

plethy

Changes in version 1.1.3:

NEW FEATURES

procoil

Changes in version 1.13.2:

pRoloc

Changes in version 1.3.19:

Changes in version 1.3.18:

Changes in version 1.3.17:

Changes in version 1.3.16:

Changes in version 1.3.15:

Changes in version 1.3.14:

Changes in version 1.3.13:

Changes in version 1.3.12:

Changes in version 1.3.11:

Changes in version 1.3.10:

Changes in version 1.3.9:

Changes in version 1.3.8:

Changes in version 1.3.7:

Changes in version 1.3.6:

Changes in version 1.3.5:

Changes in version 1.3.4:

Changes in version 1.3.3:

Changes in version 1.3.2:

Changes in version 1.3.1:

Changes in version 1.3.0:

PWMEnrich

Changes in version 3.5:

Changes in version 3.1.4:

QDNAseq

Changes in version 1.0.0 (2014-04-14):

INITIAL RELEASE

qpgraph

Changes in version 1.20:

USER VISIBLE CHANGES

NEW FEATURES

BUG FIXES

QuasR

Changes in version 1.4.0:

NEW FEATURES

r3Cseq

Changes in version 1.9.2 (2013-11-11):

Changes in version 1.9.1 (2013-10-21):

RamiGO

Changes in version 1.9.5:

Changes in version 1.9.1:

Rariant

Changes in version 1.0.0:

rBiopaxParser

Changes in version 2.1.7:

Changes in version 2.1.5:

Changes in version 2.1.3:

Changes in version 2.1.1:

Changes in version 1.3.3:

RDAVIDWebService

Changes in version 1.1.4:

BUG FIXED

Changes in version 1.1.3:

MINOR CHANGES

Changes in version 1.1.2:

CODE CHANGES

NEW FEATURES

DOCUMENTATION

Changes in version 1.1.1:

DOCUMENTATION

CODE CHANGES

DEPENDENCY CHANGES

Changes in version 1.1.0:

MINOR CHANGES

ReactomePA

Changes in version 1.7.2:

RedeR

Changes in version 1.12.0:

RefNet

Changes in version 1.0.0:

NEW FEATURES

ReQON

Changes in version 1.9.1:

Rgraphviz

Changes in version 2.7:

rhdf5

Changes in version 2.8.0:

NEW FEATURES

USER VISIBLE CHANGES

BUG FIXES

roar

Changes in version 0.99.6:

NEW FEATURES

BUG FIXES

rols

Changes in version 1.5.2:

Changes in version 1.5.1:

Changes in version 1.5.0:

rpx

Changes in version 0.99.9:

Changes in version 0.99.8:

Changes in version 0.99.7:

Changes in version 0.99.6:

Changes in version 0.99.5:

Changes in version 0.99.4:

Changes in version 0.99.3:

Changes in version 0.99.2:

Changes in version 0.99.1:

Changes in version 0.99.0:

rqubic

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

Rsamtools

Changes in version 1.15.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Rsubread

Changes in version 1.14.0:

NEW FEATURES

rTANDEM

Changes in version 1.3.9:

Changes in version 1.3.8:

BUG FIXES

Changes in version 1.3.7:

NEW FEATURES

Changes in version 1.3.5:

NEW FEATURES

Changes in version 1.3.4:

NEW FEATURES

BUG FIXES

Changes in version 1.3.3:

NEW FEATURES

Changes in version 1.3.2:

NEW FEATURES

RTN

Changes in version 1.2.0:

rTRM

Changes in version 1.2:

SANTA

Changes in version 1.3.10 (2014-03-03):

NOTES:

sapFinder

Changes in version 0.99.4:

BUG FIXES

Changes in version 0.99.3:

NEW FEATURES

BUG FIXES

Changes in version 0.99.2:

BUG FIXES

Changes in version 0.99.0:

SCAN.UPC

Changes in version 2.5.8:

NEW FEATURES

NOTES

SeqArray

Changes in version 1.3.2:

Changes in version 1.3.1:

shinyTANDEM

Changes in version 1.1.4:

BUG FIXES

Changes in version 1.1.3:

BUG FIXES

Changes in version 1.1.2:

NEW FEATURES

BUG FIXES

ShortRead

Changes in version 1.21:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

snm

Changes in version 1.11:

SomaticSignatures

Changes in version 1.0.0:

supraHex

Changes in version 1.1.17:

NEW FEATURES

Changes in version 1.1.2:

NEW FEATURES

synapter

Changes in version 1.5.7:

Changes in version 1.5.6:

Changes in version 1.5.5:

Changes in version 1.5.4:

Changes in version 1.5.3:

Changes in version 1.5.1:

Changes in version 1.5.0:

TargetSearch

Changes in version 1.20.0:

BUG FIXES

TCC

Changes in version 1.3.2:

tigre

Changes in version 1.16.1:

TransView

Changes in version 1.7.4:

BUG FIXES

Changes in version 1.7.3:

BUG FIXES

Changes in version 1.7.2:

NEW FEATURES

Changes in version 1.7.1:

BUG FIXES

unifiedWMWqPCR

Changes in version 0.9.9:

SIGNIFICANT USER-VISIBLE CHANGES

VariantAnnotation

Changes in version 1.10.0:

NEW FEATURES

MODIFICATIONS

DEPRECATED and DEFUNCT

BUG FIXES

VariantFiltering

Changes in version 0.99:

USER VISIBLE CHANGES

VariantTools

Changes in version 1.6.0:

NEW FEATURES

USER-VISIBLE CHANGES

wateRmelon

1.3.1: thanks to several users for bug reports!

xcms

Changes in version 1.39.6:

USER VISIBLE CHANGES

BUG FIXES

Changes in version 1.39.4:

BUG FIXES

Changes in version 1.39.3:

BUG FIXES

Changes in version 1.39.1:

BUG FIXES

REQUIRED CHANGES

yaqcaffy

Changes in version 1.23.1:

Packages removed from the release

The following packages are no longer in the release:

Agi4x44PreProcess, maDB, pgUtils

Fred Hutchinson Cancer Research Center