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.
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/.
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)
Package maintainers can add NEWS files describing changes to their packages. The following package NEWS is available:
Changes in version 2.5.2 (2014-10-03):
Changes in version 2.5.1 (2014-10-03):
Changes in version 2.5.0:
Changes in version 1.37.2 (2014-09-28):
Changes in version 1.37.1 (2014-08-25):
Changes in version 1.37.0 (2014-04-11):
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
Changes in version 0.99.0:
NEW FEATURES
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.
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* 1.8.0 SERIES NEWS *
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**************************************************
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.
Changes in version 1.6.0:
NEW FEATURES
Changes in version 2.1.2 (2014-09-23):
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):
Changes in version 0.99.2:
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.
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
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
Changes in version 1.4.0:
USER VISIBLE CHANGES
Support for markdown documents
Add \Githubpkg markup command
Changes in version 2.0.4:
Category Class
Category Functionality
Category Dependencies
Category Deprecation
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
Changes in version 0.99.1:
SIGNIFICANT USER-VISIBLE CHANGES
NEW FEATURES
BUG FIXES
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
PLANS
Changes in version 1.7.10:
NEW FEATURES
Changes in version 1.7.1:
NEW FEATURES
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.
Changes in version 1.1.2:
Changes in version 1.1.21:
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:
Changes in version 1.1.15:
Changes in version 1.1.14:
Changes in version 1.1.13:
Changes in version 1.1.12:
Changes in version 1.1.10:
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:
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:
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>
Changes in version 1.5.8:
Changes in version 1.5.7:
Changes in version 1.5.6:
Changes in version 1.5.5:
Changes in version 1.5.4:
Changes in version 1.5.3:
Changes in version 1.5.2:
Changes in version 1.5.1:
Changes in version 1.3.8 (2014-09-28):
Changes in version 1.3.7 (2014-05-08):
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):
Changes in version 1.3.4 (2014-04-30):
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):
Changes in version 1.3.1 (2014-04-25):
Changes in version 1.1.9 (2014-07-26):
Changes in version 1.1.7 (2014-04-24):
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):
Changes in version 1.4.0:
BUG FIXES
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:
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:
Changes in version 1.0.0:
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).
Changes in version 0.99.1:
USER VISIBLE CHANGES
Changes in version 0.99.5:
Changes in version 1.3.10:
NEW FEATURE
Changes in version 1.3.8:
NEW FEATURE
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
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
Changes in version 1.0.0:
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.
Changes in version 1.5.5:
BUG FIXES
Changes in version 1.5.4:
BUG FIXES
Changes in version 1.5.3:
BUG FIXES
Changes in version 1.3.6:
NEW FEATURES
BUG FIXES
Changes in version 1.3.4:
NEW FEATURES
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
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
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
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
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
Changes in version 0.99.0:
NEW FEATURES
Changes in version 0.99.0:
NEW FEATURES
Preparing to submit to Bioconductor.
Added tests and vignette.
Changes in version 0.99.0:
NEW FEATURES
Preparing to submit to Bioconductor.
Added tests and vignette.
SIGNIFICANT USER-VISIBLE CHANGES
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.
Changes in version 1.12.0:
Changes in version 1.1.1 (2014-05-06):
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
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).
Changes in version 2.3.6:
Changes in version 2.3.5:
Changes in version 2.3.4:
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:
Changes in version 2.3.1:
Changes in version 2.1.15:
Changes in version 2.1.14:
Changes in version 2.1.13:
Changes in version 2.1.12:
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:
Changes in version 2.1.9:
Changes in version 2.1.8:
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:
Changes in version 2.1.5:
Changes in version 2.1.4:
Changes in version 2.1.3:
Changes in version 2.1.2:
Changes in version 2.1.1:
Changes in version 2.1.0:
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’
Changes in version 1.5.4:
Changes in version 1.5.3:
BUG FIXES
Changes in version 1.5.2:
NEW FEATURES
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.
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.
Changes in version 0.99.8:
NEW FEATURES
Changes in version 1.6.0:
NEW FEATURES
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:
Changes in version 1.3.9:
Changes in version 1.3.8:
Changes in version 1.3.7:
Changes in version 1.3.6:
Changes in version 1.3.5:
Fails gracefully on daemonization request on Windows
Deprecates the ‘proxy’ argument to ‘startEpiviz’
Changes in version 1.3.4:
Changes in version 0.99.4:
BUG FIXES AND MINOR IMPROVEMENTS
Changes in version 0.99.1:
BUG FIXES AND MINOR IMPROVEMENTS
Changes in version 0.99.0:
NEW FEATURES
ISSUES
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
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
Changes in version 1.4.1 (2014-07-02):
fixed bug: sometimes bed file is not displayed properly
added “NEWS” section
added reference information
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
Changes in version 1.3.9:
Changes in version 1.3.7:
Changes in version 1.3.5:
Changes in version 1.3.4:
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 …)
Changes in version 1.1.1:
DOCUMENTATION
Changes in version 0.99.4 (2014-10-03):
NEW FEATURES
Changes in version 0.99.3:
NEW FEATURES
Changes in version 0.99.2:
NEW FEATURES
Changes in version 0.99.1:
NEW FEATURES
Changes in version 0.99.0:
NEW FEATURES
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
Changes in version 2.3.0:
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
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’
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
Changes in version 1.9.2:
Changes in version 2.8.0:
NEW FEATURES
BUG FIXES
Changes in version 1.7.1:
NEW FEATURES
BUG FIXES
Changes in version 1.21.1:
Changes in version 1.20.1:
Added an argument to the readGff3 function to enable quietness.
Corrected some R CMD check warnings
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.
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
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).
Changes in version 1.19.27:
NEW FEATURES
Changes in version 1.19.7:
NEW FEATURES
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
Changes in version 3.27.5:
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).
Changes in version 0.99.17:
BUG FIXES
Changes in version 0.99.16:
GENERAL UPDATES
Changes in version 0.99.15:
GENERAL UPDATES
Changes in version 0.99.14:
BUG FIXES
UPDATED FEATURES
GENERAL UPDATES
Changes in version 0.99.13:
UPDATED FEATURES
Changes in version 0.99.12:
UPDATED FEATURES
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
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
BUG FIXES
GENERAL UPDATES
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
Changes in version 0.99.6:
UPDATED FEATURES
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
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
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
Changes in version 1.23.2:
Changes in version 1.23.1:
Changes in version 1.99.3:
CHANGES
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
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
Changes in version 1.11.4 (2014-10-01):
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.
Changes in version 1.9.0:
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.9.8:
USER VISIBLE CHANGES
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:
Changes in version 1.11.31:
Changes in version 1.11.22:
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:
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:
Changes in version 1.11.17:
Changes in version 1.11.16:
Changes in version 1.11.15:
Changes in version 1.11.14:
Changes in version 1.11.13:
Changes in version 1.11.12:
Changes in version 1.11.11:
Changes in version 1.11.10:
Changes in version 1.11.9:
Changes in version 1.11.8:
Changes in version 1.11.7:
Changes in version 1.11.6:
Changes in version 1.11.5:
Changes in version 1.11.4:
Changes in version 1.11.3:
Changes in version 1.11.1:
Changes in version 0.99.4 (2014-10-01):
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):
Changes in version 0.99.1 (2014-05-14):
Changes in version 0.99.0 (2014-04-17):
Changes in version 0.99.9:
Changes in version 0.99.8:
Changes in version 0.99.7:
Changes in version 0.99.6:
Changes in version 0.99.5:
Changes in version 0.99.4:
NEW FEATURES
plotdisFeature(), function to plot distance distribution to feature boundary.
Includes sites.ctrl dataset to compliment sites dataset.
Changes in version 0.99.3:
NEW FEATURES
DEPRECATED AND DEFUNCT
BUG FIXES
0.99.0: Added examples for almost all functions
0.99.0: Removed Subread support
Changes in version 1.9.5:
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
Access the contact map is now ALWAYS performed using chromosomes’ name such as ygi/xgi, i.e. rownames/colnames of contact maps
Update of the setGenomicFeatures method and speed improvment
BUG FIXES
Update of isComplete method
Update of import functions
Changes in version 1.9.4:
NEW FEATURES
ICE normalization can now be applied on both HTCexp and HTClist objects
New methods for HTClist-class : isComplete, isPairwise, forcePairwise, forceSymmetric
New methods for HTCexp-class : forceSymmetric
New methods (not exported) for HTClist-class : getCombinedIntervals, getCombinedContacts
SIGNIFICANT USER-VISIBLE CHANGES
Update of the binningC method. Improvement of speed and memory usage. The binningC function can now be applied on Hi-C data (or any already binned data). The goal is to move from a very high resolution map (for instance 40kb) to a lower resolution ( for instance 1Mb) by aggregationg and summing the bins.
Update of the importC/exportC functions which are now based on a new format (list with interactor1/interactor2/count + BED files). This format is recommanded to store sparse data because only the non null values are exported/imported.
Update of the import.my5C/export.m5C functions. Only the matrix format is now supported. For the list format, see the importC/exportC functions.
BUG FIXES
Changes in version 1.9.3:
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
Update output of summary method to add the seqlevels of both interactors
Speed improvement; seqlevels
Update import.my5C function
BUG FIXES
Fix bug in HTCexp constructor. Only intrachromosomal data can be force to be symmetrical
Fix bug in summary function for HTClist object
Fix bug in mapC function, in case of empty matrices (only zero values)
Changes in version 3.15.3:
Changes in version 3.15.2:
Changes in version 3.15.1:
start next dev cycle
remove count_transcripts and count_ncRNA_nongenic from QA
Changes in version 3.14.1:
3.14.1 release
fixed the fragmentLength NA bug spotted by Jinfeng
Changes in version 0.7.2 (2014-10-02):
Changes in version 0.7.1 (2014-09-21):
The vignette now reads the GenomeStudio example file from the IlluminaDataTestFiles package instead of the internet.
Updated CITATION.
Added citation to vignette.
Changes in version 0.7.0 (2014-04-11):
Changes in version 1.0.1:
FEATURES
Package allows systematically explore the IMPC dataset’s multiple dimensions until the correct combination of filters has been selected.
Package helps to obtain datasets from IMPC database.
The data retrieved from IMPCdata package can be directly used by PhenStat – an R package that encapsulates the IMPC statistical pipeline, available at <URL: http://bioconductor.org/packages/release/bioc/html/PhenStat.html>.
Changes in version 1.10.0:
CHANGES IN VERSION 2.0.0
NEW FEATURES
o Add mapCoords() and pmapCoords() as replacements for map() and pmap().
o Add coercion from list to RangesList.
o Add slice,ANY method as a convenience for slice(as(x, "Rle"), ...).
o Add mergeByOverlaps(); acts like base::merge as far as it makes sense.
o Add overlapsAny,Vector,missing method.
SIGNIFICANT USER-VISIBLE CHANGES
o Move Annotated, DataTable, Vector, Hits, Rle, List, SimpleList, and
DataFrame classes to new S4Vectors package.
o Move isConstant(), classNameForDisplay(), and low-level argument
checking helpers isSingleNumber(), isSingleString(), etc... to new
S4Vectors package.
o Rename Grouping class -> ManyToOneGrouping. Redefine Grouping class as
the parent of all groupings (it formalizes the most general kind of
grouping).
o Change splitAsList() to a generic.
o In rbind,DataFrame method, no longer coerce the combined column to the
class of the column in the first argument.
o Do not carry over row.names attribute from data.frame to DataFrame.
o No longer make names valid in [[<-,DataFrame method.
o Make the set operations dispatch on Ranges instead of IRanges; they
usually return an IRanges, but the input could be any implementation.
o Add '...' to splitAsList() generic.
o Speed up trim() on a Views object when trimming is actually not needed
(no-op).
o Speed up validation of IRanges objects by 2x.
o Speed up "flank" method for Ranges objects by 4x.
DEPRECATED AND DEFUNCT
o Defunct map() and pmap().
o reduce() argument 'with.mapping' is now defunct.
o splitAsListReturnedClass() is now defunct.
o Deprecate seqapply(), mseqapply(), tseqapply(), seqsplit(), and seqby().
BUG FIXES
o Fix rbind,DataFrame method when first column is a matrix.
o Fix a memory leak in the interval tree code.
o Fix handling of minoverlap > 1 in findOverlaps(), so that it behaves
more consistently and respects 'maxgap', as documented.
o Fix findOverlaps,IRanges method for select="last".
o Fix subset,Vector-method to handle objects with NULL mcols(x) (e.g.
Rle object).
o Fix internal helper rbind.mcols() for DataFrame (and potentially other
tables).
o ranges,SimpleRleList method now returns a SimpleRangesList (instead of
CompressedRangesList).
o Make flank() work on Ranges object of length 0.
Changes in version 1.0.0:
Changes in version 1.7.6:
NEW FEATURES
Changes in version 1.7.5:
NEW FEATURES
Changes in version 1.7.4:
NEW FEATURES
Changes in version 1.7.3:
NEW FEATURES
Changes in version 1.7.2:
NEW FEATURES
Changes in version 1.7.1:
NEW FEATURES
Changes in version 3.22.0:
New functions goana() and topGO() provide gene ontology analyses of differentially genes from a linear model fit. The tests include the ability to adjust for gene length or abundance biases in differential expression detection, similar to the goseq package.
Improvements to diffSplice. diffSplice() now calculates Simes adjusted p-values for gene level inferences, in addition to the exon level t-tests and gene level F-tests. topSplice() now has three ranking methods (“simes”, “F” or “t”), with “simes” now becoming the default. diffSplice() also has a new argument ‘robust’ giving access to robust empirical Bayes variance moderation.
New function plotExons() to plot log-fold-changes by exon for a given gene.
New function voomWithQualityWeights() allows users to estimate sample quality weights or allow for heteroscedasticity between treatment groups when doing an RNA-seq analysis.
Improvement to arrayQualightyWeights(). It now has a new argument ‘var.design’ which allows users to model variability by treatment group or other covariates.
Improved plotting for voomaByGroup().
barcodeplot() can now plot different weights for different genes in the set.
Improvements to roast() and mroast(). The directional (up and down) tests done by roast() now use both the original rotations and their opposite signs, effectively doubling the number of effective rotations for no additional computational cost. The two-sided tests are now done explicitly by rotation instead of doubling the smallest one-sided p-value. The two-sided p-value is now called “UpOrDown” in the roast() output. Both functions now use a fast approximation to convert t-statistics into z-scores, making the functions much faster when the number of rotations or the number of genes is large. The contrast argument can now optionally be a character string giving a column name of the design matrix.
zscoreT() can optionally use a fast approximation instead of the slower exact calculation.
symbols2indices() renamed to ids2indices().
Improvements to removeBatchEffect(). It can now take into account weights and other arguments that will affect the linear model fit. It can now accept any arguments that would be acceptable for lmFit(). The behavior of removeBatchEffect() with design supplied has also changed so that it is now consistent with that of lmFit() when modelling batches as additive effects. Previously batch adjustments were made only within the treatment levels defined by the design matrix.
New function plotWithHighlights(), which is now used as the low-level function for plotMA() and plot() methods for limma data objects.
The definition of the M and A axes for an MA-plot of single channel data is changed slightly. Previously the A-axis was the average of all arrays in the dataset - this has been definition since MA-plots were introduced for single channel data in April 2003. Now an artificial array is formed by averaging all arrays other than the one to be plotted. Then a mean-difference plot is formed from the specified array and the artificial array. This change ensures the specified and artificial arrays are computed from independent data, and ensures the MA-plot will reduce to a correct mean-difference plot when there are just two arrays in the dataset.
plotMDS() can now optionally plot samples using symbols instead of text labels. It no longer has a ‘col’ argument, which instead is handled by ….
vennDiagram() now supports circles of different colors for any number of circles. Previously this was supported only up to three sets.
getEAWP() will now find a weights matrix in an ExpressionSet object if it exists.
update to helpMethods().
Substantial updates to the two RNA-seq case studies in the User’s Guide. In both cases, the short read data has been realigned and resummarized.
Improvements to many Rd files. Many keyword entries have been revised. Many usage and example lines been reformated to avoid over long lines.
biocViews keywords updated.
Subsetting columns of a MArrayLM object no longer subsets the design matrix.
Bug fix for read.maimages: default value for ‘quote’ was not being set correctly for source=”agilent.mean” or source=”agilent.median”.
Bug fix to topTableF() and topTable(). The ordering of Amean values was sometimes incorrect when sorting by F-statistic and a lfc or p.value filter had been set.
Bug fix to read.ilmn() when sep=”,”.
Changes in version 0.99.1:
0.9.4: New functions: vns_default function, MEIGO, vns_optset, get_VNS_settings, rosen10
0.9.4: Lots of clean-up in other functions with some new prototypes: e.g., CeSSR, rvnds_hamming, rvnds_local.R, ssm_localsolver.R
Changes in version 1.0.4:
Changes in version 1.0.3:
Changes in version 1.0.2:
Changes in version 1.0.1:
CHANGES IN VERSION 0.99
o Function clean.fix renamed to MetReport
o The function raw.peaks has been removed.
o Improved speed and error messages.
o MetReport is now able to extract directly the area and/or the base peak of an AMDIS report.
o The new function MetReportNames allows users to extract sample’s abundances from an AMDIS report based only in sample’s names.
o The new function buildLib allows users to convert an AMDIS library to a csv file in the format required by Metab.
o Function Htest allows users to adjust p-values for multiple comparisons.
Changes in version 1.7 (2014-05-07):
Added function plotBubble
Added parallel (multi-core) options to fitPA, fitDO
Fixed bug for fitMeta when useCSSoffset=FALSE and model matrix ncol==2
(1.7.10) Updated default quantile estimate (.5) for low estimates
(1.7.10) Added short description on how to do multiple group comparisons
(1.7.15) Output of fitZig (eb) is now a result of limma::eBayes instead of limma::ebayes
(1.7.16) plotMRheatmap allows for sorting by any stat (not just sd)
(1.7.18) fitTimeSeries Including times series method for differentially abundant time intervals
(1.7.20) Fixed minor bug for OTU level time series analyses and added plotClassTimeSeries
(1.7.26) Added warning / fix if any samples are empty in cumNormStat
(1.7.27) Added a few unit tests
(1.7.29) Added interactiveDisplay to namespace (display function allows interactive exploration / plots through browser)
Changes in version 1.3.5 (2014-09-30):
NEW FEATURES
Re-analysis based on saved gene models is now faster.
Added the ability to save time-consuming part of analyses also when count.type=”gene”.
BUG FIXES
Changes in version 1.3.4 (2014-09-03):
NEW FEATURES
BUG FIXES
Fixed more problems occured with the change of biomaRt attributes for newer organisms.
Fixed bug causing report crash when no genes are passing FDR threshold in paired comparisons.
Changes in version 1.3.3 (2014-08-21):
NEW FEATURES
Added the ability to retrieve annotation for genes/exons from UCSC or RefSeq through connection to UCSC Genome Browser public SQL database. The GC-content for each region is retrieved through BSgenome packages.
Added details regarding the number of genes returned by each algorithm when conducting combined analysis.
BUG FIXES
Fixed minor bug with warning level logging.
Fixed problem occured with the change of biomaRt attributes for newer organisms.
Changes in version 1.3.2 (2014-05-05):
NEW FEATURES
Function to merge exons belonging to different isoforms to a set of “virtual” exons to help construct a single gene model with unique exons
Simplified the usage of read2count()
BUG FIXES
Major bug in “exon” mode that inflated the number of reads for certain genes with many isoforms
Minor bug in argument checking, not allowing to not save the gene model in “exon” mode
Changes in version 0.99.9:
BUG FIXES
Changes in version 0.99.1 (2014-08-08):
Changes in version 1.0.0:
Changes in version 0.99.2:
Changes in version 0.99.1:
Changes in version 0.99.0:
Changes in version 1.11:
Updated CITATION.
Added dropLociWithSnps for easy exclusion of certain methylation loci.
Add getAnnotationObject for easy printing of contents of the annotation object.
Changes in 1.10 imported into 1.11.
Fixed an issue with bumphunter calling the bumphunter package in a wrong way.
Added getOOB and getSnpBeta convenience functions for accessing the OOB probes and the SNP probes.
read.450k.sheet now forces a column named Slide to be character.
The NOOB background correction method is now available throguh preprocessNoob.
One can now supply the permutations to be used in permutation analysis. This is useful for cases in which the total number of possilbe permutations is small and one wants to use them all or in cases in which one wants to assure balance, for example, between cases and controls.
The bumphunter method now has the option to create null distributions using a bootstrap approach.
Fixed a man page issue.
Added GitHub URL to DESCRIPTION.
Functional normalization now supports background correction by NOOB (see preprocessNoob); this is recommended (and the new default).
Changes in version 0.99.9:
Changes in version 0.99.7:
Changes in version 0.99.6:
Changes in version 0.99.5:
Changes in version 0.99.4:
0.99.6: plot_genes_jitter, plot_genes_in_pseudotime, and plot_genes_positive_cells now accept a new parameter, labe_by_short_name, to help control faceting
0.99.6: orderCells() now accepts the name of the root cell, so you can fix the beginning of the pseudotime trajectory
0.99.6: CellDataSet objects accept an argument for the VGAM family to be used for the distribution of expression values (e.g. negbinomial())
0.99.6: Dimensionality reduction, plotting, model fitting, and differential analyis routines now recognize CellDataSet expression families and alter their behavior when expression is count based. Allows analysis of absolute, as opposed to relative, single cell expression data.
0.99.5: Final changes from BioC for inclusion in development branch
0.99.4: A number of changes to the vignette
0.99.3: orderCells() now accepts the root_cell_name argument to specify the root of the ordering tree.
0.99.3: various fixes to accomodate the BioConductor build system and coding standards. Thanks to Sonali Arora for help with this.
0.99.0: INITIAL RELEASE
Changes in version 1.99.4:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.99.3:
BUG FIXES
Changes in version 1.99.2:
SIGNIFICANT USER-VISIBLE CHANGES
mosaicsFit(): Sets bgEst=”rMOM” as default.
Help documents are polished and updated.
Vignette is updated.
Changes in version 1.99.1:
SIGNIFICANT USER-VISIBLE CHANGES
mosaicsFitHMM() & mosaicsPeakHMM(): Hidden-Markov-Model-based MOSAiCS model fitting & peak calling, respectively, to identify broad peaks such as histone modifications.
Add new class ‘MosaicsHMM’ with methods show(), plot(), & estimates().
mosaicsFit(): Introduces a new argument ‘trans’.
mosaicsFit(): Stability & robustness of model fitting were improved.
Polish help documents of constructBins(), generateWig(), and mosaicsRunAll().
Tested to work with >= R 3.0 properly.
BUG FIXES
constructBins() & export(): Use correct base for BED file (one base shift).
Reflect the changes in Rcpp packages that mosaics package depends on.
Changes in version 1.9.9:
NEW FEATURES
BUG FIXES
Changes in version 1.9.8:
NEW FEATURES
BUG FIXES
Changes in version 1.9.7:
NEW FEATURES
BUG FIXES
Changes in version 1.9.6:
NEW FEATURES
BUG FIXES
Changes in version 1.9.5:
NEW FEATURES
BUG FIXES
Changes in version 1.9.4:
NEW FEATURES
BUG FIXES
Changes in version 1.9.3:
NEW FEATURES
BUG FIXES
Changes in version 1.9.2:
NEW FEATURES
BUG FIXES
Changes in version 0.99.6:
Changes in version 0.99.5:
Changes in version 0.99.4:
Changes in version 0.99.3:
Refactoring of shiny part of code
Change how mzR is used. Now connections are opened and closed whenever raw data is needed
Fix to namespace
Added warning to RStudio users about potential problems due to mzR problems
Changes in version 0.99.1:
Changes in version 0.99.0:
Changes in version 0.99.3:
Changes in version 0.99.2:
Added introduction to vignette
Added sessionInfo to vignette
Removed calls to library(MSGFplus) in tests
Changes in version 0.99.1:
Changes in version 0.99.0:
Submission to Bioconductor
Update MS-GF+ to v10072
Changes in version 1.13.16:
width generic if non-existant [2014-09-03 Wed]
fix undocumented S4 methods warnings [2014-09-27 Sat]
Changes in version 1.13.15:
msMap(MSmap)<- method [2014-08-12 Tue]
Typo in MIAPE man [2014-08-29 Fri]
Changes in version 1.13.14:
Fix xic example [2014-08-08 Fri]
importing lattice, ggplot2 (was depends) and suggesting rgl [2014-08-09 Sat]
MSmap infrastructure [2014-08-09 Sat]
Changes in version 1.13.13:
Changes in version 1.13.12:
Don’t import width from IRanges [2014-07-23 Wed]
qual slot is populated again [2014-07-23 Wed]
Changes in version 1.13.11:
Changes in version 1.13.10:
new averageMSnSet function to generate an average over a list of MSnSets. [2014-06-17 Tue]
new non-parametric coefficent of variation function [2014-06-17 Tue]
Using/importing IRanges::width [2014-06-18 Wed]
Changes in version 1.13.9:
new listOf helper function [2014-06-16 Mon]
compfnames to compare and document differences in MSnSet feature names [2014-06-16 Mon]
suggesting Vennerable (compfnames example) and roxygen2 (generate rd) [2014-06-16 Mon]
Changes in version 1.13.8:
Changes in version 1.13.7:
Changes in version 1.13.6:
new isEmpty method for Spectrum instances [2014-05-14 Wed]
removePeaks does not try for empty Spectra [2014-05-14 Wed]
isEmpty unit test [2014-05-14 Wed]
Changes in version 1.13.5:
export .get.amino.acids function [2014-05-08 Thu]
removePeaks for centroided data [2014-05-08 Thu]
add new exported function get.atomic.mass [2014-05-08 Thu]
Spectrum[2] prototype sets centroided=FALSE by default (instead of logical()) [2014-05-08 Thu]
fnamesIn also supports y = “data.frame” [2014-05-14 Wed]
Using BiocParallel for parallel support; replaced parallel argument with BPPARAM [2014-05-14 Wed]
Changes in version 1.13.4:
Document difference between traceable and non-traceable FeaturesOfInterest instances [2014-04-30 Wed]
ignoring desciptions with length > 1 [2014-04-30 Wed]
Changes in version 1.13.3:
Changes in version 1.13.2:
add compareSpectra to compare Spectrum objects [2014-04-09 Wed]
add bin method for Spectrum objects [2014-04-09 Wed]
recreate inst/extdata/msx.rda for R 3.1 and Biobase 2.24 [2014-04-13 Sun]
add plot,Spectrum,Spectrum method [2014-04-14 Mon]
add calculateFragments,character,Spectrum and calculateFragments,character,missing methods [2014-04-15 Tue]
updated readMSData test unit to ignore object@.classVersion that fails with latest R/Bioc versions [2014-04-15 Tue]
formatRt conversion from ‘mm:sec’ to sec and unit test [2014-04-17 Thu]
Update nprot/npsm.prot/npsm.pep/npep.prot feature variables and relevant man/tests/argument defaults [2014-04-17 Thu]
Changes in version 1.13.1:
add precursor method to Spectrum2 normalisation method [2014-04-08 Tue]
add smooth for MSnExp and Spectrum classes [2014-04-10 Thu]
add pickPeaks for MSnExp and Spectrum classes [2014-04-10 Thu]
updated show,MSnExp to display only first/last files when > 2 [2014-04-11 Fri]
Changes in version 1.13.0:
Changes in version 0.99.3:
Changes in version 0.99.2:
Updated Rcpp dependency
Updated contact info to match the bioc-devel mailing list
Changes in version 0.99.1:
Changes in version 0.99.0:
Minor bug fixes
Added unit tests for filter optimization and assessment of non-tryptic and missed cleavages
Version bump for Bioconductor submission
Changes in version 0.1.0:
Changes in version 0.99.1:
Changes in version 0.99.3:
OTHER CHANGES
Removed suppressWarnings() from plot calls of interactiveGraph(), and made arrowheads be ‘none’ – to avoid trivial warnings about zero-length arrows of indeterminate angle
Cleaned up usage of switch() function calls in graphCell() and generateGeneSets() functions
Changes in version 0.99.2:
BUG FIXES
OTHER CHANGES
Added suppressWarnings() to plot calls of interactiveGraph (to avoid trivial warnings about edges that are too short to be plotted, which can happen when the number of GO terms is large in the call to graphCell)
Updated nested if/else statements to ‘switch’ function calls
Changed many ‘cat’ function calls to ‘message’ or ‘warning’
Made ‘for’ loops more robust through use of ‘seq_along’, ‘seq_len’, and ‘seq.int’
Changes in version 0.99.1:
OTHER CHANGES
Modified Description field in DESCRIPTION file
Reordered import() lines in NAMESPACE file in an attempt to avoid the following two Bioconductor warnings: Warning: multiple methods tables found for ‘unsplit’ Warning: replacing previous import by ‘IRanges::unsplit’ when loading ‘GenomeInfoDb’ (mvGST does not call ‘unsplit’ in any way)
Changes in version 0.99.0:
OTHER CHANGES
Changes in version 0.1.3:
NEW FEATURES
Added package vignette
Made graphCell more flexible with ‘background’ colors for graph elements of lesser interest.
Made p.adjust.SFL more flexible to control FWER at a user-supplied FWER (rather than automatic 0.05).
Implemented minsize and maxsize arguments to restrict sizes of gene sets of interest.
BUG FIXES
OTHER CHANGES
Changes in version 0.1.2:
NEW FEATURES
BUG FIXES
OTHER CHANGES
Cleaned up package dependencies in DESCRIPTION and NAMESPACE files
Cleaned up some .Rd files (especially examples)
Changes in version 0.1.1:
NEW FEATURES
The default method for accounting for gene name translation issues is now ‘method = 2’.
The arguments ‘contrasts’ and ‘gene.names’ in ‘profileTable’ are now optional. The information may be passed to ‘profileTable’ as the row and column names of the argument ‘pvals’.
The function ‘pickOut’ now returns a data frame with the GO descriptions and p-values for each contrasts tested as well as the GO ID.
The function ‘graphCell’ now has an optional argument that allows the user to enter the returns from ‘pickOut’ as the only argument.
BUG FIXES
OTHER CHANGES
Minor clarifications in help files.
‘pvals’ is now the first argument in ‘profileTable’.
Changes in version 1.3.6:
Huge restructuring in documentation
Fixed a bug that would throw an error when an empty mzID object was flattened
Restructuring of unit tests so they conform with ‘new’ guidelines and gets called during check
Changes in version 1.3.5:
Changes in version 1.3.4:
Changes in version 1.3.3:
Added method removeDecoy, to remove decoy specific information from an mzID or mzIDCollection object thus decreasing its size.
Added formal getter methods to extract specific information from mzID and mzIDCollection objects
All attribute names are now parsed as-is despite inconsitency between schema versions. Controlling compatability is now done using the safeName parameter in flatten and getter methods
Substantial cleanup in documentation
Changes in version 1.3.2:
Changes in version 1.3.1:
Changes in version 1.99.4:
Changes in version 1.99.3:
Changes in version 1.99.2:
Changes in version 1.99.1:
annoucning pwiz in vignette and that it will become the default backend in Bioc 3.1 [2014-09-25 Thu]
adding a dummy close for pwiz backend to avoid breaking code that properly closes the previous ramp backend [2014-09-21 Sun]
Not using ListBuilder to make psms data.frame and fix segfautls, via KK [2014-09-27 Sat]
Changes in version 1.99.0:
New pwiz backend and support for mzid, contributed by Qiang Kou as part of GSoC 2014.
Using BiocStyle for vignette [2014-08-26 Tue]
Changes in version 1.9.2:
NEW FEATURES
Corrected bug in getBindingProfiles.R concerning chromosome-name processing.
Modified wig2CSARScore.c increase the max. number of chromosomes allowed in the WIG file.
Package title modified from “Analysis of Variation in ChIP-Seq using Functional PCA Statistics” to “Shape-based Analysis of Variation in ChIP-Seq using Functional PCA Statistics”
Changes in version 2.11.39:
Enhancement
update ‘samples’ slot of ‘ncdfFlowList’ class from ‘character’ to ‘named integer’ to speed up look up
replace ‘coerce’ method with ‘ncdfFlowList’ constructor function
update validity check of ‘ncdfFlowList’ class
add ‘subset.ncdfFlowList’ and ‘subset.ncdfFlowSet’ S3 functions to subset the ncdfFlowSet/ncdfFlowList based on ‘pData’
wrap “[[” logic into c++ to speed it up
add ‘save_ncfs’ and ‘load_ncfs’ functions to save/load a ncdfFlowSet object to/from disk.
Changes in version 1.1.6:
plotCytoscapeGML: a new function to export network plots as GML files, for Cytoscape 3.0 compatibility.
getGetsetNetworks now can return pathway-class objects, used by graphite package, which allows fast topology-based geneset analyses.
getGenesets now can export the results in GMT file format, readily parsed by most GSEA packages.
Bug fixes on KGML signaling network construction.
Changes in version 1.1.3:
Changes in version 1.1.2:
Added x-axis labels to plots
Changed ‘z’ to ‘covars’ in the npGSEA function
Added a new function ‘pValues’ which returns all appropriate p-values for a given npGSEAResult object
Added a new function slot to the npGSEAResult objects, betaHats. This vector contains the betaHats for each gene in the gene set. Users can thus now see each gene’s individual contribution to the test statistics.
Changes in version 1.1.1:
Changes in version 0.99.2 (2014-07-14):
Changes in version 0.99.1 (2014-07-14):
Minor changes for BioConductor submission:
extended description
minor changes to vignette
improved documentation of posets
Changes in version 0.99.0 (2014-06-26):
Changes in version 1.3.17:
Enhancements
more robust csv parsing
register wrapper function for quadGate.seq
parse ‘subSample’ argument from ‘gating_args’ column in csv template to allow subsampling the data prior to gating.
pass … from quantileGate to quantile function
add method for multipleFitlerResult
support multi-dimensions in framework by deprecating x,y with channels.
bug fixes
Changes in version 1.0.0:
GENERAL
Changes in version 1.5.4:
adjust run-time messages into 3 consistent classes: Info (on progress), Note and Warning.
include paths.hsa data, the full list of human pathway ID/names from KEGG, as to help user specify target pathways when calling pathview.
updated korg to included over 80 newly added species, such as sheep, apple, mandarin orange etc. Pathview can work with 3050 species now.
adjust the definitions of 7 arguments for pathview function: discrete, limit,bins, both.dirs, trans.fun, low, mid, high. These used to be a list of two logical elements with “gene” and “cpd” as the names. They can be vectors of two or one element(s) now. This makes pathview easier to use now.
Vigette has been reformatted: add a Citation section, and some example on reading user data into R, fix a few typos.
Changes in version 2.0.0:
NEW FEATURES
Two new statistical methods implemented RR (Reference Range Plus) and TF (Time Fixed Effect) that can be called from testDataset() function with argument method set to RR and TF correspondingly.
Additional measure of biological effect added: Percentage Change to summaryOutput() and vectorOutput functions.
New function is added to suggest analysis paths for dataset: recommendMethod()
Function to implement the RR method: RRTest().
Functions to implement the TF method: TFDataset() creates dataset suitable for TF, startTFModel(), finalTFModel creates model and fits it.
Changes in function summaryOutput() - additional information and clearer layout.
COMPTABILITY ISSUES
The vectorOutput() had additional elements which have increased its length.
The function boxplotSexGenotypeBatch() has been deprecated and replace with scatterplotSexGenotypeBatch().
Additional argument (phenotypeThreshold) with default value 0.01 has been added to the summaryOutput() function
BUG FIXES
Changes in version 1.9.15:
BUG FIXES
phyloseq_to_deseq2
was adding an unnecessary pseudocount of 1
to the count matrix. No longer.
Originally described at https://github.com/joey711/phyloseq/issues/387
Changes in version 1.9.14:
BUG FIXES
distance
erroneously transformed Rao distance results for method DPCoA. Now Fixed.
Originally described at https://github.com/joey711/phyloseq/issues/390
Changes in version 1.9.13:
USER-VISIBLE CHANGES
distance
function now supports “wunifrac” option, for UniFrac(..., weighted=TRUE)
distance
function regexpr-matching for range of variants for weighted-UniFrac, unweighted-UniFrac method option
distance
function regexpr-matching for type
argument range of alternatives
Proposed in https://github.com/joey711/phyloseq/pull/384
Changes in version 1.9.12:
BUG FIXES
psmelt
function now properly handles single-OTU data
Related to https://github.com/joey711/phyloseq/issues/338
Builds on https://github.com/joey711/phyloseq/pull/373
Changes in version 1.9.11:
USER-VISIBLE CHANGES
More robust plot_ordination
behavior with clearer warning/error messages.
Coordinates automatically checked/assigned to OTU or samples
Attempt to calculate OTU or sample weighted-average coordinates via vegan::wascores
, if-needed
Species weighted-average via vegan::wascores
supported now in phyloseq::scores.pcoa
Related to https://github.com/joey711/phyloseq/pull/364
Changes in version 1.9.10:
USER-VISIBLE CHANGES
Massive speed/memory improvement for UniFrac calculations (via UniFrac
or distance
)
Added unit-tests for the correctness of UniFrac results (no bugs detected. results from pycogent)
Moved all unit tests to tests/testthat as recommended by CRAN maintainers and testthat doc
Changes in version 1.9.9:
USER-VISIBLE CHANGES
plot_net
faster, more-flexible network plot with improved defaults
https://github.com/joey711/phyloseq/pull/353
Changes in version 1.9.8:
USER-VISIBLE CHANGES
mt
includes other corrections, FDR by default.
Resolves Issue 59
Changes in version 1.9.7:
BUG FIXES
Now requires ggplot2 version 1.0.0
Fixes bug in which ggplot 1.0 breaks in a phyloseq vignette
Resolves Issue 347
Changes in version 1.9.6:
USER-VISIBLE CHANGES
New sortby
argument in plot_richness
function.
Sort discrete x by one or more alpha-diversity measures
Solves Issue 342
Resolves/merges Pull 343
Changes in version 1.9.5:
USER-VISIBLE CHANGES
microbio_me_qiime
function now handles string study number for first argument. This is in addition to numeric study
number, already supported.Changes in version 1.9.4:
BUG FIXES
rarefy_even_depth()
function no longer enforces an orientation.
It used to always coerce to OTU-by-sample orientation.
Solves Issue 320 https://github.com/joey711/phyloseq/issues/320
Changes in version 1.9.3:
USER-VISIBLE CHANGES
Massive Revision to plot_tree()
plot_tree
now uses the psmelt
function
All covariates are available for aesthetic mapping.
plot_tree
substantial speed improvement
Uses native ape-package C code for tree computation
Efficient data.table
consolidated graphic data passed to ggplot2
Additional arguments: treetheme
and justify
tree_layout
- new, user-accessible function
for building alternative trees from phyloseq data.
Foundation for solving Issue 313 and Issue 331
https://github.com/joey711/phyloseq/issues/313
https://github.com/joey711/phyloseq/issues/331
Changes in version 1.9.2:
BUG FIXES
Large files cause import_usearch_uc() to have error. Error in paste0(readLines(ucfile), collapse = “\n”) : result would exceed 2^31-1 bytes
Solves Issue 327: https://github.com/joey711/phyloseq/issues/327
Changes in version 1.9.1:
BUG FIXES
Bug in psmelt
causing unnecessary error for phyloseq datasets with empty components.
Solves Issue 319: https://github.com/joey711/phyloseq/issues/319
Changes in version 1.6.0:
NEW FEATURES
Changes in version 1.3.1:
NEW FEATURES
Added the ‘retrieveMatrix’ method
Added the ‘tsplot’ method
Added the ‘mvtsplot’ method
SIGNIFICANT USER VISIBLE CHANGES
Removed dependency on the ‘batch’ package
Exported ‘proc.sanity’
Added dependency on ggplot2
Changes in version 1.37.1:
GeneExpression' and
MassSpectrometry’ –moved Biobase and MASS from Depends' to
Imports’Changes in version 9.1:
fixed bug where read names were incorrect in output fasta files
updated vignette
added biocViews
fixed coding style Package submission, version 0.99.0, 18 July 2014
Changes in version 1.5.3:
Introduced new parameter paired_ended_reads. When the data contains paired-ended reads, this parameter should be set to TRUE. Otherwise, the two read mates will be treated as independent units.
Introduced new parameter ignore_strand. If set to TRUE then the strand from which read comes is ignored when counting overlaps. If you use strand-specific RNA-seq protocol, you should set it to FALSE, otherwise set it to TRUE.
Changes in version 1.5.19:
Changes in version 1.5.18:
Changes in version 1.5.17:
Changes in version 1.5.16:
new pRolocGUI section [2014-08-15 Fri]
new foi section [2014-08-16 Sat]
Changes in version 1.5.15:
svmOpt sigma defaults changed from 10^(-2:3) to 10^(-3:2) [2014-08-15 Fri]
in xxxOptimisation, the best parameter(s) for the validation classification runs are now chosen at random instead of using the first best param (see change in pRoloc:::getBestParam that got a sample argument defaulted to TRUE) [2014-08-15 Fri]
When calculating macroF1 scores (xval and validation), NAs are set to 0 (via MLInterfaces:::.macroF1(…, naAs0 = TRUE)). The macro F1 will not be NA (when mean of F1s is calculated) but lowered. This avoids having an NA macro F1 when 1 (or more) classe(s) end(s) up with NA (also set to 0) precision(s) or recall(s) [2014-08-15 Fri]
Changes in version 1.5.14:
Changes in version 1.5.13:
Changes in version 1.5.12:
Changes in version 1.5.11:
Remove plot2D outliers param [2014-07-10 Thu]
fix subsetAsDataFrame for keepColNames and write unit test [2014-07-11 Fri]
Changes in version 1.5.10:
Changes in version 1.5.9:
Export single steps of lopims [2014-06-23 Mon]
Rephrase classifier parameter optimisation proceudres [2014-06-23 Mon]
Changes in version 1.5.8:
nndistx_matrix function added to allow use of query matrix when calculating knn distances [2014-06-18 Wed]
nndist[x]_[matrix | msnset] are now available using the experted nndist method [2014-06-18 Wed] |
markerSet and unknownSet renamed to markerMSnSet and unknownMSnSet [2014-06-19 Thu]
functions sampleMSnSet and testMSnSet added [2014-06-19 Thu]
Changes in version 1.5.7:
Changes in version 1.5.6:
Changes in version 1.5.5:
replaced MSVBAR::rmultnorm with mvtnorm::rmvnorm since the former has been removed from CRAN and don’t import [2014-05-21 Wed]
Bug tracking [2014-05-26 Mon]
Changes in version 1.5.4:
testMarkers gets an error argument [2014-05-14 Wed]
plotDist now has a ylim argument [2014-05-21 Wed]
Changes in version 1.5.3:
import all MLInterfaces [2014-04-30 Wed]
new param optim secion in ml vignette [2014-05-05 Mon]
various ml typos and pRolocmakers man update [2014-05-06 Tue]
Changes in version 1.5.2:
In plotDist, … is now passed to matlines instead of plot and has a new lty parameter [2014-04-17 Thu]
new highlightOnPlot function, using the new features of interest infrastructure [2014-04-29 Tue]
Changes in version 1.5.1:
new dunkley2006 pdunit object created with mclust 4.3 [2014-04-08 Tue]
addMarker also accepts fcol and addMarkers unit test [2014-04-14 Mon]
Changes in version 1.5.0:
Changes in version 0.99.12:
Changes in version 0.99.11:
Add screenshot to README [2014-09-05 Fri]
fix bug when features of fois are not present
move data tab to the end
Changes in version 0.99.10:
Updated README [2014-09-04 Thu]
Remove old R code file [2014-09-04]
Changes in version 0.99.9:
Changes in version 0.99.8:
Changes in version 0.99.7:
display feature meta-data instead of protein name when hovering [2014-07-27 Tue]
better feature highlighting [2014-07-27 Tue]
only 1 vignette [2014-07-27 Tue]
Changes in version 0.99.6:
Changes in version 0.99.5:
Changes in version 0.99.4:
Changes in version 0.99.3:
multiple objects can be passed to pRolocVis by using a list [2014-06-03 Tue]
improve query search (submit and select check box) [2014-06-02 Mon]
add unit tests for helper functions and add manual unit test [2014-06-03 Tue]
Changes in version 0.99.2:
Changes in version 0.99.1:
fix biocViews [2014-05-27 Tue]
misc refactoring [2014-05-27 Tue]
Changes in version 0.99.0:
Changes in version 1.1.10:
Changes in version 1.1.9:
Changes in version 1.1.8:
update function “chargeStat”
change file name
Changes in version 1.1.7:
Changes in version 1.1.6:
Changes in version 1.1.5:
Changes in version 1.1.4:
Changes in version 1.1.3:
Changes in version 1.1.2:
change the figure of missed cleavages
fix several typos in vignette
Changes in version 1.1.1:
Changes in version 1.1.0:
support mz[X]ML format file
add identification-independent metrics
Changes in version 1.0.0:
NEW FEATURES
Changes in version 1.3.1:
Changes in version 1.3.0:
Changes in version 1.2.0 (2014-10-14):
RELEASE
IMPROVEMENTS
segmentBins() supports another transformation option besides log2: sqrt(x + 3/8), which stabilizes the variance
plot() can skip plotting of segments and calls by specifying doSegments=FALSE and doCalls=FALSE
exportBins() also supports BED files
BUG FIXES
Changes in version 1.0.5 (2014-06-13):
BUG FIXES
Changes in version 1.0.4 (2014-05-23):
BUG FIXES
Changes in version 1.0.3 (2014-05-23):
IMPROVEMENTS
added exportBins() for exporting to a file
switch graphics in the vignette to PNG
Changes in version 1.0.2 (2014-05-15):
IMPROVEMENTS
plot() honors user-specified values for xlab and xaxt
plot() allows omission of labels for the standard deviation and the number of data points
improve diagnostic messages
Changes in version 1.0.1 (2014-04-17):
BUG FIXES
Changes in version 2.00:
USER VISIBLE CHANGES
Function qpGraph() has been replaced by a class of objects called qpGraph whose constructor implements the functionality that the qpGraph() function was providing. However, a couple of arguments have changed and it returns an object of the new defined class qpGraph. Please consult its manual page for more information.
Removed methods qpCItest() and qpEdgeNrr() taking an ‘smlSet’ object as input.
Added a new (first version) vignette showing the new functionality to estimate eQTL networks from genetical genomics data.
NEW FEATURES
BUG FIXES
Bugfix in qpEdgeNrr() when using arguments restrict.Q and fix.Q and input was ‘data.frame’ or ‘ExpressionSet’.
Bugfix in the calculation of marginal covariances with missing observations.
Bugfix in qpAnyGraph()
Changes in version 1.4.1:
NEW FEATURES
Changes in version 1.3.1:
BUG FIXED
DAVIDGODag
bug was fixed. Now in case that pvalueCutoff value is lower than every value present an empty goDag is returned
(Thanks to Ulrik Stervbo)Changes in version 1.3.0:
MINOR CHANGES
Changes in version 1.9.4:
Changes in version 1.9.3:
Changes in version 1.9.2:
Changes in version 1.9.1:
Changes in version 1.14.0:
Changes in version 1.1.8:
NEW FEATURES
Changes in version 0.99.0:
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
Updated the vignette and the package to work with recent versions of the packages this package depends on.
Renamed the package from derfinderReport to regionReport and generateReport() to derfinderReport(). In the future we will add another report for a general GRanges object.
Simplified derfinderReport()’s call by using advanced arguments.
Added Travis integration.
Changes in version 2.9:
Changes in version 0.99.2:
BUG FIXES
Changes in version 0.99.1:
NEW FEATURES
added new functions: RGSEAsd() RGSEApredict() RGSEAfix()
added a vignette to explain functionality of RGSEA
add unit tests for RGSEA.
Changes in version 2.10.0:
NEW FEATURES
Added support for HDF5 property lists.
Added property list arguments to H5Dcreate and H5Dopen.
New function h5readAttributes implemented that reads all HDF5 attributes of one object.
New function h5version implemented.
fillValue parameter added to h5createDataset.
New low level general library functions H5Lcreate_external, H5Fis_hdf5, H5Fget_filesize, H5Fget_name, H5Pcreate, H5Pcopy, H5Pget_class, H5Pclose, H5Pclose_class, H5Pset_char_encoding, H5Pset_create_intermediate_group, H5Pset_chunk_cache, H5Pset_layout, H5Pset_chunk, H5Pget_chunk, H5Pset_deflate, H5Pset_fill_value, H5Pset_fill_time, H5Pset_alloc_time, H5Pequal implemented.
Support for parallel Make (make -j)
USER VISIBLE CHANGES
BUG FIXES
Error in h5write for 0-length objects, as a consequence of automatic determining chunk size
missing size parameter message in h5createDataset now correctly display
checking for open file identifiers in h5read and h5ls now only searches for file names in open files, groups and datasets.
assignment has now correct pointer target type (void *) in H5Pset_fill_value
Changes in version 1.1.2:
NEW FEATURES
BUG FIXES
Changes in version 1.7.2:
Removing (temporarily) allIds(“GO”)) example as currently returns illegal message to fix testing error [2014-10-07 Tue]
Updating roxygem inline docs to fix errors in generated Rds [2014-10-07 Tue]
Changes in version 1.7.1:
Changes in version 1.7.0:
1.6.0: () Major documentation cleanup. () Added two sided hypotheses to RRHO() with signed pvalue plotting. () Added comparison of three lists using RRHOCOmparison(). () Added an option for log10 pvalues in RRHO. () Added error handling to RRHO so that failed plotting does not crash the computation.
Changes in version 1.17.0:
NEW FEATURES
pileup visits entire file if no ‘which’ argument specified for ‘ScanBamParam’ parameter of pileup. Buffered functionality with ‘yieldSize’ available to manage memory consumption when working with large BAM files
pileup ‘read_pos_breaks’ parameter renamed to ‘cycle_bins’: cycle_bins allows users to differentiate pileup counts based on user-defined regions within a read.
pileup uses PileupParam and ScanBamParam instances to calculate pileup statistics for a BAM file; returns a data.frame with columns summarizing information extracted from alignments overlapping each genomic position
scanBam,BamSampler-method returns requested and actual yieldSize, and total reads
seqinfo,BamFileList-method returns the merged seqinfo of each BamFile; seqlevels and seqlengths behave similarly.
scanBamHeader accepts a ‘what’ argument to control input of the targets and / or text portion of the header, and is much faster for BAM files with many rnames.
SIGNIFICANT USER-VISIBLE CHANGES
rename PileupParam class and constructor -> ApplyPileupsParam
seqinfo,BamFile-method orders levels as they occur in the file, reverting a change introduced in Rsamtools version 1.15.28 (version 1.17.16).
BUG FIXES
scanBam(BamSampler(), param=param) with a ‘which’ argument no longer mangles element names, and respects yield size
applyPileups checks that seqlevels are identical across files
scanFa documentation incorrectly indicated that end coordinates beyond the range of the sequence would be truncated; they are an error.
applyPileups would fail on cigars with insertion followed by reference skip, e.g., 2I1024N98M (bug report of Dan Gatti).
Changes in version 1.16.0:
NEW FEATURES
Subread aligner (align function) can accurately map micro RNA (miRNA) sequencing reads. A full index without gaps should be built for the reference genome before mapping miRNA-seq reads.
Subjunc requires the number of consensus subreads to be at least 30 percent of the total number of extracted subreads when reporting hits for exonic reads. This improves the mapping accuracy of such reads.
Reads are allowed to be extended in featureCounts.
Minimum required number of overlapped bases can be specified when assigning reads to features in featureCounts.
By default, Subread and Subjunc aligners do not allow more than three mismatches in the reported alignments. This however can be tuned via the `maxMismatches’ parameter.
A number of bug fixes.
Changes in version 1.26:
NEW FEATURES
ucscGenomes() retrieves organism information
New function exportToTabix() exports a GRanges to a tabix-indexed tab separated file that contains all of the metadata columns. Use import,TabixFile to load specific ranges of data back into a GRanges.
BigWig import/export to/from Integer/Numeric/RleList is now much more efficient, and uses a more efficient storage format within the BigWig file, when possible.
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
Changes in version 1.4:
Improvements to user interface and general look and feel. Fontawesome icons are used now. Fixed behavior of some web controls (sliders). Updated tutorial. Data tables are paginated (and the number of entries per page customizable).
Target transcription factor selection process improved. Now all possible transcription factors are added to a searchable dropdown menu.
Changes in version 0.1:
Created S4 methods for RUV* functions
Created Vignette
Initial submission to Bioconductor
CHANGES IN VERSION 0.4.0
NEW FEATURES
o Add isSorted() and isStrictlySorted() generics, plus some methods.
o Add low-level wmsg() helper for formatting error/warning messages.
o Add pc() function for parallel c() of list-like objects.
o Add coerce,Vector,DataFrame; just adds any mcols as columns on top of the
coerce,ANY,DataFrame behavior.
o [[ on a List object now accepts a numeric- or character-Rle of length 1.
o Add "droplevels" methods for Rle, List, and DataFrame objects.
o Add table,DataTable and transform,DataTable methods.
o Add prototype of a better all.equals() for S4 objects.
SIGNIFICANT USER-VISIBLE CHANGES
o Move Annotated, DataTable, Vector, Hits, Rle, List, SimpleList, and
DataFrame classes from the IRanges package.
o Move isConstant(), classNameForDisplay(), and low-level argument
checking helpers isSingleNumber(), isSingleString(), etc... from the
IRanges package.
o Add as.data.frame,List method and remove other inconsistent and not
needed anymore "as.data.frame" methods for List subclasses.
o Remove useless and thus probably never used aggregate,DataTable method
that followed the time-series API.
o coerce,ANY,List method now propagates the names.
BUG FIXES
o Fix bug in coercion from list to SimpleList when the list contains
matrices and arrays.
o Fix subset() on a zero column DataFrame.
o Fix rendering of Date/time classes as DataFrame columns.
Changes in version 2.1.0 (2014-09-12):
NOTES:
Changes in version 1.3.0:
NEW FEATURES
Changes in version 2.7.1:
FIXES
ParseMetaFromGtfFile improvements (ambiguous function call, spaces in FASTA descriptors)
BrainArray summarization when probe maps to multiple genes/probesets
NEW FEATURES
Changes in version 0.99.0:
Changes in version 1.5.2:
Changes in version 1.5.1:
fix a bug in ‘seqVCF2GDS’ when the values in the FILTER column are all missing
enhance ‘seqVCF.Header’
support the LinkingTo mechanism
Changes in version 0.99.4:
PACKAGE
plotHeatmap function returns cluster report as GRanges structure
redundant parameters removed from plotting functions
plotHeatmap function have “embed” parameter for plotHeatmap - allows to plot 1st heatmap without using grid system, intended to use with complex plots
BUGFIX
motif plot orientation properly dependents on strand
GUI - reordering the heatmap respects previously set include/exclude parameters
Changes in version 0.99.1:
PACKAGE
heatmap plotting function returns cluster report ad data.table
getPlotSetArray function have “verbose” parameter that controls messages and warnings output
references added to documentation
BUGFIX
plotHeatmap and plotAverage generic methods for SeqPlots-classes respect the parameters
package passes tests and check on 32bit Windows (plotting only, because no rtrackalyer::BigWigFile support for Win32)
Changes in version 0.99:
GENERAL
PACKAGE
package really on reference class system including MotifSetup, PlotSetArray, PlotSetList and PlotSetPair
generic subset and data manipulation methods for SeqPlots-classes including ‘[’, “[[” and “unlist”, which allows to switch between classes
automatic tests for class system, calculations and plotting functions
documentation for all functions and classes
PDF vignette engine replaced by HTML one
QuickStart vignette added
GUI
BUGFIX
CHANGES IN VERSION 0.99.42
BUG FIXES
o trimFastq also includes record identifiers in output files
(=read title), e.g. SRR014849.1 EIXKN4201CFU84 length=93.
CHANGES IN VERSION 0.99.40
NEW FEATURES
o Included this NEWS file
Changes in version 1.23:
NEW FEATURES
alphabetScore,PhredQuality-method implemented
reverse, reverseComplement methods for ShortReadQ objects
srlist, to access SRList data as a base R list.
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
report() prints adapter contaminants correctly when user has stringsAsFactors=FALSE
qa(…, sample=FALSE) no longer tries to re-match ‘pattern’ argument
Changes in version 0.99.2:
an option to create an integer snp.id when converting from PLINK
a new function ‘snpgdsFst’ to estimate Fst
Changes in version 0.99.0:
initial submission to Bioconductor
moving from CRAN to Bioconductor
Changes in version 2.0.0:
Major refractioning
Reduce external dependenies: stringr, h5vc, h5vcData
Changes in version 0.99.23:
USER VISIBLE CHANGES
added methods for specLSet class: ionlibrary, rt.input, rt.normalized
fixed Sys.time() units in message.
USER UNVISIBLE CHANGES
Changes in version 0.99.22:
USER VISIBLE CHANGES
Changes in version 0.99.21:
USER VISIBLE CHANGES
specLSet class
replace print by show and write.Spectronaut method in specL and specLSet classes
Changes in version 0.99.20:
USER VISIBLE CHANGES
replaced mclapply by BiocParalle::bplapply
print method
include iRTpeptide data
Changes in version 0.99.3:
Changes in version 0.99.2:
added pseudo option to getCountMatrix to handle bam files that do not have count information
changed outputs to “message” instead of “print”
Changes in version 0.99.1:
Changes in version 1.0.0:
Changes in version 1.22.0:
BUG FIXES
Changes in version 3.5.4:
bug fix in ‘.coverage.hist’ regarding calculation of cumulative coverage fractions (affects values in the ‘sensitivity.txt’ output table and the sensitivity barplots in the multiTEQCreport)
bug fix in ‘htmlDuplicatesBarplot’: also working now for paired-end data
Changes in version 3.5.3:
Changes in version 3.5.2:
Changes in version 3.5.1:
Changes in version 1.1.1:
NEW FEATURES
BUG FIXES
Changes in version 1.12.0:
NEW FEATURES
allow GRanges in ‘rowData’ to hold user-defined metadata cols (i.e., cols other than paramRangeID, REF, ALT, etc.)
add isSNV() family of functions
add faster method for converting a list matrix to an array
add ‘c’ method for typed Rle classes so class is preserved
add CITATION file
rework writeVCF(): - FORMAT and genotype fields are parsed in C - output file is written from C - chunking added for large VCFs
MODIFICATIONS
add ‘row.names’ to readVcf()
deprecate restrictToSNV(); replaced by isSNV() family
remove use of seqapply()
show info / geno headers without splitting across blocks
use mapCoords() in predictCoding() and locateVariants()
deprecate refLocsToLocalLocs()
propagate strand in predictCoding()
replace deprecated seqsplit() with splitAsList()
ensure GT field, if present, comes first in VCF output
modify DESCRIPTION Author and Maintainer fileds with @R
add ‘row.names’ to info,VCF-method
BUG FIXES
modify expand() to work with no ‘info’ fields are imported
remove duplicate rows from .splicesites()
fix handling of real-valued NAs in geno omatrix construction in writeVcf()
Changes in version 1.2:
USER VISIBLE CHANGES
Added the calculation of the position of each variant within the cDNA (when it applies), adding also a new ‘Transcript’ tab in the shiny app
Showing the number of individuals in the ‘VariantFilteringParam’ object, taken from the input VCF file
BUG FIXES
Some bugfixes in the shiny app
Replaced a .gz file in the ‘extdata’f older by the corresponding .bgz file
Changes in version 1.8.0:
NEW FEATURES
Changes in version 1.41.1:
BUG FIXES
fix sampclass generation from phenoData if some combinations of factors don’t exist
disable parallel code in manpages to avoid issues on BioC windows build farm machines
VERSION xps-1.25.2
VERSION xps-1.25.1
Changes in version 3.00:
Changes in version 1.25.1:
The following packages are no longer in the release:
Resourcerer, RMAPPER, virtualArray