October 14, 2014

Bioconductors:

We are pleased to announce Bioconductor 3.0, consisting of 934 software packages, 219 experiment data packages, and 870 up-to-date annotation packages.

There are 114 new software packages, and many updates and improvements to existing packages; Bioconductor 3.0 is compatible with R 3.1, 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 3.0

New Software Packages

NEWS from new and existing packages

Packages removed from the release

Getting Started with Bioconductor 3.0

To update to or install Bioconductor 3.0:

Install R 3.1. Bioconductor 3.0 has been designed expressly for this version of R. Follow the instructions at http://bioconductor.org/install/.

New Software Packages

There are 114 new packages in this release of Bioconductor.

ALDEx2 - A differential abundance analysis for the comparison of two or more conditions. For example, single-organism and meta-RNA-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected false discovery rate given the biological and sampling variation using the Wilcox rank test or Welches t-test (aldex.ttest) or the glm and Kruskal Wallis tests (aldex.glm). Reports both P and fdr values calculated by the Benjamini Hochberg correction.

ASGSCA - The package provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables. The method is based on Generalized Structured Component Analysis (GSCA).

ballgown - Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.

blima - Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.

BridgeDbR - Use BridgeDb functions and load identifier mapping databases in R

CFAssay - The package provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.

ClassifyR - The software formalises a framework for classification in R. There are four stages. Data transformation, feature selection, and prediction. The requirements of variable types and names are fixed, but specialised variables for functions can also be provided. The classification framework is wrapped in a driver loop, that reproducibly does a couple of cross-validation schemes. Functions for differential expression, differential variability, and differential distribution are included. Additional functions may be developed by the user, if they have better performing methods.

compEpiTools - Tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples.

CoRegNet - This package provides methods to identify active transcriptional programs. Methods and classes are provided to import or infer large scale co-regulatory network from transcriptomic data. The specificity of the encoded networks is to model Transcription Factor cooperation. External regulation evidences (TFBS, ChIP,…) can be integrated to assess the inferred network and refine it if necessary. Transcriptional activity of the regulators in the network can be estimated using an measure of their influence in a given sample. Finally, an interactive UI can be used to navigate through the network of cooperative regulators and to visualize their activity in a specific sample or subgroup sample. The proposed visualization tool can be used to integrate gene expression, transcriptional activity, copy number status, sample classification and a transcriptional network including co-regulation information.

cosmiq - cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.

COSNet - Package that implements the COSNet classification algorithm. The algorithm predicts node labels in partially labeled graphs.

csaw - Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

DEGreport - Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.

derfinder - Fast differential expression analysis of RNA-seq data at base-pair resolution

derfinderHelper - Helper package for speeding up the derfinder package when using multiple cores.

derfinderPlot - Plotting functions for derfinder

DOQTL - DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.

DupChecker - Meta-analysis has become a popular approach for high-throughput genomic data analysis because it often can significantly increase power to detect biological signals or patterns in datasets. However, when using public-available databases for meta-analysis, duplication of samples is an often encountered problem, especially for gene expression data. Not removing duplicates would make study results questionable. We developed a Bioconductor package DupChecker that efficiently identifies duplicated samples by generating MD5 fingerprints for raw data.

EBSeqHMM - The EBSeqHMM package implements an auto-regressive hidden Markov model for statistical analysis in ordered RNA-seq experiments (e.g. time course or spatial course data). The EBSeqHMM package provides functions to identify genes and isoforms that have non- constant expression profile over the time points/positions, and cluster them into expression paths.

EnrichmentBrowser - The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.

erccdashboard - Technical performance metrics for differential gene expression experiments using External RNA Controls Consortium (ERCC) spike-in ratio mixtures.

facopy - facopy is an R package for fine-tuned cancer CNA association modeling. Association is measured directly at the genomic features of interest and, in the case of genes, downstream gene-set enrichment analysis can be performed thanks to novel internal processing of the data. The software opens a way to systematically scrutinize the differences in CNA distribution across tumoral phenotypes, such as those that relate to tumor type, location and progression. Currently, the output format from 11 different methods that analyze data from whole-genome/exome sequencing and SNP microarrays, is supported. Multiple genomes, alteration types and variable types are also supported.

FEM - FEM can dentify interactome hotspots of differential promoter methylation and differential ex-pression, where an inverse association between promoter methylation and gene expression is assumed.

flowcatchR - flowcatchR is a set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides the steps from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations (e.g. how good the segmentation was). The main novel contribution investigates the issue of tracking flowing cells such as in blood vessels, to categorize the particles in flowing, rolling and adherent. This classification is applied in the study of phenomena such as hemostasis and study of thrombosis development.

flowCHIC - A package to analyze flow cytometric data of complex microbial communities based on histogram images

flowClean - A quality control tool for flow cytometry data based on compositional data analysis.

flowDensity - This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data.

focalCall - Detection of genomic focal aberrations in high-resolution DNA copy number data

FourCSeq - FourCSeq is an R package dedicated to the analysis of (multiplexed) 4C sequencing data. The package provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions. The statistical analysis in R starts with individual bam files for each sample as inputs. To obtain these files, the package contains a python script (extdata/python/demultiplex.py) to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated.

geecc - Use log-linear models to perform hypergeometric and chi-squared tests for gene set enrichments for two (based on contingency tables) or three categories (contingency cubes). Categories can be differentially expressed genes, GO terms, sequence length, GC content, chromosmal position, phylostrata, ….

GenomicInteractions - R package for handling Genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots / statistics

GenomicTuples - GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.

GenoView - Superimposing input data over existing genomic references allows for fast, accurate visual comparisons. The GenoView package is a novel bioinformatics package which condenses genomic data tracks to offer a comprehensive view of genetic variants. Its main function is to display mutation data over exons and protein domains, which easily identifies potential genomic locations of interest.

GOexpress - The package contains methods to visualise the expression levels of genes from a microarray or RNA-seq experiment and offers a clustering analysis to identify GO terms enriched in genes with expression levels best clustering predefined two or more groups of samples. Annotations for the genes present in the expression dataset are obtained from Ensembl through the biomaRt package. The random forest framework is used to evaluate the ability of each gene to cluster samples according to the factor of interest. Finally, GO terms are scored by averaging the rank (alternatively, score) of their respective gene sets to cluster the samples. An ANOVA approach is also available as an alternative statistical framework.

GOsummaries - A package to visualise Gene Ontology (GO) enrichment analysis results on gene lists arising from different analyses such clustering or PCA. The significant GO categories are visualised as word clouds that can be combined with different plots summarising the underlying data.

groHMM - A pipeline for the analysis of GRO-seq data.

GSAR - Gene set analysis using specific alternative hypotheses. Tests for differential expression, scale and net correlation structure.

GSReg - A package for gene set analysis based on the variability of expressions. It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods.

HDTD - Characterization of intra-individual variability using physiologically relevant measurements provides important insights into fundamental biological questions ranging from cell type identity to tumor development. For each individual, the data measurements can be written as a matrix with the different subsamples of the individual recorded in the columns and the different phenotypic units recorded in the rows. Datasets of this type are called high-dimensional transposable data. The HDTD package provides functions for conducting statistical inference for the mean relationship between the row and column variables and for the covariance structure within and between the row and column variables.

hiAnnotator - hiAnnotator contains set of functions which allow users to annotate a GRanges object with custom set of annotations. The basic philosophy of this package is to take two GRanges objects (query & subject) with common set of seqnames (i.e. chromosomes) and return associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands). The package comes with three types of annotation functions which calculates if a position from query is: within a feature, near a feature, or count features in defined window sizes. Moreover, each function is equipped with parallel backend to utilize the foreach package. In addition, the package is equipped with wrapper functions, which finds appropriate columns needed to make a GRanges object from a common data frame.

hiReadsProcessor - hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.

IdeoViz - Plots data associated with arbitrary genomic intervals along chromosomal ideogram.

IMPCdata - Package contains methods for data retrieval from IMPC Database.

interactiveDisplayBase - The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects.

kebabs - The package provides functionality for kernel-based analysis of DNA, RNA, and amino acid sequences via SVM-based methods. As core functionality, kebabs implements following sequence kernels: spectrum kernel, mismatch kernel, gappy pair kernel, and motif kernel. Apart from an efficient implementation of standard position-independent functionality, the kernels are extended in a novel way to take the position of patterns into account for the similarity measure. Because of the flexibility of the kernel formulation, other kernels like the weighted degree kernel or the shifted weighted degree kernel with constant weighting of positions are included as special cases. An annotation-specific variant of the kernels uses annotation information placed along the sequence together with the patterns in the sequence. The package allows for the generation of a kernel matrix or an explicit feature representation in dense or sparse format for all available kernels which can be used with methods implemented in other R packages. With focus on SVM-based methods, kebabs provides a framework which simplifies the usage of existing SVM implementations in kernlab, e1071, and LiblineaR. Binary and multi-class classification as well as regression tasks can be used in a unified way without having to deal with the different functions, parameters, and formats of the selected SVM. As support for choosing hyperparameters, the package provides cross validation - including grouped cross validation, grid search and model selection functions. For easier biological interpretation of the results, the package computes feature weights for all SVMs and prediction profiles which show the contribution of individual sequence positions to the prediction result and indicate the relevance of sequence sections for the learning result and the underlying biological functions.

M3D - This package identifies statistically significantly differentially methylated regions of CpGs. It uses kernel methods (the Maximum Mean Discrepancy) to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles.

MAIT - The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.

MBAmethyl - This package provides a function for reconstructing DNA methylation values from raw measurements. It iteratively implements the group fused lars to smooth related-by-location methylation values and the constrained least squares to remove probe affinity effect across multiple sequences.

MBASED - The package implements MBASED algorithm for detecting allele-specific gene expression from RNA count data, where allele counts at individual loci (SNVs) are integrated into a gene-specific measure of ASE, and utilizes simulations to appropriately assess the statistical significance of observed ASE.

MEIGOR - Global Optimization

metabomxtr - The functions in this package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions.

Metab - Metab is an R package for high-throughput processing of metabolomics data analysed by the Automated Mass Spectral Deconvolution and Identification System (AMDIS) (http://chemdata.nist.gov/mass-spc/amdis/downloads/). In addition, it performs statistical hypothesis test (t-test) and analysis of variance (ANOVA). Doing so, Metab considerably speed up the data mining process in metabolomics and produces better quality results. Metab was developed using interactive features, allowing users with lack of R knowledge to appreciate its functionalities.

metagene - This package produces metagene plots to compare the behavior of DNA-interacting proteins at selected groups of genes/features. Pre-calculated features (such as transcription start sites of protein coding gene or enhancer) are available. Bam files are used to increase the resolution. Multiple combination of group of features and or group of bam files can be compared in a single analysis. Bootstraping analysis is used to compare the groups and locate regions with statistically different enrichment profiles.

MethylAid - A visual and interactive web application using RStudio’s shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.

MethylMix - MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression.

methylPipe - Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.

MGFM - The package is designed to detect marker genes from Microarray gene expression data sets

miRNAtap - The package facilitates implementation of workflows requiring miRNA predictions, it allows to integrate ranked miRNA target predictions from multiple sources available online and aggregate them with various methods which improves quality of predictions above any of the single sources. Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation).

missMethyl - Normalisation and testing for differential variability for data from Illumina’s Infinium HumanMethylation450 array. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene’s test.

monocle - Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.

MoPS - Identification and characterization of periodic fluctuations in time-series data.

MPFE - Estimate distribution of methylation patterns from a table of counts from a bisulphite sequencing experiment given a non-conversion rate and read error rate.

mQTL.NMR - mQTL.NMR provides a complete mQTL analysis pipeline for 1H NMR data. Distinctive features include normalisation using most-used approaches, peak alignment using RSPA approach, dimensionality reduction using SRV and binning approaches, and mQTL analysis for animal and human cohorts.

MSGFgui - This package makes it possible to perform analyses using the MSGFplus package in a GUI environment. Furthermore it enables the user to investigate the results using interactive plots, summary statistics and filtering. Lastly it exposes the current results to another R session so the user can seamlessly integrate the gui into other workflows.

MSGFplus - This package contains function to perform peptide identification using MS-GF+

MSnID - Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.

MultiMed - Implements permutation method with joint correction for testing multiple mediators

mvGST - mvGST provides platform-independent tools to identify GO terms (gene sets) that are differentially active (up or down) in multiple contrasts of interest. Given a matrix of one-sided p-values (rows for genes, columns for contrasts), mvGST uses meta-analytic methods to combine p-values for all genes annotated to each gene set, and then classify each gene set as being significantly more active (1), less active (-1), or not significantly differentially active (0) in each contrast of interest. With multiple contrasts of interest, each gene set is assigned to a profile (across contrasts) of differential activity. Tools are also provided for visualizing (in a GO graph) the gene sets classified to a given profile.

mygene - MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It’s designed with simplicity and performance emphasized. mygene, is an easy-to-use R wrapper to access MyGene.Info_ services.

netbiov - A package that provides an effective visualization of large biological networks

NGScopy - NGScopy provides a quantitative caller for detecting copy number variations in next generation sequencing (NGS), including whole genome sequencing (WGS), whole exome sequencing (WES) and targeted panel sequencing (TPS). The caller can be parallelized by chromosomes to use multiple processors/cores on one computer.

OncoSimulR - Functions for simulating and plotting cancer progression data, including drivers and passengers, and allowing for order restrictions. Simulations use continuous-time models (based on Bozic et al., 2010 and McFarland et al., 2013) and fitness functions account for possible restrictions in the order of accumulation of mutations.

oposSOM - This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data.

PAA - PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After pre-processing (background correction, batch filtering, normalization) univariate feature pre-selection is performed (e.g., using the “minimum M statistic” approach - hereinafter referred to as “mMs”). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.

paxtoolsr - The package provides a basic set of R functions for interacting with BioPAX OWL files and the querying Pathway Commons (PC) molecular interaction data server, hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

Pbase - A set of classes and functions to investigate and understand protein sequence data in the context of a proteomics experiment.

pepStat - Statistical analysis of peptide microarrays

pepXMLTab - Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.

polyester - This package can be used to simulate RNA-seq reads from differential expression experiments with replicates. The reads can then be aligned and used to perform comparisons of methods for differential expression.

Polyfit - Polyfit is an add-on to the packages DESeq which ensures the p-value distribution is uniform over the interval [0, 1] for data satisfying the null hypothesis of no differential expression, and uses an adpated Storey-Tibshiran method to calculate q-values.

proBAMr - Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.

pRolocGUI - The package pRolocGUI comprises functions to interactively visualise organelle (spatial) proteomics data on the basis of pRoloc, pRolocdata and shiny.

proteoQC - This package creates a HTML format QC report for MS/MS-based proteomics data. The report is intended to allow the user to quickly assess the quality of proteomics data.

PSEA - Deconvolution of gene expression data by Population-Specific Expression Analysis (PSEA).

Pviz - Pviz adapts the Gviz package for protein sequences and data.

quantro - A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.

rain - This package uses non-parametric methods to detect rhythms in time series. It deals with outliers, missing values and is optimized for time series comprising 10-100 measurements. As it does not assume expect any distinct waveform it is optimal or detecting oscillating behavior (e.g. circadian or cell cycle) in e.g. genome- or proteome-wide biological measurements such as: micro arrays, proteome mass spectrometry, or metabolome measurements.

regionReport - Generate HTML reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder.

RGSEA - Combining bootstrap aggregating and Gene set enrichment analysis (GSEA), RGSEA is a classfication algorithm with high robustness and no over-fitting problem. It performs well especially for the data generated from different exprements.

riboSeqR - Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.

Rnits - R/Bioconductor package for normalization, curve registration and inference in time course gene expression data

Rqc - Rqc is an optimised tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.

rRDP - Seamlessly interfaces RDP classifier (version 2.9).

RUVnormalize - RUVnormalize is meant to remove unwanted variation from gene expression data when the factor of interest is not defined, e.g., to clean up a dataset for general use or to do any kind of unsupervised analysis.

RUVSeq - This package implements the remove unwanted variation (RUV) methods of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.

S4Vectors - The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

SemDist - This package implements methods to calculate information accretion for a given version of the gene ontology and uses this data to calculate remaining uncertainty, misinformation, and semantic similarity for given sets of predicted annotations and true annotations from a protein function predictor.

seqplots - SeqPlots is a tool for plotting next generation sequencing (NGS) based experiments’ signal tracks, e.g. reads coverage from ChIP-seq, RNA-seq and DNA accessibility assays like DNase-seq and MNase-seq, over user specified genomic features, e.g. promoters, gene bodies, etc. It can also calculate sequence motif density profiles from reference genome. The data are visualized as average signal profile plot, with error estimates (standard error and 95% confidence interval) shown as fields, or as series of heatmaps that can be sorted and clustered using hierarchical clustering, k-means algorithm and self organising maps. Plots can be prepared using R programming language or web browser based graphical user interface (GUI) implemented using Shiny framework. The dual-purpose implementation allows running the software locally on desktop or deploying it on server. SeqPlots is useful for both for exploratory data analyses and preparing replicable, publication quality plots. Other features of the software include collaboration and data sharing capabilities, as well as ability to store pre-calculated result matrixes, that combine many sequencing experiments and in-silico generated tracks with multiple different features. These binaries can be further used to generate new combination plots on fly, run automated batch operations or share with colleagues, who can adjust their plotting parameters without loading actual tracks and recalculating numeric values. SeqPlots relays on Bioconductor packages, mainly on rtracklayer for data input and BSgenome packages for reference genome sequence and annotations.

seqTools - Analyze read length, phred scores and alphabet frequency and DNA k-mers on uncompressed and compressed fastq files.

SGSeq - RNA-seq data are informative for the analysis of known and novel transcript isoforms. While the short length of RNA-seq reads limits the ability to predict and quantify full-length transcripts, short read data are well suited for the analysis of individual alternative transcripts events (e.g. inclusion or skipping of a cassette exon). The SGSeq package enables the prediction, quantification and visualization of alternative transcript events from BAM files.

shinyMethyl - Interactive tool for visualizing Illumina’s 450k array data

SigCheck - While gene signatures are frequently used to classify data (e.g. predict prognosis of cancer patients), it it not always clear how optimal or meaningful they are (cf David Venet, Jacques E. Dumont, and Vincent Detours’ paper “Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome”). Based partly on suggestions in that paper, SigCheck accepts a data set (as an ExpressionSet) and a gene signature, and compares its classification performance (using the MLInterfaces package) against a) random gene signatures of the same length; b) known, (related and unrelated) gene signatures; and c) permuted data.

simulatorZ - simulatorZ is a package intended primarily to simulate collections of independent genomic data sets, as well as performing training and validation with predicting algorithms. It supports ExpressionSets and SummarizedExperiment objects.

SNPRelate - Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP format in this package is also being used by the GWASTools package with the support of S4 classes and generic functions.

specL - specL provides a function for generating spectra libraries which can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software.

ssviz - Small RNA sequencing viewer

STAN - STAN (STrand-specic ANnotation of genomic data) implements bidirectional Hidden Markov Models (bdHMM), which are designed for studying directed genomic processes, such as gene transcription, DNA replication, recombination or DNA repair by integrating genomic data. bdHMMs model a sequence of successive observations (e.g. ChIP or RNA measurements along the genome) by a discrete number of ‘directed genomic states’, which e.g. reflect distinct genome-associated complexes. Unlike standard HMM approaches, bdHMMs allow the integration of strand-specific (e.g. RNA) and non strand-specific data (e.g. ChIP).

STATegRa - Classes and tools for multi-omics data integration.

switchBox - The package offer different classifiers based on comparisons of pair of features (TSP), using various decision rules (e.g., majority wins principle).

systemPipeR - R package for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and many others. An important feature is support for running command-line software, such as NGS aligners, on both single machines or compute clusters. This includes both interactive job submissions or batch submissions to queuing systems of clusters.

ToPASeq - Implementation of seven methods for topology-based pathway analysis of both RNASeq and microarray data: SPIA, DEGraph, TopologyGSA, TAPPA, TBS, PWEA and a visualization tool for a single pathway.

tracktables - Methods to create complex IGV genome browser sessions and dynamic IGV reports in HTML pages.

TSCAN - TSCAN enables users to easily construct and tune pseudotemporal cell ordering as well as analyzing differentially expressed genes. TSCAN comes with a user-friendly GUI written in shiny. More features will come in the future.

wavClusteR - Infer PAR-CLIP induced transitions and discriminate them from sequencing error, SNPs, contaminants and additional non-experimental causes, using a non-parametric mixture model. wavClusteR resolves cluster boundaries at high resolution and provides robust estimation of cluster statistics. In addition, the package allows to integrate RNA-Seq data to estimate FDR over the entire range of relative substitution frequencies. Furthermore, the package provides post-processing of results and functions to export results for UCSC genome browser visualization and motif search analysis. Key functions support parallel multicore computing. While wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other Next-Generation Sequencing data obtained from substitution inducing experimental procedures (e.g. BisSeq)

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 2.5.2 (2014-10-03):

Corrected help for “inputToADaCGH”

Changes in version 2.5.1 (2014-10-03):

Fixed bug reading files when R object was called “inputData”

Changes in version 2.5.0:

Bumped BioC version.

affxparser

Changes in version 1.37.2 (2014-09-28):

Minor modifications due to the move to GitHub.

Changes in version 1.37.1 (2014-08-25):

CLEANUP: Removed R CMD check NOTEs that appeared in recent R versions.

Changes in version 1.37.0 (2014-04-11):

The version number was bumped for the Bioconductor devel version, which is now BioC v2.15 for R (>= 3.1.0).

ALDEx2

Changes in version 0.99.2:

NEW FEATURES

made aldex.clr into a class

allowed input of SummarizedExperiment object instead of a reads data frame

prioritized use of the BiocParallel package for multicore processing. If BiocParallel is not installed then the parallel package used, if neither packages are installed, then serial processing is used

Changes in version 0.99.1:

NEW FEATURES

changed conditional tests for multiprocessor use, defaults to FALSE

Changes in version 0.99.0:

NEW FEATURES

first submission to Bioc-devel

annotate

Changes in version 1.43:

NEW FEATURES

blastSequences accepts an argument timeout limiting waiting time for a response; in an interactive session and after the timeout is reached, the user may opt to retry the query.

blastSequences accepts an argument as controlling the representation of the return value, either a DNAMultipleAlignment, a data.frame, or the XML.

AnnotationForge

************************************************** * * * 1.8.0 SERIES NEWS * * * **************************************************

NEW FEATURES

o Adds support for making orgDb objects/databases for all NCBI taxIDs where there is sufficient data (for adding to AnnotationHub). This makes objects for 1100 organisms.

AnnotationHub

Changes in version 1.6.0:

NEW FEATURES

add query and subset,AnnotationHub=methods

aroma.light

Changes in version 2.1.2 (2014-09-23):

Minor tweaks due to the move to GitHub.

Changes in version 2.1.1 (2014-09-16):

IMPORTANT/CLEANUP: The matrixStats package is no longer attached with this package. In other words, you now might have to add library(‘matrixStats’) to your scripts.

CLEANUP: Now importing R.utils (instead of only suggesting it).

Fixed some new R CMD check NOTEs.

Changes in version 2.1.0 (2014-04-11):

The version number was bumped for the Bioconductor devel version, which is now BioC v2.15 for R (>= 3.1.0).

ASGSCA

Changes in version 0.99.2:

Minor bioconductor submission issues resolved

Changes in version 0.99.1:

Added real data in examples

Changed biocViews tag

Changes in version 0.99.0:

Initial release to Bioconductor.

Added NEWS file.

ballgown

9.7: new methods for accessing gene and transcript names and IDs

9.7: development package (on GitHub) now has Travis CI integration, so the package’s is built/tested with every new push and a status image is visible on the package README

9.6: ballgownrsem can now handle gzipped input files

9.6: small fixes to eliminate warnings/errors on R CMD CHECK

9.5: “subset” function now behaves appropriately if sampleNames contain “dot” characters

9.4: Tablemaker source code moved out of Ballgown repository (both GitHub and BioC svn repos)

9.3: exprfilter function added

9.2: ballgownrsem function added (now compatible with RSEM output)

9.2: RSEM slot added to ballgown S4 class

9.2: bug fixes in subset function

9.2: library size adjustment in stattest is now CSS normalization (using log FPKM) by default and is more customizable

0.99.1:

9.0: “meas” argument added to constructor function

9.0: unit tests added

9.0: vignette updated

9.0: several bug fixes in plotting functions and statistical testing function Alpha release, 30 March 2014:

9.0: package announced

BiocParallel

CHANGES IN VERSION 1.0.0

NEW FEATURES

o Add vignette sections for cluster managers, AMI o Add bpiterate generic and methods o Add REDUCE to bpiterate() o Add 'reduce.in.order' to bpiterate()

MODIFICATIONS

o Update vignette examples, reorganize sections o Allow 'workers' in BiocParallelParam to be character or integer o Enhance bpresume() man page; add examples o Enhance register() man page; add examples o Improve default registration for SnowParam: - max 8 cores - use detectcores() / mc.cores if available o Modify .convertToSimpleError() to convert NULL to NA_character_

BUG FIXES

o Fix recursion problem for BPPARAM as list o Modify bpaggregate() to run in parallel

BiocStyle

Changes in version 1.4.0:

USER VISIBLE CHANGES

Support for markdown documents

Add \Githubpkg markup command

biosvd

Changes in version 2.0.4:

Category Class

Class EigensystemPlotParam has been added, to allow all plot-related settings to be specified in an object of this class.

Category Functionality

The plots function now provides up to ten visualizations. This function generates a heatmap of the eigenfeatures by assays with use of the given contrast factor (eigenfeatureHeatmap), a heatmap of the features by eigenassays with use of the given contrast factor (eigenassayHeatmap), a heatmap of the features by assays with features sorted according to their correlation with two eigenfeatures (sortedHeatmap), a bar plot with the eigenexpression fractions of all eigenfeatures (fraction), a screeplot for the eigenexpression fractions (scree), a bar plot with the eigenexpression fractions of the eigenfeatures without the dominant eigenfeature(s) (zoomedFraction), the intensity levels of selected eigenfeatures across the assays (by default eigenfeatures 1-4) (lines), the intensity levels of all eigenfeatures across the assays (allLines), polar plot for the assays according to their correlation with two eigenassays (eigenassayPolar), and polar plot for the features according to their correlation with two eigenfeatures (eigenfeaturePolar).

Category Dependencies

The package now longer depends on ReportingTools.

Category Deprecation

The sort function has been deprecated, and replaced by the function project. This function returns the rectangular and polar coordinates of the eigensystem projection onto two specified eigenfeatures and eigenassays.

BitSeq

Changes in version 1.10.0 (2014-10-01):

NEW FEATURES

This release corresponds to C++ BitSeq version 0.7.5.

adding “unstranded” option to parseAlignment, to allow read pairs with various directions to be used

enable excluding singletons (single-mate alignments of paired reads) in parseAlignment

BridgeDbR

Changes in version 0.99.1:

SIGNIFICANT USER-VISIBLE CHANGES

No changes

NEW FEATURES

New package

BUG FIXES

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

CGEN

Changes in version 3.0:

USER VISIBLE CHANGES

The functions score.test, GxE.scan, GxE.scan.partition and GxE.scan.combine have been added.

The functions snp.logistic and snp.scan.logistic can now handle imputed genotypes.

BUG FIXES

The function snp.logistic checks that the snp variable is used in main.vars or int.vars.

PLANS

The next release will have a new Wald test function.

chimera

Changes in version 1.7.10:

NEW FEATURES

Fusions data generated by fusionCatcher can be imported.

Changes in version 1.7.1:

NEW FEATURES

Fusions data generated by Rsubread can be imported.

chipenrich

Changes in version 1.3.4:

PKG FEATURES

A new method, broadenrich, is available in the chipenrich function which is designed for gene set enrichment on broad genomic regions, such as peaks resulting from histone modificaiton based ChIP-seq experiments.

Methods chipenrich and broadenrich are available in multicore versions (on every platform except Windows). The user selects the number of cores when calling the chipenrich function.

Peaks downloaded from the ENCODE Consortium as .broadPeak or .narrowPeak files are supported directly.

Peaks downloaded from the modENCODE Consortium as .bed.gff or .bed.gff3 files are also supported directly.

Support for D. melanogaster (dm3) genome and enrichment testing for GO terms from all three branches (GOBP, GOCC, and GOMF).

New gene sets from Reactome (http://www.reactome.org) for human, mouse, and rat.

New example histone data set, peaks_H3K4me3_GM12878, based on hg19.

ChIPQC

Changes in version 1.1.2:

Big fixes/man page fixes

ChIPseeker

Changes in version 1.1.21:

use data.table instead of data.frame to optimize covplot <2014-10-06, Mon>

Changes in version 1.1.20:

update annotatePeak to store the seqinfo information <2014-09-30, Tue>

modified runValue(x) to sapply(x, runValue) <2014-09-30, Tue>

Changes in version 1.1.19:

implement csAnno S4 object <2014-09-28, Sun>

modify plot function for csAnno instance <2014-09-28, Sun>

implement vennpie function <2014-09-28, Sun>

Changes in version 1.1.17:

deprecate plotChrCov to new function covplot <2014-08-18, Mon>

add new paramter chrs and xlim to covplot <2014-08-18, Mon>

Changes in version 1.1.16:

optimize plotChrCov, running time reduce drastically <2014-08-15, Fri>

Changes in version 1.1.15:

remove un-mappable peak to prevent fail in peak annotation <2014-08-14, Thu>

Changes in version 1.1.14:

bug fixed in plotDistToTSS <2014-08-14, Thu>

Changes in version 1.1.13:

change TranscriptDb to TxDb according to GenomicFeatures <2014-07-29, Tue>

Changes in version 1.1.12:

bug fixed in plotChrCov <2014-07-21, Mon>

Changes in version 1.1.10:

bug fixed in calculating distances from peak end <2014-06-18, Wed>

Changes in version 1.1.9:

add level parameter to annotatePeak, and set it to “transcript” by default. Now annotatePeak will annotate peaks in transcript level except user specify level = “gene” <2014-06-16, Mon>

add addFlankGeneInfo parameter to annotatePeak. If it set to true, all features within the flankDistance will be annotated. <2014-06-16, Mon>

Changes in version 1.1.8:

bug fixed when peak overlap with feature <2014-06-11, Wed>

optimize for getting overlap features of peaks <2014-06-11, Wed>

update plotAnnoPie, separate the pie and legend to prevent label overlap <2014-06-12, Thu>

Changes in version 1.1.7:

bug fixed in calculating distanceToTSS <2014-06-03, Tue>

Changes in version 1.1.6:

add chainFile parameter in enrichAnnoOverlap and enrichPeakOverlap to support different genome version comparision <2014-06-01, Sun>

fixed color bug in peakHeatmap.internal2 and plotAnnoBar <2014-06-02, Mon>

update vignettes <2014-06-02, Mon>

Changes in version 1.1.5:

export getPromoters and getTagMatrix <2014-05-31, Sat>

rename plotAvgProf to plotAvgProf2 and implement plotAvgProf based on tagMatrix <2014-05-31, Sat>

implement tagHeatmap for visualize heatmap of the tagMatrix or a list of tagMatrix <2014-05-31, Sat>

implement shuffle function to generate a random ChIP data based on a real one <2014-05-31, Sat>

implement enrichPeakOverlap to calcuate significant of ChIP experiments based on the genome coordinations <2014-05-31, Sat>

implement enrichAnnoOverlap to calculate significant of ChIP experiments based on their nearest gene annotation <2014-05-31, Sat>

incorporate GEO database for mining significant overlap of ChIP data <2014-05-31, Sat> + getGEOspecies summarize the collected data by species + getGEOgenomeVersion summarize the colleted data by genome version + getGEOInfo extract the information by genome version query + downloadGEObedFiles download all bed files of a particular genome version + downloadGSMbedFiles download the bed files of the input GSM list.

Changes in version 1.1.4:

in the annotation column of output of annotatePeak function, if Exon/Intron, the output change to ‘Transcript_Name/GeneID, Exon no. of total_no.’ <2014-05-14, Wed>

Changes in version 1.1.3:

bug fixed when metadata(TranscriptDb) contained NA <2014-04-30, Wed>

support ID type of Ensembl in annotatePeak (Entrez was supported) <2014-04-30, Wed>

Changes in version 1.1.2:

implemented plotChrCov <2014-04-25, Fri>

implemented plotAvgProf and peakHeatmap <2014-04-24, Thu>

Changes in version 1.1.1:

output of annotatePeak now contain chromosome length information <2014-04-22, Tue>

re-implement plotAnnoPie to use ordinary pie plot instead of pie3D <2014-04-21, Mon>

cisPath

Changes in version 1.5.8:

documentation improvements

Changes in version 1.5.7:

Fix a bug

Changes in version 1.5.6:

Fix a bug

Changes in version 1.5.5:

improvements

Changes in version 1.5.4:

improvements

Changes in version 1.5.3:

A method has been added to format PPI data (SIF format) downloaded from PINA2.

Changes in version 1.5.2:

Fix a bug

Changes in version 1.5.1:

Fix a bug

cleaver

Changes in version 1.3.8 (2014-09-28):

Use title case in the “Title:” field of the DESCRIPTION file.

Changes in version 1.3.7 (2014-05-08):

Create an IRangesList using split instead of lapply in the cleavageRanges,AAStringSet-method is more than two times faster.

Changes in version 1.3.6 (2014-05-03):

Add cleavageRanges method for character, AAString and AAStringSet.

cleave,AAString returns an AAStringSet instead of an AAStringSetList object.

Fix return value of cleavageSites,AAStringSet.

Changes in version 1.3.5 (2014-04-30):

Fix defintion of cleavageSites,AAStringSet.

Changes in version 1.3.4 (2014-04-30):

Add cleavageSites method for character, AAString and AAStringSet.

Changes in version 1.3.3 (2014-04-28):

Avoid duplicated digest of peptides results in a hugh speed improvement and a hugh memory reduction (removes fix from 1.1.8 and partly reintroduces original algorithm).

Remove memory test and “memoryThreshold” argument (fails on different platforms and is not important anymore using the “new” cleavage algorithm).

Change default of “unique” argument to “unique=TRUE”.

Changes in version 1.3.2 (2014-04-25):

Introduce simple memory test and “memoryThreshold” argument to avoid the calculation of ridiculous high numbers of “missedCleavages” and peptide combinations.

Changes in version 1.3.1 (2014-04-25):

Add “custom” argument to allow the user defining own cleavage rules.

Clomial

Changes in version 1.1.9 (2014-07-26):

Adding QC for the situation when only 1 sample is provided.

Changes in version 1.1.7 (2014-04-24):

The function Clomial.generate.data() can now model sequencing error.

Changes in version 1.1.2 (2014-04-18):

Some bugs fixed regarding ignoring samples.

Some bugs fixed regarding loading saved results when running in parallel.

Some typos fixed in the man files.

More efficient job submissions.

The function compute.errors() is now exported, and can be accessed by the user.

Changes in version 1.1.0 (2014-03-11):

Approved by Bioconductor.

clonotypeR

Changes in version 1.4.0:

BUG FIXES

Minor packaging corrections (NAMESPACE, etc.).

clusterProfiler

Changes in version 1.99.0:

set version to 1.99.0 and will release version 2.0.0 in next BioConductor release. <2014-09-03, Wed> + In version 2.0.0, the package was extended to support about 20 species for both of GO and KEGG analyses. + support gene set enrichment analysis algorithm for both of GO and KEGG. + support enrichMap visualization.

support about 20 species of KEGG analyses. <2014-09-03, Wed>

update man file to indicate that enrichGO is now support more than 20 species <2014-09-03, Wed>

Changes in version 1.13.3:

add keepGOlevel, keepGOterm, excludeGOlevel, excludeGOterm, not exported yet <2014-08-28, Thu>

Changes in version 1.13.2:

implement gseGO and gseKEGG for gene set enrichment analysis <2014-07-31, Thu>

import enrichMap from DOSE <2014-07-31, Thu>

add corresponding section in vignettes <2014-07-31, Thu>

Changes in version 1.13.1:

update man files according to the change of roxygen2 (ver 4.0.0) <2014-05-16, Fri>

Changes in version 1.0.0:

initial version with the following functions implemented: + GRbaseCoverage + GRcoverage + GRcoverageInbins + GRcoverageSummit + GRenrichment + countOverlapsInBins + stallingIndex + TSS + distanceFromTSS + GRangesInPromoters + GRmidpoint + GRannotate + GRannotateSimple + makeGtfFromDb + enhancers + matchEnhancers + topGOres + simplifyGOterms + findLncRNA + getPromoterClass + heatmapData + palette2d + heatmapPlot + plotStallingIndex + GR2fasta + overlapOfGRanges + GRsetwidth + unionMaxScore + GRanges2ucsc + ucsc2GRanges

CompGO

Changes in version 1.1.3:

Added ability to plot absolute values of Z-scores in plotZScores()

Fixed vignette to include Abs() plotting

Changes in version 1.1.2:

Included static vignette for illustration purposes. Some steps in our pipeline require either writing to disk or the use of a registered email, which are difficult to include in a dynamically-compiled vignette. Using a vignette that is able to show each of the steps in the pipeline with a helpful degree of detail is better than having a dynamic but less expressive one.

The vignette included uses the example datasets from He (2011) to run through the entire pipeline, illustrating the major steps and providing a useful template for analysis.

Changes in version 1.1.1:

Added functionality to plot differentially-enriched KEGG pathways using software package pathview

Added interactive plotting function to generate comparisons of many lists at once using PCA and dendrogram plots

Added several example datasets of .bed files from He, A. (2011).

cosmiq

Changes in version 0.99.1:

USER VISIBLE CHANGES

reduced rt window to decreasse the overall vignette compilation time

COSNet

Changes in version 0.99.5:

Modified the Section 1 of vignettes. USER VISIBLE CHANGES BUG FIXES PLANS

CRISPRseek

Changes in version 1.3.10:

NEW FEATURE

gRNAs are automatically output to a bed file for view in the UCSC genome browser

Changes in version 1.3.8:

NEW FEATURE

Added calculategRNAefficiency to calculate gRNA cleavage efficiency using DoenchNBT2014 predictive logistic model

Changes in version 1.3.7:

NEW FEATURE

Added searchDirection to compare2Sequences to allow search one against the other and many to many sequence search

Added exception handling to catch no gRNA found error in compare2Sequences

Changes in version 1.3.5:

BUG FIX

TopN offtarget total score was sometimes missing for sequences containing gRNAs with less than 6 offtargets in version 1.3.3

Changes in version 1.3.3:

NEW FEATURE

Search for off-targets is much faster when more than 10 gRNAs are searched

Added new optional parameter orgAnn in offTargetAnalysis

Added gene ID and optional gene symbol in off-target output file

Added gRNA target region, GC content of gRNA and number of Ts in the last 4 postion of gRNA (not including PAM sequence) in the summary output file

csaw

Changes in version 1.0.0:

New package csaw, for de novo detection of differential binding in ChIP-seq data.

cummeRbund

2.7.1: Bugfixes: - Fixed ‘fullnames’ argument to cuffData::*Matrix() methods so that it does what it’s supposed to do. - Added ‘showPool’ argument to fpkmSCVPlot. When TRUE, empirical mean and standard deviation are determined across all conditions as opposed to cross-replicate. This is set to TRUE anytime you have n<2 replicates per condition. - Added stat=”identity” to expressionBarplot to comply with ggplot 0.9.3 enforcement. - ‘labels’ argument to csScatter is now working as it’s supposed to. You can pass a vector of ‘gene_short_name’ identifiers to labels and these will be specifically called out in red text on scatterplot. - Added repFpkmMatrix() and replicates() methods to CuffFeature objects. - Removed unnecessary Joins to optimize retrieval speed for several key queries. - Fixed bug in csVolcano matrix that forced ylimits to be c(0,15) New Features: - Added csNMF() method for CuffData and CuffFeatureSet objects to perform non-negative matrix factorization. As of now, it’s merely a wrapper around the default settings for NMFN::nnmf(), but hope to expand in the future. * Does not adjust sparsity of matrices after output, must be done by user as needed. - Added csPie() method for CuffGene objects. Allows for visualization of relative isoform, CDS, and promoter usage proportions as a pie chart by condition (or optionally as stacked bar charts by adding + coord_cartesian() ). - Added ‘method’ argument to csCluster and csHeatmap to allow custom distance functions for clustering. Default = “none” = JSdist(). You can now provide a function that returns a ‘dist’ object on rows of a matrix. - Added varModel.info tracking for compatibility with cuffdiff >=2.1. Will now find varModel.info file if exists, and incorporate into database. - dispersionPlot() method added for CuffSet object. This now appropriately draws from varModel.info and is the preferred visualization for dispersion of RNA-Seq data with cummeRbund. - Added diffTable() method to CuffData and CuffFeatureSet objects to allow a ‘one-table’ snapshot of results for all Features (CuffData) or a set of Features (CuffFeatureSet). This table outputs key values including gene name, gene short name, expression estimates and per-comparison fold-change, p-value, q-value, and significance values (yes/no). A convenient ‘data-dump’ function to merge across several tables. - Added coercion methods for CuffGene objects to create GRanges and GRangeslist objects (more BioC friendly!). Will work on making this possible on CuffFeatureSet and CuffFeature objects as well. - Added pass-through to select p.adjust method for getSig (method argument to getSig) - Added ability to revert to cuffdiff q-values for specific paired-wise interrogations with getSig as opposed to re-calculating new ones (useCuffMTC; default=FALSE) Notes: - Removed generic for ‘featureNames’. Now appropriately uses featureNames generic from Biobase. As a consequence, Biobase is now a dependency. - Added passthrough to as.dist(…) in JSdist(…) - Added ‘logMode’ argument to csClusterPlot. - Added ‘showPoints’ argument to PCAplot to allow disabling of gene values in PCA plot. If false, only sample projections are plotted. - Added ‘facet’ argument to expressionPlot to disable faceting by feature_id. - shannon.entropy now uses log2 instead of log10 to constrain specificity scores between 0 and 1.

customProDB

Changes in version 1.5.5:

BUG FIXES

Fix a bug in function OutputNovelJun.R

Changes in version 1.5.4:

BUG FIXES

Fix a bug, novel junction coding sequence on ‘-‘ strand, in function OutputNovelJun.R

Changes in version 1.5.3:

BUG FIXES

Fix a bug, ID mapping, in function OutputNovelJun.R

dagLogo

Changes in version 1.3.6:

NEW FEATURES

add test files for fetchSequence function

BUG FIXES

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

Changes in version 1.3.4:

NEW FEATURES

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

BUG FIXES

fetchSequences(): when using proteome object created from AAStringSet, the columns 2 and 3 in the sequences data frame do not contain the expected values.

testDAU(): the counts() function returned NA for letters that were missing in a given matrix; that lead to NaNs in the background matrix and to errors during dagLogo() plotting. changed counts() to return 0 for missing letters.

fix the typo in dagLogo()

Changes in version 1.3.3:

NEW FEATURES

add background Noise into test

column label relative to the anchor when draw logos

BUG FIXES

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

deepSNV

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

Updates

A few changes to shearwater vignette

Renamed arguments pi.gene and pi.backgr in makePrior()

Bugfixes

Fixed bug in bf2Vcf() when no variant is called

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

Updates

Updated CITATION

Added verbose option to bam2R to suppress output

Changed mode() to “integer” for value of loadAllData()

Bugfixes

Fixed bug when only one variant is called in bf2Vcf()

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

Updates

Using knitr for prettier vignettes

Including shearwater vignette

Bugfixes

fixed issues with deletions in bf2Vcf()

makePrior() adds background on all sites

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

Updates

New shearwater algorithm

Including VCF output through summary(deepSNV, value=”VCF”)

Changes in version 1.11.1:

Bugfixes

Report correct table in summary(…, value=”VCF”); Thanks to David Gacquer.

DEGreport

0.99.12: 09-04-2014 Lorena Pantano lorena.pantano@gmail.com CORRECT DOC OF createReport

0.99.11: 09-02-2014 Lorena Pantano lorena.pantano@gmail.com ADD ncores TO REPORT CREATION

0.99.10: 08-16-2014 Lorena Pantano lorena.pantano@gmail.com REMOVE BIOMART FROM VIGNETTES DUE TO WINDOWS UNKNOWN BUILD ISSUES

0.99.9: 08-02-2014 Lorena Pantano lorena.pantano@gmail.com ADDING PARALLELIZATION TO BAYESIAN INFERENCE

0.99.4: 05-19-2014 Lorena Pantano lorena.pantano@gmail.com CODING STYLE * replacing tab by 4 spaces * cleaning up function * adding unit tests

derfinder

Changes in version 0.99.0:

NEW FEATURES

Preparing to submit to Bioconductor.

derfinderHelper

Changes in version 0.99.0:

NEW FEATURES

Preparing to submit to Bioconductor.

Added tests and vignette.

derfinderPlot

Changes in version 0.99.0:

NEW FEATURES

Preparing to submit to Bioconductor.

Added tests and vignette.

SIGNIFICANT USER-VISIBLE CHANGES

plotOverview() and plotCluster() can now plot FWER adjusted p-values if calculated with derfinder::mergeResults()

DESeq2

Changes in version 1.6.0:

DESeq() and results() gets a ‘parallel’ argument.

results() gets an ‘addMLE’ argument.

results() gets a ‘test’ argument, for constructing Wald tests after DESeq() was run using the likelihood ratio test.

results() argument ‘format’ for GRanges or GRangesList results.

new plotCounts() function.

Less outlier calling from Cook’s distance for analyses with many samples and many conditions.

More robust beta prior variance and log fold change shrinkage.

DiffBind

Changes in version 1.12.0:

Mostly bug fixes!

DMRforPairs

Changes in version 1.1.1 (2014-05-06):

The publication describing DMRforPairs was accepted in BMC Bioinformatics. The citation info of the package has been updated accordingly. Please use this updated reference when citing DMRforPairs: Rijlaarsdam MA, Zwan YGvd, Dorssers LC, Looijenga LH. DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles. BMC Bioinformatics. 2014(in press).

DOQTL

Changes in version 0.99.1:

NEW FEATURES

Added limited support for Heterogeneous Stock mice.

assoc.plot Added strain distribution patterns above the association mapping plot.

CHANGES

rankZ Fixed bug relating to NA values.

Changes in version 0.99.0:

NEW FEATURES

read.vcf reads Sanger SNP VCF files.

assoc.map imputes Sanger SNPs onto DO genomes and performs association mapping.

Fixed bug in kinship.probs in which kinship per chromosome was not calculated correctly.

Improved gene layout algorithm in gene.plot.

CHANGES

scanone returns p-values and -log10(p-values).

doqtl.plot plots either LOD or -log10(p-values).

DOSE

Changes in version 2.3.6:

add readable parameter in simplot <2014-10-09, Thu>

Changes in version 2.3.5:

implement enrichMap <2014-07-28, Wed>

Changes in version 2.3.4:

return ggplot2 objects in gseaplot <2014-07-21, Mon>

Changes in version 2.3.3:

geneSim can only accept one gene ID vector and perform as mgeneSim in GOSemSim <2014-06-23, Mon>

update man files <2014-06-23, Mon>

Changes in version 2.3.2:

bug fixed in scaleNodeColor <2014-06-08, Sun>

Changes in version 2.3.1:

upgrade man file according to roxygen2 (ver 4.0.0) . <2014-05-16, Fri>

easyRNASeq

Changes in version 2.1.15:

Removed an apparently unnecessary require call.

Changes in version 2.1.14:

Fixed a missing documentation link and a missing object documentation as well as the move of two objects’ (DataFrame, SimpleList) generic from IRanges to S4Vectors

Changes in version 2.1.13:

Bioconductor Core Team changes to underlying packages

Changes in version 2.1.12:

Bioconductor Core Team changes to underlying packages

Changes in version 2.1.11:

Fixed more IRanges -> S4Vectors import changes.

Relaxed the BAM header validation of the SO field. Thanks to John (Zang Jianhua) for finding the issue and providing the fix. Same changes as in release 2.0.9.

Changes in version 2.1.10:

Bioconductor core changes Iranges -> S4Vectors

Changes in version 2.1.9:

Ported changes from version 2.0.7

Changes in version 2.1.8:

Ported changes from the release version 2.0.5 and 2.0.6

Changes in version 2.1.7:

Changed to use roxygen 4.0.0

Corrected a dependency mismatch. Beats me why it did not work in v2.1.6…

Changes in version 2.1.6:

Corrected a dependency mismatch.

Changes in version 2.1.5:

Same changes as 2.0.3 and adapted dependencies from IRanges to S4Vectors

Changes in version 2.1.4:

Some haphazard modification from Bioc.

Changes in version 2.1.3:

Same changes as 2.0.2

Changes in version 2.1.2:

Completed the previous commit

Changes in version 2.1.1:

Same changes as 2.0.1

Changes in version 2.1.0:

None, Bioc new devel branch

EBImage

Changes in version 4.8.0:

NEW FEATURES

‘otsu’ thresholding method (contributed by Philip A. Marais, University of Pretoria, South Africa)

Support for dimnames in Image objects

‘bg.col’ argument to ‘affine’ transformations

‘reenumerate’ argument to ‘rmObjects’

‘names’ argument to ‘readImage’

‘as.array’ method for Image objects

‘as.nativeRaster’ function

SIGNIFICANT USER-VISIBLE CHANGES

Performance improvements to ‘Image’, ‘selectChannel’, ‘combine ‘ and ‘reenumerate’

Use a more efficient ‘nativeRaster’ representation in ‘displayRaster’

Cleaner output of the ‘show-Image’ method; print true object class name and dimorder (if set)

‘readImage’ sets Image dimnames to corresponding file names

‘filter2’ and ‘affine’ return object of the same class as input

Renamed ‘getNumberOfFrames’ to ‘numberOfFrames’

BUG FIXES

Handling of dimensions of character arrays

Drawing of grid lines in ‘displayRaster’

Passing of ‘…’ arguments in ‘readImage’

EBSeq

Changes in version 1.5.4:

An extra numerical approximation step is implemented in EBMultiTest() function to avoid underflow. The underflow is likely due to large number of samples. A bug in EBMultiTest() is fixed. The bug will cause error when there is exactly 1 gene/isoform that needs numerical approximation.

Changes in version 1.5.3:

BUG FIXES

Fixed a bug that may generate NA FC estimates when there are no replicates.

Changes in version 1.5.2:

NEW FEATURES

An extra numerical approximation step is implemented in EBTest() function to avoid underflow. The underflow is likely due to large number of samples.

EDASeq

Changes in version 1.99:

“exprs” and “exprs<-“ are now deprecated: use “counts” and “counts<-“ instead (for compatibility with the DESeq class).

“counts” now accesses the original counts (even after normalization) and “normCounts” accesses the normalized counts.

Added the slot “normalizedCounts” to the SeqExpressionSet class: now the normalization functions will save the normalized counts in this new slot while keeping the original counts in “counts.”

Added option to “MDPlot” to visualize control genes in red.

withinLaneNormalization and betweenLaneNormalization now always store the normalized counts in the normalizedCounts slot, even when offset=TRUE is used.

Added a new method plotPCA for Principal Components Analysis (PCA) plots.

Updated the vignette to reflect these changes.

DESCRIPTION and NAMESPACE cleaned up.

edgeR

Changes in version 3.8.0:

New goana() methods for DGEExact and DGELRT objects to perform Gene Ontology analysis of differentially expressed genes using Entrez Gene IDs.

New functions diffSpliceDGE(), topSpliceDGE() and plotSpliceDGE() for detecting differential exon usage and displaying results.

New function treatDGE() that tests for DE relative to a specified log2-FC threshold.

glmQLFTest() is split into three functions: glmQLFit() for fitting quasi-likelihood GLMs, glmQLFTest() for performing quasi-likelihood F-tests and plotQLDisp() for plotting quasi-likelihood dispersions.

processHairpinReads() renamed to processAmplicons() and allows for paired end data.

glmFit() now stores unshrunk.coefficients from prior.count=0 as well as shrunk coefficients.

estimateDisp() now has a min.row.sum argument to protect against all zero counts.

APL calculations in estimateDisp() are hot-started using fitted values from previous dispersions, to avoid discontinuous APL landscapes.

adjustedProfileLik() is modified to accept starting coefficients. glmFit() now passes starting coefficients to mglmOneGroup().

calcNormFactors() is now a S3 generic function.

The SAGE datasets from Zhang et al (1997) are no longer included with the edgeR package.

EnrichmentBrowser

Changes in version 0.99.8:

NEW FEATURES

Initial release of ‘EnrichmentBrowser’ package

ensemblVEP

Changes in version 1.6.0:

NEW FEATURES

Add VEPParam77 class to support Ensembl 77

epivizr

Changes in version 1.3.20:

Standalone mode introduced, a version of epiviz with reduced capabilities is now included as part of epivizr. The epiviz web app is run locally using ‘httpuv’s http server

Add and remove seqinfo (e.g., chromosome info) to any epiviz session

Changes in version 1.3.11:

Add NEWS file

Update documentation on ‘slideshow’ function

Changes in version 1.3.10:

Changed default on ‘slideshow’ to show all ranges

Changes in version 1.3.9:

Added ‘heatmapChart’ convenience function

Changes in version 1.3.8:

Fixed bug in ‘startEpiviz’ not sending ‘seqName’ parameter correctly

Changes in version 1.3.7:

Fixed bug in ‘EpivizBpData’ that sent ‘metadata’ info in wrong format

Changes in version 1.3.6:

Changes slots using lists in ‘EpivizDeviceMgr’ to environments to avoid crashing RStudio due to inspection of manager objects

Changes in version 1.3.5:

Fails gracefully on daemonization request on Windows

Deprecates the ‘proxy’ argument to ‘startEpiviz’

Changes in version 1.3.4:

Upgrading to Epiviz v2 webapp

erccdashboard

Changes in version 0.99.4:

BUG FIXES AND MINOR IMPROVEMENTS

Updated saveERCCPlots, description file, and citation file.

Changes in version 0.99.1:

BUG FIXES AND MINOR IMPROVEMENTS

Fixed bug in erccROC and estLODR code to only use P-values from ERCCs by coding “ERCC-00” prefix instead of “ERCC-“ which in some cases might find endogenous transcripts named with this prefix.

Changes in version 0.99.0:

NEW FEATURES

Version set to 0.99.0 for submission to Bioconductor

ISSUES

CMD check still takes too long (> 5 minutes), probably due to differential expression testing in underlying package. This will be difficult to change.

Changes in version 0.9.12:

BUG FIXES AND MINOR IMPROVEMENTS

Shortened vignette to reduce installation time

Fixed userMixFile as.factor bug

Updated namespace to pull in mgcv and nlme package functionality

ISSUES

CMD check still takes too long (> 5 minutes), probably due to differential expression testing in underlying package. This will be difficult to change.

Changes in version 0.9.11:

BUG FIXES AND MINOR IMPROVEMENTS

Added examples to several functions including “dontrun” to minimize installation time

Updated Namespace to include gplots

exomePeak

Changes in version 1.4.1 (2014-07-02):

fixed bug: sometimes bed file is not displayed properly

added “NEWS” section

added reference information

FGNet

Changes in version 3.0:

NEW FEATURES

Graphical User Interface (GUI)

New FEA tools: topGO and gage (GSA)

Plot gene expression (up/down) in the functional networks (Available since devel. version 2.1)

plotGoAncestors, plotKegg

INTERFACE CHANGES

Functions renamed or replaced:

toMatrix/adjMatrix: fea2incidMat

plotMetagroupsDistance: clusterDistance

query_gtLinker & getResults_gtLinker: fea_gtLinker & fea_gtLinker_getResults

query_david & getResults_david: fea_david & format_david

report_gtLinker & report_david: FGNet_report

intersectionNetwork: is now included in functionalNetwork

flipflop

Changes in version 1.3.9:

[pre-processing] redefine extreme boundary of segments (first and last), see calculateBound in readgroup.cpp

Changes in version 1.3.7:

solve non-portable flags issues, see Makevars

Changes in version 1.3.5:

solve compilation isue on Mavericks (using clang), see Makevars.

Changes in version 1.3.4:

properly take into account ‘S’, ‘X’ and ‘=’ characters (soft clipping, strict mismatch and match) in the CIGAR of the sam file

Changes in version 1.3.2:

Solve small bugs in the graph construction

Update the optimization solver for refit. More accurate and faster!

Remove warnings from spams (to continue …)

flowBin

Changes in version 1.1.1:

DOCUMENTATION

Minor fixes to errors or incompleteness in man files.

flowcatchR

Changes in version 0.99.4 (2014-10-03):

NEW FEATURES

Final fixes. Accepted in the current status at Bioconductor.

Changes in version 0.99.3:

NEW FEATURES

Changes in the code to be adapted to the latest devel version of EBImage (new functions were added for the Frames class).

Changes in version 0.99.2:

NEW FEATURES

Updated/added documentation.

Changes in version 0.99.1:

NEW FEATURES

Adapted after first round of review.

Changes in version 0.99.0:

NEW FEATURES

Initial submit to Bioconductor.

flowCore

Changes in version 1.31.15:

Deprecation

‘filterSet’ and ‘workFlow’ are deprecated by ‘flowWorkspace::GatingSet’

update vignette by using ‘GatingSet’

Enhancement

support ‘SPILLOVER in read.FCS` besides the existing keywords (“SPILL”, “spillover”)

support reading( read.FCS ) bad FCS files exported by flowJo that do not follow standards strictly

support ‘ncdfFlowList’ in ‘findTimeChannel’ function

flowType

Changes in version 2.3.0:

To maintain some backwards compatibility, allow users to specify method=’thresholds’ as either capital or lower case.

flowViz

Changes in version 1.29.30:

bug fixes

fix the error when xyplot on rare cells

error when xyplot on rare cell

enhancements

speed up xyplot by subsampling the data

support multiple overlays in xyplot

flowWorkspace

Changes in version 3.11.32:

Enhancements

stores the axis information in ‘axis’ slot of ‘GatingSet’ class to be used by plotGate

allow different orders of colnames of flow data when merging multiple ‘GatingSet’s into ‘GatingSetList’

add hidden nodes support

annotate hidden and boolean nodes in ‘gating tree’

wrap ‘getNodes’ logic into c++ to speed it up

add ‘flowJoTrans’ function to construct the flowJo-type biexponentioal transformation function

add multiple overlays support to plotGate method

add raw.scale argument to plotGate

add ‘subset’ S3 function to subset the GatingSet/GatingSetList based on ‘pData’

add ‘long’ format output from ‘getPopStats` method

add ‘transform’ method for ‘GatingSet’ to transform the flow data associated with the GatingSet and save the transformation functions within ‘GatingSet’

add some internal functions (‘merge-GatingSet.R’) to handle merging ‘GatingSets’

focalCall

Changes in version 0.99.3 (2014-10-06):

IMPROVEMENTS

Fixed unit tests

Changed column names in CNVset in example data

Changes in version 0.99.2 (2014-10-06):

IMPROVEMENTS

Added initial unit testing

Fixed indenting in .Rd files

Added this NEWS file

Changed all hard coded column numbers to name of column

Added example to BierkensCNA.Rd

Changed names example data (“BierkensCNA”)

Fixed NAMESPACE file

Changes in version 0.99.1 (2014-10-02):

IMPROVEMENTS

Changed F to FALSE

Fixed /value section in man pages

Added runnable examples for all man pages

Updated DESCRIPTION file

Changes in version 0.99.0 (2014-04-14):

RELEASE

initial submitted version

gCMAP

Changes in version 1.9.2:

BUGFIX: Updated geneIndex method to accept both symbols2indices and id2indices functions from limma, depending on the limma version.

GeneAnswers

Changes in version 2.8.0:

NEW FEATURES

New function getListGIF is added to interact with ListGIF web server (http://listgif.nubic.northwestern.edu). ListGIF provides a quick analysis solution to identify the overrepresented biomedical concepts from a list of query genes. Result is rendered as a wordle.

BUG FIXES

Reactome hyperlink has been fixed.

GeneNetworkBuilder

Changes in version 1.7.1:

NEW FEATURES

No changes classified as ‘new features’ (package under active development)

BUG FIXES

Fixed no matching function bug under Mac OS X Mavericks

genomeIntervals

Changes in version 1.21.1:

Ported version 1.20.1 changes

Changes in version 1.20.1:

Added an argument to the readGff3 function to enable quietness.

Corrected some R CMD check warnings

GenomicFeatures

CHANGES IN VERSION 1.18

NEW FEATURES

o Add extractUpstreamSeqs(). o makeTranscriptDbFromUCSC() now supports the "flyBaseGene" table (FlyBase Genes track). o makeTranscriptDbFromBiomart() now knows how to fetch the sequence lengths from the Ensembl Plants db. o makeTranscriptDbFromGFF() is now more tolerant of bad strand information.

SIGNIFICANT USER-VISIBLE CHANGES

o Replace toy TxDb UCSC_knownGene_sample.sqlite (based on hg18) with hg19_knownGene_sample.sqlite (based on hg19) and use hg19 instead of hg18 in all examples (and unit tests). o Rename TranscriptDb class -> TxDb. o Now when GTF files are processed into TxDbs with exon ranking being inferreed, if the exons are on separate chromosomes, we toss out that transcript (since we cannot possibly guess the exon ranking correctly).

DEPRECATED AND DEFUNCT

o extractTranscripts() and extractTranscriptsFromGenome() are now defunct. o Deprecate sortExonsByRank().

BUG FIXES

o Bug fixes and improvements to makeTranscriptDbFromBiomart(): (a) Fix long standing bug where the code in charge of inferring the CDSs from the UTRs would return CDSs spanning all the exons of a non-coding transcript. (b) Fix an issue that was preventing the function from extracting the CDS information added recently to the datasets in the Ensembl Fungi, Ensembl Metazoa, Ensembl Plants, and Ensembl Protists databases. (c) Make the code in charge of extracting the CDSs more robust by taking advantage of new attributes (genomic_coding_start and genomic_coding_end) added by Ensembl in release 74 (Dec 2013), and by adding more sanity checks.

GenomicFiles

Changes in version 1.2.0:

NEW FEATURES

Add pack / unpack generics and methods

Add GenomicFiles class

Add reduceByFile / reduceByRange methods for GenomicFiles class that expect ‘file’ to be character and ‘ranges’ a GRanges

Move yieldReduce() from Rsamtools to GenomicFiles and rename as reduceByYield()

Allow GRange or GRangesList as @rowData in GenomicFiles class

MODIFICATIONS

Remove unused .FileList, VCFFileViews and FaFileViews class

Add checks for ‘summarize=FALSE’ when REDUCER is used

Clean up vignette introduction

Change REDUCER() signature to single argument reguardless of the value of ‘iterate’

Rework reduceByYield() arguments for consistency with other reduceBy* functions

GenomicRanges

CHANGES IN VERSION 1.18.0

NEW FEATURES

o Add 'use.mcols' arg to "ranges" method for GRangesList objects. o "assays<-" methods may be invoked with 'withDimnames' arg. o Add mapCoords() generic and methods (replacing map()). o Add granges,GenomicRanges method. o Add strand<-,GRangesList,character method for global replacement (i.e., all strands become 'value'). o Add resize,GRangesList-method. o Add DelegatingGenomicRanges class and vignette on how to extend GenomicRanges. o Document subsetting a named list-like object by a GRanges subscript.

SIGNIFICANT USER-LEVEL CHANGES

o Modify "show" methods for GRanges and GRangesList objects so they print a 1-line summary of the seqinfo component. o Remove as.data.frame,GRangesList-method; use as.data.frame,List. o "trim" method for GenomicRanges only trims out-of-bound ranges on non-circular sequences whose length is not NA. This behavior is consistent with the GenomicRanges validity method. o Changes to flank(), resize() and start/end/width setters: - no longer trim the result ranges when called on a GRanges - warning is issued by GenomicRanges validity method when out-of-bound ranges are on non-circular sequences whose length is not NA Note this behavior is now consistent with that of shift(). o Speed up validation of GenomicRanges objects by 1.2x. o Speed up trim() on GenomicRanges objects by 1.2x. o Improve warning when GenomicRanges object contains out-of-bound ranges. o Work on vignette HOWTOs: - split 'How to read BAM files into R' into 3 HOWTOs - split 'How to prepare a table of read counts for RNA-Seq differential gene expression' into 3 HOWTOs - split 'How to extract DNA sequences of gene regions' into 2 HOWTOs - make individual HOWTOs subsections of single HOWTO section o Follow renaming of TranscriptDb class to TxDb. o Replace references to plantsmart21 with plantsmart22.

DEPRECATED AND DEFUNCT

o Defunct map() (skip deprecation). Replace with mapCoords().

BUG FIXES

o [cr]bind,SummarizedExperiment methods respect derived classes. o assays(se, withDimnames=TRUE) <- value no longer tries to access a slot 'withDimnames'. o cbind and rbind,SummarizedExperiment-methods respect derived classes o "ranges" method for GRangesList objects should not propagate inner metadata columns by default. o GRanges() constructor now preserves the seqlevels in the order supplied by the user. o Ensure tileGenome() breakpoints do not extend past end of genome. o Fix "show" method for GenomicRanges objects when 'showHeadLines' global option is set to Inf. o [rc]bind,SummarizeExperiment-methods now compare all elements. o Remove "==" and "<=" methods for GenomicRanges objects (not needed).

genoset

Changes in version 1.19.27:

NEW FEATURES

rangeMeans for numeric gets a na.rm argument and uses 50% less time for na.rm = FALSE ands 25% less time for na.rm=TRUE.

Changes in version 1.19.7:

NEW FEATURES

The version introduces the rangeMeans family of functions, which are closely related to IRanges::viewMeans family of functions. These new functions take an RleDataFrame and an IRanges (or matrix) of row ranges and compute summary stats. These are useful for summaries like the average DNA copy number or coverage in a gene, by sample. These functions differ from view* in that they are more time efficient and they offer a ‘simplify’ argument to return a matrix, rather than a list.

Changes in version 1.19.0:

NEW FEATURES

This version introduces the RleDataFrame class. This class extends SimpleRleList and DataFrame. It stores a collection of like-length Rle objects. With the AtomicList features it behaves much like a matrix. For example, log2(x) - 1 works. We also have row and column sums and means. rangeSampleMeans functions like viewMeans. This object can be used to store runs of data along the genome for multiple samples, like coverage or DNA copy number. It can be used as an assayDataElement in a genoset (or any eSet).

segTable and segPairTable are dramatically faster. Stacking data.frames with segTable(RleDataFrame,stack=TRUE) argument is now instantaneous.

DEPRECATED AND DEFUNCT

Previously we used a DataFrame for storing collections of Rle objects. This practice is now deprecated. Similarly, colMeans on a DataFrame is now deprecated.

GGBase

Changes in version 3.27.5:

clipPCs and regressOut now work for SummarizedExperiment instances

gmapR

CHANGES IN VERSION 1.8.0

NEW FEATURES

o GmapGenomes can be built from any file supported by rtracklayer (so 2bit now works, as well as fasta). o Tally BAM files by codon given a set of transcript structures. This happens at the read level, i.e., a codon is observed within an individual read. o Tally BAM files strand by XS tag (inferred strand of transcription, instead of strand of alignment).

GOexpress

Changes in version 0.99.17:

BUG FIXES

NAs were introduced in the average score and rank of GO terms following analysis of microarray data (ANOVA and randomForest) for GO terms without associated features in the ExpressionSet. The problem was not found in any case for analysis of RNA-Seq data. This was causing issues during the subset_scores function and subsequent plots, such as main titles made of multiple lines and NAs. GO terms without associated probesets are now given average score of 0 and average rank equal to the maximum in the dataset plus 1.

Changes in version 0.99.16:

GENERAL UPDATES

Included co-authors who participated in the generation and analysis of data used to test the package.

Changes in version 0.99.15:

GENERAL UPDATES

Updated man pages GO_analyse to describe the recently added subset slot in the result variable.

Changes in version 0.99.14:

BUG FIXES

The anova method of the GO_analyse method was broken since the introduction of ExpressionSet, release 0.99.4.

UPDATED FEATURES

The subset argument was also added to the GO_analyse method. This allows the identification of genes clustering a subset of groups, at a subset of time-points, etc. while plotting the expression profile of the entire dataset, if desired.

GENERAL UPDATES

Updated man pages GO_analyse to allow only one example to be run. This saves time during CMD check, while making the man page more easily readable.

Changes in version 0.99.13:

UPDATED FEATURES

All expression plots were updated to a default ylim range corresponding to the minimum and maximum expression values found in the entire ExpressionSet. This is meant to avoid mis-interpretation of the amplitude of variation between sample groups, as suggested in the paper: Rougier, N.P., Droettboom, M., and Bourne, P.E. (2014). Ten simple rules for better figures. PLoS computational biology 10, e1003833.

Changes in version 0.99.12:

UPDATED FEATURES

All expression plots were given new arguments for more control: xlab allows users to change the default title for the X-axis, ylim allows users to override the lower and upper boundaries of the Y axis.

GENERAL UPDATES

Updated man pages AlvMac, AlvMac_results, microarray2dataset, and prefix2dataset. Replaced the LaTeX describe statement by an itemise statement to make the man page more readable in a terminal window.

Moved functions between the post_analysis script and the toolkit script. From now on, only functions accessible to the users should be present in the post_analysis script, while toolkit should contain method called internally.

The User’s Guide was updated to redirect the users to the new support site for Bioconductor rather than the bioc-devel mailing list.

Changes in version 0.99.11:

NEW FEATURES

The new subEset() method subsets an ExpressionSet given a list where item names are column names of the phenoData slots and item values are vectors of values corresponding to sample to retain (e.g. list(Time=c(“2H”, “6H”)) will retain samples with value “2H” or “6H” in the “Time” column of the phenoData slot).

UPDATED FEATURES

All relevant visualisation methods have been added an argument to subset samples to plot to those with a given set of values for a given column in the phenoData (uses the new function subEset described above).

The example analysis results was renamed from “raw_results” to “AlvMac_results”, so that it can now loaded running data(AlvMac_results). The new name is meant to be more specific to the package.

Changes in version 0.99.10:

GENERAL UPDATES

Replaced \format by \value sections to the following man pages: AlvMac.Rd, microarray2dataset.Rd, prefix2dataset.Rd, raw_results.Rd to avoid having an empty value section, as recommended by the Bioconductor package tracker. Hopefully, it does not require a non-empty \format section as well…

Restricted lines to less than 80 characters and indentation by multiple of four space characters.

Changes in version 0.99.9:

UPDATED FEATURES

all post analysis functions were given more sanity checks to verify that the “result” argument contains the required slots of a GO_analyse() output and the the arguments pointing at a phenotypic data column are valid column names.

BUG FIXES

expression_plot_symbol and expression_profiles symbol used the default value of col.palette and colourF instead of forwarding the user-defined one to the expression_plot and expression_profiles functions.

GENERAL UPDATES

Added cross-reference in UsersGuide to point at examples of usages of factor and numeric values for the expression plots

Changes in version 0.99.8:

GENERAL UPDATES

Resaved R data files to reduced package disk size. No more WARNING in R CMD check.

Removed reference to GitHub in the README file. The weblink is given in the DESCRIPTION file anyway if users are interested.

Changes in version 0.99.7:

UPDATED FEATURES

fixed a typo in the code of heatmap_GO which made it crash for any other dataset than the example dataset.

Changes in version 0.99.6:

UPDATED FEATURES

expression_profiles_symbol() method was missing the “index” argument to select the feature identifier to plot alone.

Changes in version 0.99.5:

NEW FEATURES

expression_profiles() method plots the expression profiles of individual samples series, as opposed to grouped samples series handled by expression_plot functions.

expression_profiles_symbol() method plots the expression profiles of individual samples series using a gene name instead of an Ensembl gene identifier.

UPDATED FEATURES

overlap_GO can print to screen, if filename argument is set to NULL (Default).

heatmap_GO, cluter_GO and plot_design can resize title font and wrap the text on multiple lines.

expression_plot and expression_plot_symbol can orient X axis labels at a given angle.

replaced return(NULL) statement by stop() when no close match is found to a gene name in the family of expression_plot functions.

GENERAL UPDATES

User’s Guide updated.

List of contributors updated in User’s Guide and DESCRIPTION.

Changes in version 0.99.4:

UPDATED FEATURES

Use of ExpressionSet instead of numeric named matrix and AnnotatedDataFrame. Better consistency with other Bioconductor packages.

GENERAL UPDATES

Implemented corrections requested following the Bioconductor review. Includes typos, consistent terminology through the package code and metafiles, additional information in help files, no reference to GitHub as an alternate installation option, use of arrow signs instead of equal signs for value assignment.

Restricted lines to 80 characters, and used 4-space tabulations.

Corrected out-of-date documentation.

Changes in version 0.99.3:

UPDATED FEATURES

Control the size of the legend text in the two expression plot figures. Updated help files accordingly.

Updated vignette with new section “Statistics”.

Complete cleaning of code files for lines shorter than 80 columns.

Cleanup of help files for lines shorter than 80 columns.

Enabled filtering of raw results on the average score of a GO term.

Changes in version 0.99.2:

UPDATED FEATURES

Metadata lines in the preamble of the Sweave file

Changes in version 0.99.1:

UPDATED FEATURES

Sweave vignette implemented.

Replaced all message() statements by cat() to make Sweave output the full message in the vignette.

Updated a missed F into FALSE

Updated an invalid biocViews (typo)

Date field added for a proper citation() method.

Changes in version 0.99.0:

UPDATED FEATURES

Replaced all cat() statements by message() to match the Biocondcutor guidelines.

GOSemSim

Changes in version 1.23.2:

fast IC-method implemented, contributed by Alexey Stukalov <2014-09-27, Sat>

Changes in version 1.23.1:

add support of species coelicolor and gondii <2014-09-03, Wed>

GOsummaries

Changes in version 1.99.3:

CHANGES

Bumped the version number to 1.99.3

Changes in version 1.1:

Added support for custom data in word clouds (see gosummaries functions)

Now it is possible to display genes instead of GO categories (see show_genes parameter in gosummaries.MArrayLM, gosummaries.prcomp and gosummaries.matrix)

Added function gosummaries.matrix that takes in a matrix that is a MDS representation of data and expression matrix and then finds most correlated features for each MDS component.

Changes in version 1.0:

NEW FEATURES

First version of the package

Changes in version 0.99.3:

NEW FEATURES

Updated Vignette to biocStyle

Form now GOsummaries is going to live in Bioconductor and this version supersedes the CRAN version 1.1

Changes in version 0.99.2:

NEW FEATURES

Reformatted code for Bioconductor

Improved Vignette

graphite

Changes in version 1.11.4 (2014-10-01):

Updated Biocarta, KEGG, NCI, HumanCyc, Panther and Reactome data.

GSAR

Changes in version 1.0.0:

This is the first version of the R package GSAR.

The package provides two-sample nonparametric multivariate statistical methods to test specific alternative hypotheses against a null hypothesis.

GSAR depends on package igraph to handle graphs in objects of class igraph and uses some functions too.

New capabilities and future changes will be reported in subsequent versions.

Gviz

Changes in version 1.9.0:

NEW FEATURES

The new CustomTrack class to allow for user-defined plotting functions.

SIGNIFICANT USER-VISIBLE CHANGES

The collapseTranscripts parameter now offers more control over the type of collapsing.

gwascat

Changes in version 1.9.8:

USER VISIBLE CHANGES

makeCurrentGwascat has new arguments, useHg38seqinfo and altseqinfo. These address the fact that the textual version of the catalog served by NHGRI has hg38 addresses. Two snapshots of the data are available, created Sept 8 2014, one direct in hg38 (gwrngs38 in data) and the other by liftOver to hg19 addresses (gwrngs19)

Changes in version 1.11.33:

Allow getting variables from sub-nodes in a GDS file (e.g., getVariable(GdsReader, “snp.annot/qual”)).

Add getNodeDescription method to GdsReader.

Added examples of converting from PLINK and VCF in Formats vignette.

Changes in version 1.11.32:

imputedDosageFile replaces ncdfImputedDosage and gdsImputedDosage

Changes in version 1.11.31:

setMissingGenotypes replaces ncdfSetMissingGenotypes and gdsSetMissingGenotypes

Changes in version 1.11.22:

convertNcdfGds and convertGdsNcdf will convert files with any variable names (not just genotype)

Changes in version 1.11.21:

Fixed bug in vcfWrite to output missing data code for ID column

Data cleaning vignette uses createDataFile instead of ncdfCreate and ncdfAddData

Data cleaning vignette uses snpgdsOpen and snpgdsClose

Changes in version 1.11.20:

Fixed bug in assocTestCPH when there is no Y chromosome in the data

Changes in version 1.11.19:

convertNcdfGds will not write entire snp and sample annotations to file

createDataFile replaces ncdfCreate and ncdfAddData

Changes in version 1.11.18:

patch from Karl Forner to allow use of open gds objects in constructors for GdsReader and GdsGenotypeReader

Changes in version 1.11.17:

removed duplicated .probToDosage function from ncdfImputedDosage.R source file

Changes in version 1.11.16:

expanded matching options in duplicateDiscordanceAcrossDatasets

Changes in version 1.11.15:

allowed truncate to be a numeric value or TRUE in qqPlot

Changes in version 1.11.14:

added pasteSorted function

Changes in version 1.11.13:

in case of missing allele code, return character genotype as NA

Changes in version 1.11.12:

bug fix in assocTestRegression when a block contains only 1 SNP

Changes in version 1.11.11:

added vcfCheck function to compare VCF file to GenotypeData object

Changes in version 1.11.10:

bug fix in gwasExactHW when a block contains only 1 genotype

Changes in version 1.11.9:

changed colors of BAF plots so points can be more easily distinguished

Changes in version 1.11.8:

added ref.allele option to vcfWrite to select either A or B as the reference allele for each SNP

Changes in version 1.11.7:

added vcfWrite function to write VCF file from GenotypeData object

Changes in version 1.11.6:

bug fix in qqPlot, manhattanPlot when requesting thinning when bins only have 1 point

Changes in version 1.11.5:

added pointsPerBin argument to manhattanPlot

Changes in version 1.11.4:

added optional thinThreshold argument to manhattanPlot and qqPlot functions

Changes in version 1.11.3:

updated gdsSubset for new gdsfmt read.gdsn syntax (also changed in release version)

Changes in version 1.11.1:

Added ylim argument to qqPlot.

HDTD

Changes in version 0.99.4 (2014-10-01):

Updated CITATION file.

Changes in version 0.99.3 (2014-09-25):

Introduced warning messages regarding the sample size.

Updated the vignette file.

Changes in version 0.99.2 (2014-08-12):

Updated the output of the core functions.

Changes in version 0.99.1 (2014-05-14):

Accepted to Bioconductor.

Changes in version 0.99.0 (2014-04-17):

Submitted to Bioconductor.

hiAnnotator

Changes in version 0.99.9:

metadatacol bug fix

Changes in version 0.99.8:

plotdis