October 31, 2017

Bioconductors:

We are pleased to announce Bioconductor 3.6, consisting of 1473 software packages, 326 experiment data packages, and 911 annotation packages.

There are 100 new software packages, and many updates and improvements to existing packages; Bioconductor 3.6 is compatible with R 3.4.2, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release will include an updated Bioconductor Amazon Machine Image and Docker containers.

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

Contents

• Getting Started with Bioconductor 3.6
• New Software Packages
• NEWS from new and existing packages
• Deprecated and Defunct Packages

Getting Started with Bioconductor 3.6

To update to or install Bioconductor 3.6:

1. Install R >=3.4.2. Bioconductor 3.6 has been designed expressly for this version of R.

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

New Software Packages

There are 100 new software packages in this release of Bioconductor.

• amplican amplican performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.

• ANF This package is used for complex patient clustering by integrating multi-omic data through affinity network fusion.

• anota2seq anota2seq provides analysis of translational efficiency and differential expression analysis for polysome-profiling and ribosome-profiling studies (two or more sample classes) quantified by RNA sequencing or DNA-microarray. Polysome-profiling and ribosome-profiling typically generate data for two RNA sources; translated mRNA and total mRNA. Analysis of differential expression is used to estimate changes within each RNA source (i.e. translated mRNA or total mRNA). Analysis of translational efficiency aims to identify changes in translation efficiency leading to altered protein levels that are independent of total mRNA levels (i.e. changes in translated mRNA that are independent of levels of total mRNA) or buffering, a mechanism regulating translational efficiency so that protein levels remain constant despite fluctuating total mRNA levels (i.e. changes in total mRNA that are independent of levels of translated mRNA). anota2seq applies analysis of partial variance and the random variance model to fulfill these tasks.

• apeglm apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.

• AUCell AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules…) in single-cell RNA-seq data. AUCell uses the “Area Under the Curve” (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.

• BASiCS Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori, e.g. experimental conditions or cell types). BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells. Unlike traditional differential expression tools, BASiCS quantifies changes in expression that lie beyond comparisons of means, also allowing the study of changes in cell-to-cell heterogeneity. The latter are quantified via a biological over-dispersion parameter that measures residual over-dispersion (with respect to Poisson sampling) after normalisation and technical noise removal.

• beachmat Provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.

• BiocSklearn This package provides interfaces to selected sklearn elements, and demonstrates fault tolerant use of python modules requiring extensive iteration.

• bnbc Tools to normalize (several) Hi-C data from replicates.

• cbaf This package contains functions that allow analysing and comparing various gene groups from different cancers/cancer subgroups easily. So far, it is compatible with RNA-seq, microRNA-seq, microarray and methylation datasets that are stored on cbioportal.org.

• CEMiTool The CEMiTool package unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.

• ChIPanalyser Based on a statistical thermodynamic framework, ChIPanalyser tries to produce ChIP-seq like profile. The model relies on four consideration: TF binding sites can be scored using a Position weight Matrix, DNA accessibility plays a role in Transcription Factor binding, binding profiles are dependant on the number of transcription factors bound to DNA and finally binding energy (another way of describing PWM’s) or binding specificity should be modulated (hence the introduction of a binding specificity modulator). The end result of ChIPanalyser is to produce profiles simulating real ChIP-seq profile and provide accuracy measurements of these predicted profiles after being compared to real ChIP-seq data. The ultimate goal is to produce ChIP-seq like profiles predicting ChIP-seq like profile to circumvent the need to produce costly ChIP-seq experiments.

• chromswitch Chromswitch implements a flexible method to detect chromatin state switches between samples in two biological conditions in a specific genomic region of interest given peaks or chromatin state calls from ChIP-seq data.

• chromVAR Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.

• ClusterJudge ClusterJudge implements the functions, examples and other software published as an algorithm by Gibbons, FD and Roth FP. The article is called “Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation” and it appeared in Genome Research, vol. 12, pp1574-1581 (2002). See package?ClusterJudge for an overview.

• coexnet Extracts the gene expression matrix from GEO DataSets (.CEL files) as a AffyBatch object. Additionally, can make the normalization process using two different methods (vsn and rma). The summarization (pass from multi-probe to one gene) uses two different criteria (Maximum value and Median of the samples expression data) and the process of gene differentially expressed analisys using two methods (sam and acde). The construction of the co-expression network can be conduced using two different methods, Pearson Correlation Coefficient (PCC) or Mutual Information (MI) and choosing a threshold value using a graph theory approach.

• consensusOV This package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.

• cytolib This package provides the core data structure and API to represent and interact with the gated cytometry data.

• DASC The package is used for identifying batches in high-dimensional dataset.

• DelayedMatrixStats A port of the ‘matrixStats’ API for use with DelayedMatrix objects from the ‘DelayedArray’ package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.

• DEP This package provides an integrated analysis workflow for robust and reproducible analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment. It requires tabular input (e.g. txt files) as generated by quantitative analysis softwares of raw mass spectrometry data, such as MaxQuant or IsobarQuant. Functions are provided for data preparation, filtering, variance normalization and imputation of missing values, as well as statistical testing of differentially enriched / expressed proteins. It also includes tools to check intermediate steps in the workflow, such as normalization and missing values imputation. Finally, visualization tools are provided to explore the results, including heatmap, volcano plot and barplot representations. For scientists with limited experience in R, the package also contains wrapper functions that entail the complete analysis workflow and generate a report. Even easier to use are the interactive Shiny apps that are provided by the package.

• diffuStats Label propagation approaches are a widely used procedure in computational biology for giving context to molecular entities using network data. Node labels, which can derive from gene expression, genome-wide association studies, protein domains or metabolomics profiling, are propagated to their neighbours in the network, effectively smoothing the scores through prior annotated knowledge and prioritising novel candidates. The R package diffuStats contains a collection of diffusion kernels and scoring approaches that facilitates their computation and benchmarking.

• DMCHMM DMCHMM is a novel profiling tool for identifying differentially methylated CpG sites using Hidden Markov Model in bisulfite sequencing data.

• Doscheda Doscheda focuses on quantitative chemoproteomics used to determine protein interaction profiles of small molecules from whole cell or tissue lysates using Mass Spectrometry data. The package provides a shiny application to run the pipeline, several visualisations and a downloadable report of an experiment.

• EpiDISH EpiDISH is a R package to infer the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user.

• epivizrChart This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used to generate interactive R markdown/notebook documents or can be visualized in the R Studio’s default viewer.

• esATAC This package provides a framework and complete preset pipeline for the quantification and analysis of ATAC-seq Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control report, to the quantification of genomic regions of interest. The package is managed by dataflow graph, and users can also build their own pipeline easily and flexibly.

• GA4GHshiny GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.

• GENIE3 This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.

• HiCcompare HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.HiCcompare differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, HiCcompare provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. HiCcompare also provides a simple yet robust permutation method for detecting differences between Hi-C datasets.

• InterMineR Databases based on the InterMine platform such as FlyMine, modMine (modENCODE), RatMine, YeastMine, HumanMine and TargetMine are integrated databases of genomic, expression and protein data for various organisms. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge. This R package provides interfaces with these databases through webservices. It makes most from the correspondence of the data frame object in R and the table object in databases, while hiding the details of data exchange through XML or JSON.

• IntramiRExploreR Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using the tool, we have identified targets for 92 intragenic miRs in D. melanogaster, using available microarray expression data, from Affymetrix 1 and Affymetrix2 microarray array platforms, providing a global perspective of intragenic miR targets in Drosophila. Predicted targets are grouped according to biological functions using the DAVID Gene Ontology tool and are ranked based on a biologically relevant scoring system, enabling the user to identify functionally relevant targets for a given miR.

• IrisSpatialFeatures IrisSpatialFeatures reads the output of the PerkinElmer inForm software and calculates a variety of spatial statistics. In addition to simple counts, it can derive average nearest neighbors for each cell-type and interaction summary profiles for each celltype. These statistics are derived across images, both overall and regions of interest as defined by user defined masks.

• IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR enabels identification and analysis of isoform switches with predicted functional consequences (such as gain/loss of protein domains etc) from quantification by Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.

• iterClust A framework for performing clustering analysis iteratively.

• ivygapSE Define a SummarizedExperiment and exploratory app for Ivy-GAP glioblastoma image, expression, and clinical data.

• JASPAR2018 Data package for JASPAR 2018. To search this databases, please use the package TFBSTools (>= 1.15.6).

• M3C A central task in genomic data analyses for stratified medicine is class discovery which is accomplished through clustering. However, an unresolved problem with current clustering algorithms is they do not test the null hypothesis and derive p values. To solve this, we developed a novel hypothesis testing framework that uses consensus clustering called Monte Carlo Consensus Clustering (M3C). M3C use a multi-core enabled Monte Carlo simulation to generate a distribution of stability scores for each number of clusters using null datasets with the same gene-gene correlation structure as the real one. These distributions are used to derive p values and a beta distribution is fitted to the data to cheaply estimate p values beyond the limits of the simulation. M3C improves accuracy, allows rejection of the null hypothesis, removes systematic bias, and uses p values to make class number decisions. We believe M3C deals with a major pitfall in current automated class discovery tools.

• MetaCyto This package provides functions for preprocessing, automated gating and meta-analysis of cytometry data. It also provides functions that facilitate the collection of cytometry data from the ImmPort database.

• methimpute This package implements functions for calling methylated and unmethylated regions and estimate variability among a population of samples.

• methInheritSim Simulate a multigeneration methylation case versus control experiment with inheritance relation using a real control dataset.

• methyvim This package provides facilities for differential methylation analysis based on variable importance measures (VIMs), a class of statistical target parameters that arise in causal inference. The estimation and inference procedures provided are nonparametric, relying on ensemble machine learning to flexibly assess functional relationship among covariates and the outcome of interest. These tools can be applied to differential methylation at the level of CpG sites, with valid inference after multiple hypothesis testing.

• mfa MFA models genomic bifurcations using a Bayesian hierarchical mixture of factor analysers.

• microbiome Utilities for microbiome analysis.

• MIRA MIRA measures the degree of “dip” in methylation level surrounding a regulatory site of interest, such as a transcription factor binding site, for instances of that type of site across the genome which can then be used to infer regulatory activity.

• miRBaseConverter A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends.

• miRmine miRmine database is a collection of expression profiles from different publicly available miRNA-seq datasets, Panwar et al (2017) miRmine: A Database of Human miRNA Expression, prepared with this data package as RangedSummarizedExperiment.

• miRsponge This package provides several functions to study miRNA sponge (also called ceRNA or miRNA decoy), including popular methods for identifying miRNA sponge interactions, and the integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of modules, and conduct survival analysis of modules.

• motifmatchr Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, which was developed by Pasi Rastas, Janne Korhonen, and Petri Martinmäki.

• mpra Tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA).

• MSstatsQC MSstatsQC is an R package which provides longitudinal system suitability monitoring tools for proteomic experiments.

• multiMiR A collection of microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).

• ndexr This package offers an interface to NDEx servers, e.g. the public server at http://ndexbio.org/. It can retrieve and save networks via the API. Networks are offered as RCX object and as igraph representation.

• omicRexposome omicRexposome systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).

• Onassis A package that allows the annotation of text with ontology terms (mainly from OBO ontologies) and the computation of semantic similarity measures based on the structure of the ontology between different annotated samples.

• oncomix This package helps identify mRNAs that are overexpressed in subsets of tumors relative to normal tissue. Ideal inputs would be paired tumor-normal data from the same tissue from many patients (>15 pairs). This unsupervised approach relies on the observation that oncogenes are characteristically overexpressed in only a subset of tumors in the population, and may help identify oncogene candidates purely based on differences in mRNA expression between previously unknown subtypes.

• oneSENSE A graphical user interface that facilitates the dimensional reduction method based on the t-distributed stochastic neighbor embedding (t-SNE) algorithm, for categorical analysis of mass cytometry data. With One-SENSE, measured parameters are grouped into predefined categories, and cells are projected onto a space composed of one dimension for each category. Each dimension is informative and can be annotated through the use of heatplots aligned in parallel to each axis, allowing for simultaneous visualization of two catergories across a two-dimensional plot. The cellular occupancy of the resulting plots alllows for direct assessment of the relationships between the categories.

• ontoProc Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.

• openPrimeR An implementation of methods for designing, evaluating, and comparing primer sets for multiplex PCR. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected. A Shiny app providing a user interface for the functionalities of this package is provided by the ‘openPrimeRui’ package.

• openPrimeRui A Shiny application providing methods for designing, evaluating, and comparing primer sets for multiplex polymerase chain reaction. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected.

• OPWeight This package perform weighted-pvalue based multiple hypothesis test and provides corresponding information such as ranking probability, weight, significant tests, etc . To conduct this testing procedure, the testing method apply a probabilistic relationship between the test rank and the corresponding test effect size.

• panelcn.mops CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.

• PathwaySplice Pathway analysis of alternative splicing would be biased without accounting for the different number of exons associated with each gene, because genes with higher number of exons are more likely to be included in the ‘significant’ gene list in alternative splicing. PathwaySplice is an R package that: (1) performs pathway analysis that explicitly adjusts for the number of exons associated with each gene (2) visualizes selection bias due to different number of exons for each gene (3) formally tests for presence of bias using logistic regression (4) supports gene sets based on the Gene Ontology terms, as well as more broadly defined gene sets (e.g. MSigDB) or user defined gene sets (5) identifies the significant genes driving pathway significance (6) organizes significant pathways with an enrichment map, where pathways with large number of overlapping genes are grouped together in a network graph

• pcxn Discover the correlated pathways/gene sets of a single pathway/gene set or discover correlation relationships among multiple pathways/gene sets. Draw a heatmap or create a network of your query and extract members of each pathway/gene set found in the available collections (MSigDB H hallmark, MSigDB C2 Canonical pathways, MSigDB C5 GO BP and Pathprint).

• phenopath PhenoPath infers genomic trajectories (pseudotimes) in the presence of heterogeneous genetic and environmental backgrounds and tests for interactions between them.

• progeny This package provides a function to infer pathway activity from gene expression using PROGENy. It contains the linear model we inferred in the publication “Perturbation-response genes reveal signaling footprints in cancer gene expression”.

• PROPS This package calculates probabilistic pathway scores using gene expression data. Gene expression values are aggregated into pathway-based scores using Bayesian network representations of biological pathways.

• Rbowtie2 This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging.

• restfulSE This package provides functions and classes to interface with remote data stores by operating on SummarizedExperiment-like objects.

• rexposome Package that allows to explore the exposome and to perform association analyses between exposures and health outcomes.

• rhdf5client Provides functionality for reading data from h5serv server from within R.

• Rhdf5lib Provides C and C++ hdf5 libraries.

• RProtoBufLib This package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.

• RTNsurvival RTNsurvival is a tool for integrating regulons generated by the RTN package with survival information. For a given regulon, the 2-tailed GSEA approach computes a differential Enrichment Score (dES) for each individual sample, and the dES distribution of all samples is then used to assess the survival statistics for the cohort. There are two main survival analysis workflows: a Cox Proportional Hazards approach used to model regulons as predictors of survival time, and a Kaplan-Meier analysis assessing the stratification of a cohort based on the regulon activity. All plots can be fine-tuned to the user’s specifications.

• runibic This package implements UbiBic algorithm in R. This biclustering algorithm for analysis of gene expression data was introduced by Zhenjia Wang et al. in 2016. It is currently considered the most promising biclustering method for identification of meaningful structures in complex and noisy data.

• RVS Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).

• Scale4C Scale4C is an R/Bioconductor package for scale-space transformation and visualization of 4C-seq data. The scale-space transformation is a multi-scale visualization technique to transform a 2D signal (e.g. 4C-seq reads on a genomic interval of choice) into a tesselation in the scale space (2D, genomic position x scale factor) by applying different smoothing kernels (Gauss, with increasing sigma). This transformation allows for explorative analysis and comparisons of the data’s structure with other samples.

• scfind Recently a very large collection of single-cell RNA-seq (scRNA-seq) datasets has been generated and publicly released. For the collection to be useful, the information must be organized in a way that supports queries that are relevant to researchers. scfind builds an index from scRNA-seq datasets which organizes the information in a suitable and compact manner so that the datasets can be very efficiently searched for either cells or cell types in which a given list of genes is expressed.

• scmap Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. scmap is a method for projecting cells from a scRNA-seq experiment on to the cell-types identified in a different experiment.

• SCnorm This package implements SCnorm — a method to normalize single-cell RNA-seq data.

• scoreInvHap scoreInvHap can get the samples’ inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for two well known inversions (8p23 and 17q21.31) and for two additional regions.

• scPipe to process single cell RNA-seq data from fastq to gene counting matrix. it can process data generated by CEL-seq, MARS-seq, Drop-seq and SMART-seq.

• seqCAT The seqCAT package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and validate the source, function and characteristics of biological samples used in scientific endeavours.

• seqcombo Provides useful functions for visualizing sequence recombination and virus reassortment events.

• SeqSQC The SeqSQC is designed to identify problematic samples in NGS data, including samples with gender mismatch, contamination, cryptic relatedness, and population outlier.

• SingleCellExperiment Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.

• slalom slalom is a scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing to identify biological drivers of cell-to-cell variability and model confounding factors.

• SPONGE This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input.

• stageR The stageR package allows automated stage-wise analysis of high-throughput gene expression data. The method is currently published as a preprint at http://biorxiv.org/content/early/2017/02/16/109082

• tenXplore Perform ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics.

• TFARM It searches for relevant associations of transcription factors with a transcription factor target, in specific genomic regions. It also allows to evaluate the Importance Index distribution of transcription factors (and combinations of transcription factors) in association rules.

• TFHAZ It finds trascription factor (TF) high accumulation DNA zones, i.e., regions along the genome where there is a high presence of different transcription factors. Starting from a dataset containing the genomic positions of TF binding regions, for each base of the selected chromosome the accumulation of TFs is computed. Three different types of accumulation (TF, region and base accumulation) are available, together with the possibility of considering, in the single base accumulation computing, the TFs present not only in that single base, but also in its neighborhood, within a window of a given width. Then, high accumulation DNA zones are defined as regions of the genome formed by contiguous bases with accumulation equal or higher than a given threshold. In addition, some functions are provided in order to analyze, visualize and compare results obtained with different input parameters.

• TMixClust Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non-parametric cubic splines estimation. The method can robustly account for the high levels of noise present in typical gene expression time series datasets.

• TnT A R interface to the TnT javascript library (https://github.com/ tntvis) to provide interactive and flexible visualization of track-based genomic data.

• topdownr The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.

• transcriptogramer R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expression are altered.

• trena Methods for reconstructing transcriptional regulatory networks, especially in species for which genome-wide TF binding site information is available.

• vulcan Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data. In order to do so, our package combines strategies from different BioConductor packages: DESeq for data normalization, ChIPpeakAnno and DiffBind for annotation and definition of ChIP-Seq genomic peaks, csaw to define optimal peak width and viper for applying a regulatory network over a differential binding signature.

• zFPKM Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data.

• zinbwave Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.

NEWS from new and existing packages

ABAEnrichment

Changes in version 1.8.0:

NEW FEATURES

• two new statistical tests are available (in addition to hypergeometric and Wilcoxon rank-sum test): 1) binomial test when genes are associated with two counts (e.g. number of amino-acid changes in two species since a common ancestor); 2) 2x2 contingency table test when genes are associated with with four counts (e.g. number of non-synonymous or synonymous variants that are fixed between or variable within species.)

• new ‘silent’ option represses all output to the screen except for warnings and error messages

USER-LEVEL CHANGES

• default ‘genes’ input is now a dataframe with gene-identifiers in column 1 and gene-associated variables, like scores or counts in the other columns (the old vector-input will still work for hypergeometric and Wilcxon rank-sum test)

• sort aba_enrich(…)[[1]] output also on structure-ID (after sorting on age category and FWER)

• sort genes in ‘get_annotated_genes’ output (mixedsort)

• rename aba_enrich() column ‘times_FWER_under_0.05’ to ‘n_significant’

IMPROVEMENTS

• performance improvements for aba_enrich and get_annotated_genes

• modified generation of temporary files allows parallel processing with mclapply

ABSSeq

Version: 2017-07-18 Date: 2017-07-18 Category: Updating! Adapt aFold model for complex design with linear model (R funtion: ABSSeqlm Text:

Version: 2017-06-02 Date: 2017-06-02 Text: 1) Updating! Introduce a new approach for normalization as qtotal (R funtion: qtotalNormalized) 2) aFold now moderates fold changes upon overall dispersion and gene-specific dispersion

Version: 2017-02-14 Date: 2017-02-14 Category: Updating! Adding new method: aFold to call DE via fold-change Text:

Version: 2016-02-29 Date: 2016-02-29 Category: Updating! Enable the paired comparison by seting up ‘paired’ parameter in ‘ABSDataSet’ object Text:

Version: 2015-08-24 Date: 2015-08-24 Category: This is the second version of ABSSeq Text: 1) Use NB distribution insead of GP to model the counts difference between conditions 2) Introduce an efficient outlier detection method: moderated MAD 3) Introduce penalty for dispersion estimation 4) Provide moderation of log2 fold-change at expression level and gene-specific dispersion

affycoretools

Version: 1.50.0 Category: Significant user-visible changes Text:

Version: 1.50.0 Category: Converted runRomer and outputRomer to S4, in the process re-factoring Text:

Version: 1.50.0 Category: they now accept either an ExpressionSet and MArrayLM object (for Text:

Version: 1.50.0 Category: Affymetrix microarray analyses), a DGEList and DGEGLM object (for Text:

Version: 1.50.0 Category: RNA-Seq analysis using edgeR) or an EList and MArrayLM object (for Text:

Version: 1.50.0 Category: either Agilent one-color microarray analysis or limma-voom RNA-Seq Text:

Version: 1.50.0 Category: analysis Text:

Version: 1.50.0 Category: affycoretools v1.43.1 Text:

Version: 1.50.0 Category: Changes Text:

Version: 1.50.0 Category: Added new functionality to automatically annotate ExpressionSets Text:

Version: 1.50.0 Category: using either ChipDb (e.g., hugene10sttranscriptcluster.db) packages Text:

Version: 1.50.0 Category: pdInfo (e.g., pd.hugene.1.0.v1) packages, or user-supplied Text:

Version: 1.50.0 Category: data.frames. Text:

ALDEx2

Changes in version 1.9.2:

NEW FEATURES (JRW, GBG

• added ability to auto-choose low variance high relative abundance features as the basis

• added new class and generic definitions to get the features used as basis

• the getDenom function can be exported

• updated documentation for above

• version bump

Changes in version 1.8.1:

NEW FEATURES (TPQ

• rennovated aldex function

• new ‘test = iterative’ uses results of one t-test as ‘denom’ input to a second

• large improvements to function documentation

• rennovated aldex.ttest function

• “progress bar” tracks progress across Monte-Carlo instances

• made aldex.ttest function faster (~300% for 10,000 features)

• now uses Wilcox signed rank test when ‘paired.test = TRUE’

• added aldex.clr method for signature ‘matrix’

amplican

Changes in version 1.0.0:

NEW FEATURES

• ampliCan first release

Anaquin

Changes in version 2.0:

• Introduced Major changes to all R functions

• Prepared upcoming sequins for germline and cancer mutations

• Prepared upcoming sequins for metagenomic sequins

AneuFinder

Version: 1.5.1 Category: SIGNIFICANT USER-LEVEL CHANGES Text:

Version: 1.5.1 Category: BUG FIXES Text: Can use BSgenomeNCBI for GC correction now (worked only for BSgenomeUCSC before).

Version: 1.5.1 Category: BUG FIXES Text: Bugfix in bam2GRanges(…, pairedEndReads=TRUE) if both alignments are not on the same chromosome.

AnnotationFilter

Changes in version 1.1.2:

NEW FEATURES

• supportFilters returns a data.frame with filter class name and field.

AnnotationHub

Changes in version 2.10.0:

NEW FEATURES

• AnnotationHub will now work offline utilizing argument ‘localHub’; will also use this option automatically if no internet connection is detected.

• Added new GDSResource class

• Added documentation for creating an AnnotationHub package

MODIFICATIONS

• Modified tags vector when passed to display to improve speed of display querying

• Moved readMetadataFromCsv from AnnotationHubData.

• Removed listResources and loadResource from AnnotationHub; not implemented and only valid in ExperimentHub

BUG FIXES

• Expose snapshot less than or equal to release date

• Force rebuild of index if index file corrput or out of date

AnnotationHubData

Changes in version 1.8.0:

NEW FEATURES

• Instead of using dropbox or ftp to deliver contributed resources to Bioconductor Core, temporary access to Annotation-Contributor user on S3 is utilized.

MODIFICATIONS

• Modified readMetadataFromCsv; make RDataPath mandatory entry and if location_prefix is Bioconductor S3 bucket the Rdatapath must start with the package name

BUG FIXES

• Add garbage collection to fix twobit memory allocation error

• Fix files not deleting do to special characters in file names

• Import dbGetQuery from DBI

• Remove hard coded biocVersion in unit tests

anota2seq

Changes in version 0.99.2:

• renaming to adhere to Bioconductor naming style for classes, functions and data objects

• correct mistake in man page of anota2seq_data

• modify default values (no NULL default value for mandatory arguments)

• fix a bug with argument fileName in the plot functions

Changes in version 0.99.1:

• the latex2 function of BiocStyle is now deprecated in the devel version of the package. Replace it by latex()

• remove inst/doc and build/ folders

• update man pages

• change default value of assayNum in anota2seqDataSetFromSE to 1

• formatting of anota2seq show method (and minor text edits in the description of the object)

• fixed issues related to sortBy parameter in anota2seqSelSigGenes

• minor text edits in messages given to user

• fixed bug regarding threshold lines in anota2seqPlotFC

• fixed bug in anota2seqSelSigGenes when useRVM = FALSE and only one gene is to be selected

Changes in version 0.99.0:

• First submitted version

apeglm

Changes in version 1.0.0:

• apeglm is released on Bioconductor! Methods can be accessed from within DESeq2 by calling ‘lfcShrink’ with type=”apeglm”.

arrayQualityMetrics

Changes in version 3.33.2:

USER VISIBLE CHANGES

• Removed reliance on SVGAnnotation as the BioCextra respository is being withdrawn. Currently SVG plots are now not interactive.

ASpli

Changes in version 1.3.12:

FEATURES

• Events named previously as ‘as’ are now names ‘Undefined AS’ for the sake of clarity.

• Enhancement to the vignettes.

BUG FIXES

• Added verbose and filterWithContrasted arguments to DUreport method.

Changes in version 1.3.11:

FEATURES

• Change the assigning of some ‘ES*’ events to ‘as’ events.

• Added verbose option of DUreportBinSplice method

• junctionDUReport methods changed to junctionDUreport to be consistent with other methods names.

BUG FIXES

• Many corrections in the vignette and man pages.

• ZNF410_E013.gr.pdf file in vignettes/images was changed to ZNF410_E013_gr.pdf to be correctly used in the latex code.

Changes in version 1.3.10:

DOCUMENTATION

• Vignette is updated to reflect changes in objects, methods and functions. Minor revisions are still required.

BUG FIXES

• PlotGenomicRegions now can make plots from unmerged bams correctly.

Changes in version 1.3.9:

BUG FIXES

• plotBins function now shows x-tick labels correctly.

Changes in version 1.3.8:

FEATURES

• PlotGenomicRegions do not requires an ASpliCounts object

BUG FIXES

• AsDiscover and DUreport can handle conditions with one samples. Results should be taken with care, but ASpli doesn’t break.

Changes in version 1.3.7:

FEATURES

• Added functions to filter elements in ASpliCounts objects by read counts and read density.

Changes in version 1.3.6:

FEATURES

• geneMode is the default mode of offset estimation.

Changes in version 1.2.1:

BUG FIXES

• AsDiscover() no longer contains mixed row data for some IR and IR* bins in irPIR table.

• DUReport() calculates correctly junction ratio for junctions sharing their end in junction.counts table.

• DUReport() no longer fails when there are no junctions that share their start or end.

• reacCounts() requires an explicit targets argument, instead of taking it from the global environment (in which may not exist with that name).

attract

Version: 1.29.1 Date: 2017-05-31 Category: Fix bug when using microarray data and the reactive gene sets Text:

AUCell

Changes in version 0.99.6:

• Interface changes to conform to Bioconductor requirements. (Function names and parameters, usage of “GeneSet” from GSEABase…)

BASiCS

Changes in version 1.1.0 (2017-08-16):

• Minor changes required to pass BiocCheck (used formatR and BiocChecks)

Changes in version 1.0.13 (2017-08-15):

• Minor changes to documentation

• Minor changes to vignette

Changes in version 1.0.12 (2017-08-14):

• ‘SummarizedExperiment’ class replaced by ‘SingleCellExperiment’

• Updated vignette

Changes in version 1.0.11 (2017-08-06):

• BASiCS_VarianceDecomp : small bugs fixed (unused Data object)

• colnames fixed on cell-specific slots ChainSC and ChainRNA

• Rcpp::checkUserInterrupt() activated in C++ code for interruptions

• ‘grDevices’ added as dependency

• ‘WithSpikes’ argument removed from ‘BASiCS_LoadChain’ function

Changes in version 1.0.10 (2017-08-06):

• BASiCS_TestDE : changes in output messages

• Gene name added in plot method for BASiCS_Chain objects

Changes in version 1.0.9 (2017-08-04):

• newBASiCS_Data : added check to ensure SpikeInfo is a data.frame

• BASiCS_TestDE : default value for EpsilonM & EpsilonD has changed

• Vignette + examples updated accordingly

Changes in version 1.0.8 (2017-08-03):

• ‘Data’ arg removed from args in: ‘HiddenHeaderDetectHVG_LVG’ + ‘HiddenVarDecomp’ + ‘BASiCS_DetectHVG’ + ‘BASiCS_DetectLVG’ + ‘BASiCS_VarThresholdSearchHVG’ + ‘BASiCS_VarThresholdSearchLVG’

• ‘object’ arg renamed as ‘Chain’ in ‘BASiCS_DetectHVG’ + ‘BASiCS_DetectLVG’ + ‘BASiCS_VarThresholdSearchHVG’ + ‘BASiCS_VarThresholdSearchLVG’

• Examples in BASiCS_MCMC updated to use built-in chain

• Removal of ‘smoothPlot’ usage in plots for ‘BASiCS_Summary’ class (avoids issues with log)

• Volcano plots added in BASiCS_TestDE function

• Resolved issues with log scale in ‘smoothScatter’

• Minor bugs fixed in BASiCS_TestDE

• ‘EviThreshold’ arg replaced by ‘ProbThreshold’ in ‘BASiCS_HVG’ + ‘BASiCS_LVG’

• Vignette updated accordingly

Changes in version 1.0.7 (2017-08-03):

• Multiple changes in BASiCS_TestDE: * Added examples of table viewing in doc * Added chain extracts to run examples * Results for differential dispersion to exclude differential mean genes * EFDR / EFNR control plot added * MA plots added

• Main hidden functions moved into individual files

• ‘graphics’ + ‘KernSmooth’ added as dependence to use ‘smoothScatter’

• ‘smooth’ argument changed to ‘SmoothPlot’ in plot functions/methods

• Added reference :: to basic functions (e.g. boxplot, var, acf, etc)

• devtools::check() OK - 1 warning : BiocStyle in vignette

Changes in version 1.0.6 (2017-08-02):

• ‘matrixStats’ added within ‘Imports’ in DESCRIPTION (to use ‘colMedians’ function)

• Minor changes function-by-function (revision of documentation + minor bugs) * BASiCS_TestDE : Improved offset plots

• Major changes function-by-function * BASiCS_TestDE : Ref/Test notation changed to Group1/2 + output table names changed (to Mean/Disp) + offset corrected objects as output + separated output tables Mean/Disp + post prob threshold moved to hidden function (avoids duplicated code)

Changes in version 1.0.5 (2017-08-01):

• Major changes function-by-function * BASiCS_TestDE : plotting functionality for offset added

• ACF plot added to BASiCS_Chain plots

Changes in version 1.0.4 (2017-08-01):

• Minor changes function-by-function (revision of documentation + minor bugs) * BASiCS_VarThresholdSearchHVG / LVG : EFDR criteria updated as in BASiCS_DetectHVG / LVG * BASiCS_TestDE : added examples

• Major changes function-by-function * BASiCS_D_TestDE : no longer in use message added

• Examples in BASiCS_MCMC updated accordingly

• Vignette updated accordingly

• Updated DESCRIPTION file (authors and description)

• Updated welcome message (with link to new wiki)

Changes in version 1.0.3 (2017-08-01):

• Minor changes function-by-function (revision of documentation + minor bugs) * BASiCS_DetectHVG / LVG: added vertical/horizontal lines in EFDR/EFND plot, subtasks moved to hidden functions (avoids repeated code)

• Major changes function-by-function * BASiCS_DetectLVG : evidence threhold to be defined by EFDR only * BASiCS_DetectHVG / LVG: fix on default prob threshold = 0.5 when optimal is < 0.5

• Examples in BASiCS_MCMC updated accordingly

• Vignette updated accordingly

Changes in version 1.0.2 (2017-08-01):

• Minor changes function-by-function (revision of documentation + minor bugs) * BASiCS_MCMC : ‘MCMC_Output’ replaced by ‘Chain’ in examples

• Major changes function-by-function * BASiCS_MCMC : chains stored a single .Rds files, with BASiCS_Chain format (rather than separate .txt files) * BASiCS_LoadChain : updated accordingly * BASiCS_DetectHVG : evidence threhold to be defined by EFDR only

• Vignette updated accordingly

Changes in version 1.0.1 (2017-07-31):

• Minor changes function-by-function (revision of documentation + minor bugs) * newBASiCS_Data : added ref to GB paper + default par value doc + Nils as author * BASiCS_Filter : added ref to GB paper + default par value doc * makeExampleBASiCS_Data : added ref to GB paper + default par value doc + Nils as author * BASiCS_MCMC : added ref to GB paper + Nils as author + fix print of system.time + updated examples

• Major changes function by function * makeExampleBASiCS_Data : Case1 param replaced by Example (vignette + unit test updated accordingly) * BASiCS_MCMC : default value for PriorDelta set to ‘log-normal’ * HiddenBASiCS_MCMC_Start : new starting values for delta (as in main repo)

Changes in version 1.0.0 (2017-07-29):

• Initial big merge with @nilseling changes (in preparation for Bioconductor submission)

• For reference, here is a summary of the changes implemented by @nilseling: * Creation of individual .R for each R function (but all ‘Hidden’ functions are in one file) * BASiCS_Data class replaced by SummarizedExperiment class (Bioconductor) * Contact email updated to ‘cvallejos@@turing.ac.uk’ * Methods for BASiCS_Data and BASiCS_D_Data objects removed (these classes no longer exist) * Adjust newBASiCS_Data function to create a SummarizedExperiment object * ‘cat’ calls replaced by ‘message’ calls * Clean up of BASiCS_D_TestDE function (removed unused args) * Clean up of BASiCS_DetectHVG_LVG function (using SummarizedExperiment class) * Clean up of BASiCS_MCMC function (using SummarizedExperiment class) * Clean up of BASiCS_Sim function (using SummarizedExperiment class; extra arg ‘muSpikes’) * Clean up of BASiCS_DetectHVG_LVG function (using SummarizedExperiment class) * Clean up of BASiCS_VarianceDecomp function (using SummarizedExperiment class) * Clean up of BASiCS_VarThresholdSearchHVG function (using SummarizedExperiment class) * Clean up of BASiCS_DenoisedCounts function (using SummarizedExperiment class) * Clean up of BASiCS_DenoisedRates function (using SummarizedExperiment class) * Clean up of HiddenBASiCS_MCMC_Start function (using SummarizedExperiment class) * Clean up of makeExampleBASiCS_Data function (using SummarizedExperiment class) * Removed methods associated to BASiCS_D_MCMC class (no longer in use) * NAMESPACE + Rd files updated accordingly * DESCRIPTION file updated accordingly * Vignette file updated accordingly

Changes in version 0.99.14 (2017-10-19):

• Added checks to ensure input SingleCellExperiment object has all info

Changes in version 0.99.13 (2017-10-17):

• @neling email added to DESCRIPTION + author contributions

Changes in version 0.99.12 (2017-10-17):

• Update of NEWS with changes by @neling

• Small typo fix in class validity from @neling last commit

• Changes in BASiCS_Chain and BASiCS_Summary classess to contain a single list slot where all parameters are stored. This allows greater flexibility to incorporate ongoing developments of BASiCS but does not affect user interface.

• BASiCS_DenoisedCounts, BASiCS_DenoisedRates, BASiCS_DetectHVG, BASiCS_DetectLVG, BASiCS_MCMC, BASiCS_TestDE, HiddenVarDecomp, newBASiCS_Chain functions and all methods updated accordingly

• ChainSC and ChainRNA example objects updated accordingly

• Unit tests updated accordingly

• Wiki page updated accordingly

• updateObject generic method imported from BiocGenerics

• New generic methods definition moved to AllGenerics.R

• Change in class definition to store current packageVersion

• BASiCS_LoadChain function updated to deal with old class definition and .txt storage.

• Shorter welcome message.

• Sanity checks in BASiCS_TestDE moved to separate file.

• Updated code indentation in BASiCS_TestDE

• Warning in BASiCS_DetectHVG and BASiCS_DetectLVG when user provides posterior probability thresholds as input

• Unused argument removed from HiddenEFDR and HiddenEFNR functions

• Minor changes to pass R CMD check

• Check library passes R CMD BiocCheck

• Tidy up NAMESPACE

• Tidy up NEWS

• Merge Devel_class into master branch

Changes in version 0.99.10 (2017-10-17):

• Updated README with BioC installation instructions and @nturaga acknowledgment

Changes in version 0.99.9 (2017-10-16):

• Updated URL and BugReports in DESCRIPTION

Changes in version 0.99.8 (2017-10-10):

• version bump to trigger a new Bioconductor build

Changes in version 0.99.7:

• inst folder has been deleted

• Removal of ... arg in segments - plot method for BASiCS_Summary

Changes in version 0.99.5 (2017-09-26):

• Change of default PriorDelta value in BASiCS_MCMC

• Unit tests modified accordingly

Changes in version 0.99.4 (2017-09-25):

• Format in BASiCS_MCMC

• Minor bug fixed in BASiCS_DetectLVG plots

• Added examples in BASiCS_DenoisedCounts + BASiCS_DenoisedRates

• Removal of Example argument in makeExampleBASiCS_D_Data

• Format in vignette

• R CMD CHECK passed

• R CMD BiocCheck passed

Changes in version 0.99.3 (2017-09-21):

• Extra unit test (parameter estimates for a given seed)

• Format + vectorisation in HiddenThresholdSearchTestDE function

• HiddenProbDE removed as no longer needed

• Additional unit test for differential test added

• Format for BASiCS_TestDE function

• Format for HiddenBASiCS_MCMC_Start function

• Format for HiddenChecksBASiCS function

• Format for BASiCS_D_TestDE

• Format for all S4 methods

• 2^ added to FC in BASiCS_TestDE TableDisp

• Format for data documentation

• Format for classes definition

• Format + vectorization for BASiCS_Filter

• Format for BASiCS_LoadChain

• Removal of second example in makeExampleBASiCS_Data (no longer required due to DataSC, DataRNA)

• Format for makeExampleBASiCS_Data

• Format for BASiCS_Sim

• Format + matrixStats usage in BASiCS_VarianceDecomp

• Unit test for HVG/LVG detection added

• Minor bug in BASiCS_TestDE resolved (related to colMeans2 use)

• Format + matrixStats usage in HiddenVarDecomp

• message replaced by cat in Methods.R

• Removal of no-longer-needed Hidden functions

• Format in HiddenHeaderDetectHVG_LVG

• Format in HiddenPlot1DetectHVG_LVG + HiddenPlot2DetectHVG_LVG

• Format + matrixStats usage in BASiCS_DetectHVG + BASiCS_DetectLVG

• Format in BASiCS_VarThresholdSearchHVG

• Format in HiddenThresholdSearchDetectHVG_LVG

• Calculations in BASiCS_DenoisedRates moved to C++ to increase speed

• Format in BASiCS_DenoisedCounts

• Edits in HiddenBASiCS_MCMCcpp and associated C++ functions * Dimensions for mu storage upto q0 only * Creation of generic storage values * Formating of long lines * Removal of no-longer-required functions and debug lines

• Edits in HiddenBASiCS_MCMCcpp and associated C++ functions * Optimization of MH updates

• Edits in HiddenBASiCS_MCMCcpp and associated C++ functions * Batch & no-batch versions merged in a single function * Avoids double transponse for chain storage

Changes in version 0.99.2:

• ‘newBASiCS_Data’: format + checks moved to HiddenChecksBASiCS_Data function

• HiddenChecksBASiCS_Data: use of colMeans2, rowMeans2

• Format in welcome message

• ‘newBASiCS_Chain’: format

Changes in version 0.99.0 (2017-08-28):

• Minor changes to complete Bioconductor submission checklist

• Version re-numbered according to Bioconductor guidelines

Changes in version 0.7.30 (2017-07-26):

• Typo fixed in ‘BASiCS:::HiddenBASiCS_MCMC_Start’ function (thanks to @bdulken for pointing out this issue)

Changes in version 0.7.29 (2017-07-24):

• ‘BASiCS:::HiddenBASiCS_MCMC_Start’ function modified regarding the definition of starting values for mu (to avoid adding +1 when it’s not necessary)

• ‘BASiCS:::HiddenBASiCS_MCMC_Start’ modified to have better starting values for delta (this is based on eq 2 from Vallejos et al, 2016)

Changes in version 0.7.28 (2017-07-21):

• Fixed dependency to ‘data.table’ to prevent errors in ‘BASiCS_LoadChain’ function(thanks to Yongchao Ge for pointing out this issue). This change affects the DESCRIPTION file as well as the ‘BASiCS_LoadChain’ function.

Changes in version 0.7.27 (2017-05-09):

• Bug fixed in ‘BASiCS_Filter’ function to stop the code crashing when there are genes with zero counts across all cells.

Changes in version 0.7.26 (2017-02-09):

• Update of ‘BASiCS_Filter’ function to include a ‘BatchInfo’ argument (thanks to Dmitriy Zhukov for suggesting this)

• Vignette file updated accordingly.

• Update of ‘newBASiCS_Data’ function to prevent issues related to unused levels when the ‘BatchInfo’ argument is set as a ‘factor’ (thanks to Kevin Rue-Albrecht for pointing out this issue)

Changes in version 0.7.25 (2017-01-11):

• Fixed typo in vignette file (thanks to Dmitriy Zhukov for pointing this out)

Changes in version 0.7.24 (2016-11-23):

• Median changed to mean when calculating identifiability constrain for the no spike case

Changes in version 0.7.23 (2016-11-21):

• Cleaning-up of identifiability constrain options for the no spike case

Changes in version 0.7.22 (2016-11-16):

• Fixed bug for ‘ConstrainType’ = 5 (affects no spike case only)

Changes in version 0.7.21 (2016-11-15):

• ‘ConstrainType’ = 4, 5 added (exclude genes with capture in less than ‘ConstrainLimit’100% of the cells)

Changes in version 0.7.20 (2016-11-14):

• ‘newBASiCS_Data’ function modified to allow no spikes case

Changes in version 0.7.19 (2016-11-14):

• RefGene information to be stored as .txt file

Changes in version 0.7.18 (2016-11-08):

• Function ‘BASiCS_LoadChain’ added to simplify the loading of pre-computed chains

• Imports from ‘testthat’ library added to NAMESPACE file

• Small changes in ‘BASiCS_D’ classes to allow offset

Changes in version 0.7.17 (2016-11-07):

• Error fixed in the definition of RefGenes

Changes in version 0.7.16 (2016-11-07):

• ConstrainType = 3 (stochastic ref) re-introduced for no-spikes case

Changes in version 0.7.15 (2016-11-07):

• ConstrainType = 1 (untrimmed) re-introduced for no-spike case (illustration purposes only)

• RefGene removed from AR report

• Added console report of RefGene choice

Changes in version 0.7.14 (2016-11-03):

• Debug message removed from ‘muUpdateNoSpikes’ function.

Changes in version 0.7.13 (2016-11-02):

• Typo on the arguments of ‘HiddenBASiCS_MCMCcppNoSpikes’ function has been fixed (‘Constrain’ instead of ‘ConstrainType’)

• Validity check ‘(y(i) > 1e-3)’ moved later on in ‘deltaUpdateNoSpikes’ to avoid breaking the code when it is not really necessary!

Changes in version 0.7.12 (2016-11-01):

• Change in defaul value of ‘PriorDelta’ (v 0.7.9) has been reverted for reproducibility issues. Message added to the start of the function so that users are aware of making the change.

• PriorDelta = ‘gamma’ is now allowed for no spikes case

Changes in version 0.7.11 (2016-10-31):

• Comments added to clarify no spikes case in ‘BASiCS_MCMC’ function.

Changes in version 0.7.10 (2016-10-31):

• Minor changes in ‘BASiCS_MCMC’ to have more meaningful variable names

• Minor changes in ‘BASiCS_MCMC’ to make no-spikes case functional

Changes in version 0.7.9 (2016-10-31):

• C++ code cleaned regarding parameter updates (no spikes case)

• Updated email in description file and welcome message

• ‘BASiCS_MCMC’ modified so that “log-normal” is the default value for PriorDelta

Changes in version 0.7.8 (2016-08-15):

• ConstrainType = 4 implemented (no spikes case only)

Changes in version 0.7.7 (2016-08-12):

• ConstrainType = 3 implemented (no spikes case only)

Changes in version 0.7.6 (2016-08-11):

• As v 0.7.5 but with extra argument for constrain limit (no spikes case only)

Changes in version 0.7.5 (2016-08-10):

• Modified constrain to include ‘expressed’ genes only (no spikes case only)

Changes in version 0.7.4 (2016-08-09):

• Modified constrain to include ‘expressed’ genes only (no spikes case only)

Changes in version 0.7.3 (2016-08-08):

• Reference set to be the gene closest to the average (no spikes case only)

Changes in version 0.7.2 (2016-08-05):

• Same as v 0.7.2 but more efficient

Changes in version 0.7.1 (2016-08-05):

• Random reference in sequential updates for mu (no spikes case only)

Changes in version 0.7.0 (2016-08-02):

• Sequential updates for mu in MCMC (no spikes case only)

Changes in version 0.6.9 (2016-08-01):

• Dirichlet-based proposals for mu in MCMC (no spikes case only)

Changes in version 0.6.8 (2016-07-28):

• Sequential updates for mu in MCMC (no spikes case only)

Changes in version 0.6.7 (2016-07-28):

• Minor changes in the validity checks of ‘BASiCS_D_Data’ objects

Changes in version 0.6.6 (2016-07-27):

• First working version of no spikes case (constrained mu’s)

Changes in version 0.6.5:

• Modified identifiability constrains for no spikes case.

Changes in version 0.6.4 (2016-06-01):

• Safety checks added to ‘phiUpdateNoSpikes’

Changes in version 0.6.3 (2016-05-31):

• Small update in wellcome message.

Changes in version 0.6.2 (2016-05-31):

• Template for ‘phiUpdateNoSpikes’ has been added.

• Minor change in ‘phiUpdate’ for all ‘HiddenBASiCS_MCMCcpp’ functions (to avoid re-writing phi0)

• Faster adaptation steps for ‘HiddenBASiCS_MCMCcppBatch’ ‘HiddenBASiCS_MCMCcppNoSpikes’

• ‘HiddenBASiCS_MCMCcppNoSpikes’ completed for testing stage (not ready for users)

Changes in version 0.6.1 (2016-05-25):

• Argument ‘WithSpikes’ added to ‘makeExampleBASiCS_Data’, generating an example data with no spikes

• Modifications to validity checks of ‘BASiCS_Data’ class to allow no spikes case (SpikeInput = 1)

• ‘show’ methods for ‘BASiCS_Data’ class modified to deal with no spike case

• Checks for ‘BASiCS_Data’ object modified to require: either spikes or batches

• ‘BASiCS_MCMC’ modified for no spikes case (if/else statement only, not yet functional)

• ‘HiddenBASiCS_MCMC_Start’ modified for no spikes case

• Function ‘HiddenBASiCS_MCMCcppNoSpikes’ added. Update for ‘phi’ is pending.

• Small vignette file for no spikes case added

Changes in version 0.5.11 (2016-05-24):

• ‘importMethodsFrom(scran, computeSumFactors)’ added to NAMESPACE

Changes in version 0.5.10 (2016-05-20):

• Updated bug in ‘HiddenBASiCS_MCMC_Start’ function (thanks to Joanna Dreux for noticing this issue)

Changes in version 0.5.9 (2016-05-19):

• Dependency to ‘scran’ added

• ‘HiddenBASiCS_MCMC_Start’ modified to use ‘scran’ estimates as starting values. This allows faster convergence.

• Updated ‘README.md’ file to build and access vignette during installation

Changes in version 0.5.8 (2016-05-18):

• After profiling of c++ functions, minor edits to improve memory usage. These do not affect user interface

• Small change in funtion ‘makeExampleBASiCS_Data’ to avoid ‘NOTICE’ message

Changes in version 0.5.7 (2016-04-27):

• Welcome message added

Changes in version 0.5.6 (2016-04-19):

• Fixed message in BASiCS_D_Test function. This does not affect functionality. Only the message that is printed in the console.

Changes in version 0.5.5 (2016-04-18):

• Small fix when checking the validity of a BASiCS_D_Data object. Thanks to Nils Eling.

• Fixed issue with documentation files.

Changes in version 0.5.4 (2016-04-15):

• Minor fixes to the documentation files

• Argument GenesSelect was added to function BASiCS_D_TestDE to allow user-defined lists of genes to be included in the comparison between cell types.

Changes in version 0.5.3 (2016-03-09):

• Slots BatchInfoTest and BatchInfoRef added to BASiCS_D_Data class.

• newBASiCS_D_Data function modified to incorporate BatchInfoTest and BatchInfoRef slots.

• CombineBASiCS_Data function modified to incorporate BatchInfoTest and BatchInfoRef slots.

• show method for BASiCS_D_Data class modified to incorporate BatchInfoTest and BatchInfoRef slots.

• GeneNames argument missing in makeExampleBASiCS_D_Data has been added.

• Slots thetaTest and thetaRef of BASiCS_D_Chain objects modified to accept matrices (necessary to allow multiple batches).

Changes in version 0.5.2 (2016-03-07):

• In function BASiCS_D_TestDE. Probability threshold set to 0.90 when EFDR fails to calibrate (simulations under the null)

• Fixed version number in description file.

Changes in version 0.5.1 (2016-03-07):

• In function BASiCS_D_TestDE. Probability threshold set to 0.95 when EFDR fails to calibrate (simulations under the null)

Changes in version 0.5.0 (2016-03-03):

• Extended package description to include comparisons between pre-specified populations of cells

• BASiCS_DV_Data, BASiCS_DV_Chain and BASiCS_DV_Summary classes replaced by BASiCS_D_Data, BASiCS_D_Chain and BASiCS_D_Summary classes, respectively.

• Slot ‘offset’ added to BASiCS_D_Chain and BASiCS_D_Summary classes.

• Slot ‘probHPD’ added to BASiCS_D_Summary class.

• Creation of CombineBASiCS_Data function to combine 2 independent BASiCS_Data objects into one BASiCS_D_Data object.

• Offset value added to the input of show method for BASiCS_D_Chain and BASiCS_D_Summary classes.

• Creation of CombineBASiCS_Chain function to combine 2 independent BASiCS_Chain objects into one BASiCS_D_Chain object.

• ‘GeneNames’ slot added to BASiCS_Data class

Changes in version 0.4.1 (2016-02-05):

• Fixed bug in vignette (usage of newBASiCS_Data function). Same bug has been fixed in documentation of class BASiCS_Data.

• Optional argument ‘Start’ added to BASiCS_MCMC function to allow running chains with a variety of user-defined starting point. In general, we do not advise to use this argument as the default option has been tuned to facilitate convergence.

• Updated documentation of ‘BASiCS_DetectHVG’ and ‘BASiCS_VarianceDecomp’ function (removing ‘GeneNames’ argument)

• Updated documentation for ‘BASiCS_DV_TestDE’ function.

• Missing @description sections added to several .Rd files.

Changes in version 0.4.0 (2015-12-21):

• Preliminary functions for differential expression analyses (mean and over-dispersion) have been added.

Changes in version 0.3.5 (2015-11-27):

• Optional argument PriorDelta added to BASiCS_MCMC function, to allow optional use of gamma or log-normal priors for delta.

• In BASiCS_MCMC function, change of default value of s2.mu to 0.5. Allows better shrinkage in situations where a gene has zero counts across all cells.

• In BASiCS_Data class. Count matrices where a gene has zero counts across all cells are now allowed. However, a warning is returned in such case. Only use such matrices when running differential expression results.

Changes in version 0.3.4 (2015-11-11):

• Fix of example code of ‘newBASiCS_Data’ function. Thanks to Simon Andrews for pointing out this issue.

Changes in version 0.3.3 (2015-11-05):

• Same method as before but improved performance of C++ code

Changes in version 0.3.2 (2015-10-23):

• Minor changes to the output of BASiCS_MCMC function (colnames of the elements related to the parameter $\theta$)

• Addition of extra optional parameter ls.phi0 to BASiCS_MCMC function. This is helpful on situations where the default value led to slow mixing to the chains related to the normalising constants $\phi_j$’s.

Changes in version 0.3.1 (2015-09-17):

• New slot GeneNames in ‘BASiCS_Data’ class

• Changes in the constructor newBASiCS_Data to allow easier construction of BASiCS_Data objects

• Minor changes to some functions’ output to use the new GeneNames slot of ‘BASiCS_Data’ class

Changes in version 0.3.0 (2015-07-31):

• New slot BacthInfo in ‘BASiCS_Data’ class

• Batch-speficic technical variability parameters are allowed

• ‘BASiCS_VarianceDecomp’ modified to accommodate batch membership (including graphical output)

Changes in version 0.2.1 (2015-07-23):

• Argument ‘GeneNames’ has been added to functions ‘BASiCS_VarianceDecomp’, ‘BASiCS_DetectHVG’, ‘BASiCS_DetectLVG’ so that users can specify gene labels or names that will be used for these functions’s output.

Changes in version 0.2.0 (2015-06-24):

• New parametrization for mRNA content size factors $\phi_j$ that improves mixing of the MCMC algorithm (using adaptive Dirichlet proposals)

• Updated vignette

Changes in version 0.1.6 (2015-06-01):

• Replacement of parameter-specific ‘displayChain’s functions by a generic method displayChainBASiCS

• Replacement of parameter-specific ‘displaySummary’s functions by a generic method displaySummaryBASiCS

• In ‘BASiCS_DetectHVG’ and ‘BASiCS_DetectLVG’: constrain added to that prob >= 0.5 is required to detect HVG and LVG

Changes in version 0.1.5 (2015-05-27):

• Small typo in ‘BASiCS_VarThresholdSearchHVG’ and ‘BASiCS_VarThresholdSearchLVG’ has been fixed.

Changes in version 0.1.4 (2015-05-21):

• ‘BASiCS_Denoise’ function added. It produces a table of normalised and denoised expression counts (after removing the effect of technical variation).

Changes in version 0.1.3 (2015-05-18):

• ‘plotBASiCSDispVsExp’: ‘log=”xy”’ argument added

• ‘BASiCS_Data’: internal checks added (pre-filter of samples and transcripts)

• ‘BASiCS_MCMC’ c++ code: Rcpp::checkUserInterrupt() added for fast user-requested interruption of MCMC sampler

• S4 method ‘plot’ for ‘BASiCS_Chain’ signature: argument ‘Column’ replaced by ‘Gene’ and ‘Cell’

• Replacement of ‘plotBASiCSNormPhi’ and ‘plotBASiCSNormS’ by S4 method ‘plot’ (‘BASiCS_Summary’ signature)

• S4 method ‘plot’ for ‘BASiCS_Summary’ signature: does not include plots for all model parameters

• S4 method ‘plot’ for ‘BASiCS_Summary’ signature: does not include scatterplots of gene-specific and cell-specific model parameters (replacing ‘plotBASiCSExpVsDisp’)

• ‘BASiCS_VarianceDecomp’ has been made visible to users (former ‘HiddenVarDecomp’ function) and output does now allow gene annotation.

• ‘BASiCS_Filter’ function added.

• Vignette has been updated according to the changes above. Instructions for installation were added.

• ‘BASiCS_Filter’ function added.

• Dependency to R (>= 3.1.0) has been added.

Changes in version 0.1.2 (2015-04-23):

• In ‘BASiCS_Sim’: change ‘sum(phi)==n’ by ‘all.equal(sum(phi),n)’

Changes in version 0.1.1 (2015-04-21):

• Improved documentation

Changes in version 0.1 (2015-04-20):

• Original release

beachmat

Changes in version 1.0.0:

• New package beachmat, which provides a C++ API for handling various R matrix types.

BgeeDB

Changes in version 2.3.2:

• Compatibility of the TopAnat part of the package with the new Bgee release 14 (www.bgee.org/bgee14/).

• Better management of potential issues with the ontology structure

Changes in version 2.3.1:

• Compatibility with the new Bgee release 14 (www.bgee.org/bgee14/) only for the processed data download part.

• The TopAnat part still temporarily uses data from Bgee release 13.2, until the webservice is ready.

• Retro compatibility with Bgee release 13.2 (www.bgee.org/bgee13/)

Biobase

Changes in version 2.37:

BUG FIXES

• ’$’ completion on eSet and ExpressionSet works in RStudio.

bioCancer

Version: 1.6.00 Category: metamorphosis: bioCancer is a radiant.data extension Text:

Version: 1.6.00 Category: reduce size of package by half 14 -> 7 mb Text:

Version: 1.5.12 Category: improve Reactome_ui functions Text:

Version: 1.5.11 Category: add switch button to ui_circomics Text:

Version: 1.5.11 Category: improve circomics functions Text:

Version: 1.5.09 Category: delete commented files and figures Text:

Version: 1.5.09 Category: cleanup ui_radiant, /Rbis, /quant, /bioCancer Text:

Version: 1.5.08 Category: switchButton Text:

Version: 1.5.07 Category: data.row.names(row.names, rowsi, i) Text:

Version: 1.5.07 Category: some row.names duplicated: 11,12,13,14 –> row.names NOT used Text:

Version: 1.5.06 Category: dplyr::mutate_each() is deprecated Text:

Version: 1.5.06 Category: dply::summarise_each() is deprecated Text:

Version: 1.5.06 Category: replace BiocStyle by prettydoc Text:

Version: 1.5.05 Category: Warning in formals(fun) : argument is not a function Text:

Version: 1.5.05 Category: Warning in body(fun) : argument is not a function Text:

Version: 1.5.04 Category: Fix setting plot size Text:

Version: 1.5.03 Category: Change the color rang of Circular layout plot as in standards Text:

Version: 1.5.02 Category: update Correlation Methods Text:

Version: 1.5.01 Category: replace .libPath() by path.package(‘bioCancer’) in portal.R file Text:

BiocCheck

Changes in version 1.14:

NEW FEATURES

• NOTE when maintainer subscription to bioc-devel mailing list cannot be checked (checking requires mailing list admin password).

BUG FIXES

• Use shell quotes to allow spaces in package paths

BiocFileCache

Changes in version 1.1:

NEW FEATURES

• (v. 1.1.7) bfcmeta() and friends allows arbitrary metadata on records and ability to query bfcmeta data.

USER-VISIBLE CHANGES

• (v. 1.1.16) if httr::HEAD fails don’t try httr::GET, just report not available

• (v. 1.1.7) bfcquery() syntax changed to grep(), rather than SQL ‘LIKE’.

• (v. 1.1.7) bfcquery() supports user-specified ‘fields=’.

• (v. 1.1.5) queryCount renamed to bfccount

• (v. 1.1.2) Add user specified extension to file in cache

• (v. 1.1.2) Use dbExecute/dbSendStatement rather than pasting query

• Files in cache retain basename and extension of original file

BiocInstaller

Changes in version 1.28.0:

NEW FEATURES

• biocLite() supports full URLs, e.g., to archived Bioconductor packages.

• Support MRAN (Microsoft R) archives.

BiocParallel

Changes in version 1.12:

BUG FIXES

• (v. 1.11.1) Change registered backend initialization to first invocation, rather than on load.

• (v 1.11.8) Ensure registry is initiailized before (public) use. Issue #65

NEW FEATURES

• (v. 1.11.2) bpiterate() gains a progress counter.

• (v. 1.11.5) ipclock(), etc: inter-process locks and counters

BiocStyle

Changes in version 2.6.0:

SIGNIFICANT USER-VISIBLE CHANGES

• Rename ‘latex2’, ‘pdf_document2’ and ‘html_document2’ to ‘latex’, ‘pdf_document’ and ‘html_document’, respectively

• Rename argument to ‘pdf_document’ from ‘use.unsrturl’ to ‘use_unsrturl’ for consistency with rmarkdown naming scheme

• Split figure/table captions on “. “ rather than “.” in order to minimize chances of hitting decimal point in numbers, etc.

BUG FIXES AND IMPROVEMENTS TO PDF STYLE

• Make knitr option ‘fig.pos’ functional in ‘pdf_document’

• Improve formatting of TOC chapter entries (https://github.com/Bioconductor/BiocStyle/issues/35)

• Adjust width of non-floating figures according to the ‘fig.wide’/’fig.small’ setting (reported by Aaron Lun)

• Robustify \texttt, e.g. by enabling backticks and fixing the substitution of control spaces

• Update LaTeX code highlighting macros for pandoc output (reported by Vince Carey)

• Silence spurious warning in ‘latex()’ emitted when the source file is missing a final EOL

• Fix broken code in knitr hook adjusting page width

• Include package version field in R Markdown documents even if they are missing an abstract (https://github.com/Bioconductor/BiocStyle/issues/29)

• Correct way of enclosing non-floating figures in LaTeX ‘adjustwidth’ environment (https://github.com/Bioconductor/BiocStyle/issues/28)

BUG FIXES AND IMPROVEMENTS TO HTML STYLE

• Correct displaying of superscript text

• Allow modifying table layout in ‘knitr::kable’ (https://github.com/Bioconductor/BiocStyle/issues/30)

• Correct padding of nested lists, and indentation of document date and multi-line headings

• Fix a bug in the function matching author affiliations (https://support.bioconductor.org/p/98155/)

• Proper horizontal alignment of ggplotly graphics (https://support.bioconductor.org/p/97609/)

• Fix compatibility with ‘runtime: shiny’ document option

biomaRt

Changes in version 2.34.0:

NEW FEATURES

• Added the listEnsemblArchives() function. This returns a table of the available Ensembl archives, and replaces the archive = TRUE argument to several functions, which was no longer working.

BUG FIXES

• The Ensembl BioMart server doesn’t always respond well if queries with more than 500 filter values are submitted. If a query that exceed this is detect biomaRt will now submit the query in batches and concatonate the result when completed.

MINOR CHANGES

• You can now provide a host with ‘http://’ at the start, or a trailing ‘/’ (typically copy/pasted from a browser) and useMarts() will cope.

BiRewire

Changes in version 3.9.1:

• Minorbug fixed (order not preserved using graph.edgelist and infinite loop in matrix with just one entry)

bnbc

Changes in version 0.99:

• Initial release to Bioconductor.

branchpointer

Version: 1.3.0 Category: Improved speed for functions Text:

Version: 1.3.0 Category: Functions combined and renamed Text:

Version: 1.3.0 Category: Updated model to single gbm Text:

Version: 1.3.0 Category: Bug fixes Text:

Version: 1.3.1 Category: Version Bump Text:

BrowserViz

Changes in version 1.9.8:

BUG FIXES

• Significant (3x) speedup. A 5000-node, 6000-edge graph transmits to Cytoscape from R in about 20 seconds.

bsseq

Changes in version 1.13:

• 1.13.6: Fix performance regression in BSmooth(). Thanks to Shan Andrews for the report (<URL: https://github.com/kasperdanielhansen/bsseq/pull/57>).

• 1.13.5: Fix major bug in combine() and combineList(). This bug led to bad BSseq objects with incorrect methylation estimates due to incorrect ‘M’, ‘Cov’, ‘coef’, and ‘se.coef’ assays. To be safe, BSseq objects created with versions 1.13.0 to 1.13.4 should be re-created using a newer version. More specifically, any BSseq objects created with combine() or combineList() should be re-created. Also, BSseq objects created using read.bismark() or read.bsmooth() with multiple ‘files’ should be re-created. Thanks to Alejandro Reyes (@areyesq89) for the report (<URL: https://github.com/kasperdanielhansen/bsseq/pull/54>).

• 1.13.4: Fix performance regression in getMeth() and getCoverage() when ‘regions’ were supplied. Thanks to Alejandro Reyes (@areyesq89) for the report (<URL: https://support.bioconductor.org/p/97611/>).

• Moved vignettes to Rmd.

CAGEr

Changes in version 1.18.1:

• getCTSS() can now load data from large BAM files. Before this update, there were “negative length vectors” errors when filtering out low quality reads from datasets with multiple dozens of millions of sequences.

CAMERA

Changes in version 1.33.3:

BUG FIXES

• Fix getPeaklist not pulling rownames correctly, closing #22, thanks to Jan Stanstrup

Changes in version 1.33.2:

BUG FIXES

• Fix getPeaklist, updated getReducedPeaklist(), Thanks to Kristian Peters

Changes in version 1.33.1:

NEW FEATURES

• allow matchedfilter alternative intval in getPeaklist (J. Stanstrup)

• pass intval from Groupcorr to calcCaS (J. Stanstrup)

• getReducedPeaklist returns just one intensity per pspec (K. Peters)

canceR

Version: 3.1 Text:

Version: 3.2 Text: dimensions levels will be plot. 1- dialogMetOption(): add “Circos” argument to make the difference between getMetDataMultipleGene() and getListMetData() 2- getGeneList(): add rm(“GeneListMSigDB””, envir=”myGlobalEnv”)

Cardinal

Changes in version 1.9.2 (2017-10-25):

BUG FIXES

• Corrected author name in all documentation

Changes in version 1.9.1 (2017-10-23):

BUG FIXES

• Fixed bug in package dependency ‘matter’ affecting the size of datasets that can be processed with ‘batchProcess’

• Fixed bug where bin sizes for units=’ppm’ were twice as wide as they should be in ‘readImzML’ and ‘reduceDimension’

categoryCompare

Version: 1.21.4 Text:

cbaf

Changes in version 1.0.0 (2017-09-10):

New Functions

• New availableData() functon to scan all the cancer studies to examine presence of RNA-seq, microRNA-seq, microarray(mRNA), microarray(miRNA) and methylation data.

• New obtainOneStudy() function to obtain and store the supported data for at least one group of genes across multiple subgroups of a cancer study. In addion, it can check whether or not all genes are included in different subgroups of a cancer study and, if not, looks for the alternative gene names.

• New obtainMultipleStudies() function to obtain and store the supported data for at least one group of genes across multiple cancer studies. It can check whether or not all genes are included in each cancer study and, if not, it looks for the alternative gene names.

• New automatedStatistics() function to calculate the statistics of the data obtained by obtainOneStudy() or obtainMultipleStudies() functions. Based on user’s preference, these statistics can include frequency percentage, frequency ratio, mean value and median value of samples greater than specific value. Furthermore, it can look for the genes that comprise the highest values in each cancer and list the top 5 genes for frequency percentage, mean value and median value.

• New heatmapOutput() function to prepare heatmap for frequency percentage, mean value and median value data provided by automatedStatistics() function. Heatmaps for every gene group are stored in separate folder.

• New xlsxOutput() function to export the output of automatedStatistics() and the gene validation result of one of the obtainOneStudy() or obtainMultipleStudies() functions as an excel file. For every gene group, an excel file will be generated and stored in the same folder as heatmaps.

• New cleanDatabase() function to remove the created databases in the cbaf package directory. This helps users to obtain the fresh data from cbioportal.org.

• New processOneStudy() function to combine obtainOneStudy(), automatedStatistics(), heatmapOutput() and xlsxOutput() functions for the ease of use.

• New processMultipleStudies() function to combine obtainMultipleStudies(), automatedStatistics(), heatmapOutput() and xlsxOutput() functions for the ease of use.

ChAMP

Changes in version 2.8.8:

• Added “force” parameter in champ.load(), which can be used for “minfi” loading method, if your data comes from different arrays, force parameter would allow minfi’s read.meth.exp function to extract their commmon probes and continue analysis.

Changes in version 2.8.7:

• Make champ.import() more robust for modifed csv file.

Changes in version 2.8.5:

• champ.DMP() works on numeric variable now

• champ.DMP() do pairewise comparison between each two categorical phenotypes.

• goseq was replaced by gometh.

• DMP.GUI() is modified heavily.

• SVD plot added legend.

• “minfi” loading method fixed.

• vignette of ChAMP and github Demo pages updated.

• Added some figures from GSE40279 in vignette.

Changes in version 2.8.3:

• Updated zzz.R file, which means the loading messages would be different.

• Fixed a warning in champ.load.Rd file.

• Fixed bug in champ.filter(), if filerDetP is false, update pd part would faile because of lacking of RemainSample variable.

Changes in version 2.8.2:

• Updated EPIC annotation to B4 version. The B4 version is downloaded from illumina website.

• Added one new parameter “method” in champ.load() function, which allows user to choose which method they want to use to read data. ChAMP or Minfi.

• champ.filter() has been totally recoded, now user can do any filtering on any data set they want. Merely champ.filter() is focused to take champ.import() result as input and generate filtered beta value for future analysis.

• Provide Whole New function champ.import() to read IDAT file to R, which is similar to minfi’s read.meth.exp() function.

• Added more strict checking in champ.runCombat(), now champ.runCombat() would check if your variable and batches conflict with each other.

• Removed some useless code in champ.DMR() to make it faster.

Changes in version 2.8.1:

• Added impute option for champ.load().

• Add ProbeCutoff and SampleCutoff parameters in champ.load().

• Added Demo on github: In respond to our reviewer’s question and to make users have better understanding on our package, we processed ChAMP fully on some data sets and saved all messages shown during processing. We upload these information to github.

ChemmineR

Changes in version 2.30.0:

NEW FEATURES

• Plots can be generated using OpenBabel library (requires ChemmineOB package and OpenBabel)

• Functions to query data from PubChem directly.

chipenrich

Changes in version 2.2.0:

NEW FEATURES

• polyenrich now supports weighting peaks by signal value

• A hybrid test, hybridenrich() is available for those unsure of which test, between chipenrich() and polyenrich() to use.

• A function to join two different results files, hybrid.join(), and it will give an adjusted set of p-values and FDR-adjusted p-values using the two.

• A new approximation method using the Score test is available for quick results for chipenrich and polyenrich. Only recommended for significantly enriched results, and not depleted results. ~30x faster.

IMPROVEMENTS

• Several updates to the vignette

ChIPpeakAnno

Changes in version 3.11.8:

• make featureAlignedExtendSignal accept GAlignments list object

Changes in version 3.11.6:

• fix the bugs Codoc mismatches from documentation object ‘peakPermTest’

Changes in version 3.11.4:

• fix the bugs when annoMcols is numeric values.

Changes in version 3.11.3:

• update the function featureAlignedSignal

Changes in version 3.11.2:

• add new function binOverGene, binOverRegions, plotBinOverRegions.

Changes in version 3.11.1:

• make FAQs availble

• Fix the bug in annoPeaks for warning of out-of-bound ranges

ChIPQC

Changes in version 1.13.2:

• Fixed bug when specifying consensus peakset as GRanges

ChIPseeker

Changes in version 1.13.1:

• fixed issue of naming intronList <2017-07-06, Thu> + https://github.com/GuangchuangYu/ChIPseeker/issues/57#issuecomment-313342399

chromstaR

Changes in version 1.3.1:

NEW FEATURES

• New parameter ‘stepsize’ allows sliding bins. This improves localization of peaks.

SIGNIFICANT USER-LEVEL CHANGES

• New default value for Chromstar(…, stepsize = 1/2 * binsize).

ClassifyR

Changes in version 1.12.0:

• Alterations to make plots compatible with ggplot versions 2.2 and greater.

• calcPerformance can calculate some performance metrics for classification tasks based on datasets with more than two classes.

• Sample-wise metrics, like sample-specific error rate and sample-specific accuracy are calculated by calcPerformance and added to the ClassifyResult object, rather than by samplesMetricMap and being inaccessible to the end-user.

cleaver

Changes in version 1.15.1 (2017-06-08):

• Don’t consider the last aminoacid as cleavage site. cleavageSites("ACK", custom="K") results in integer() instead of 3 now. Thanks Apurva Hegde ahegde@tgen.org for reporting this issue.

• Remove superfluous “missedCleavages” argument in cleavageSites.

clustComp

Changes in version 1.5.2:

• A new feature is added to flatVShier(); if the expanded version of the dendrogram is plotted, a coloured bar on the right hand side displays how genes are distributed across the flat clusters.

• New arguments ‘bar1.col’ and ‘bar2.col’ in flatVShier() allow tuning the coloured bars when the expanded dendrogram is plotted.

• Argument ‘weights’ in flatVSflat() is replaced by ‘flat1’ and ‘flat2’ for analogy with flatVShier().

• New argument ‘greedy’ in flatVSflat() allows displaying the one-to-one mapping between superclusters as in flatVShier() after finding the best layout for the bi-graph.

• New argument ‘greedy.colours’ allows setting up the visualisation of the mapping between superclusters, as in flatVShier().

• The visualisation of superclusters in SCmapping() includes new labels with their sizes.

• Internal function drawTreeGraph() includes new arguments ‘flat.obj’, ‘bar1.col’ and ‘bar2.col’ to display the second coloured bar and control the colours.

clusterExperiment

Changes in version 1.3.7 (2017-10-24):

Changes

• Added function tableClusters for tabling clusters by name.

• Added largeDataset option to subsampleClustering

• allow mergeInfo to be called in plotDendrogram to use stored merge info in plotting.

Bugs

• Fixed bug in .makeMergeDendrogram in getFeatures

Changes in version 1.3.6 (2017-10-18):

Changes

• MAJOR CHANGE TO DEFINITION OF CLASS: Added slots to ClusterExperiment object so that the object keeps the information about the merging, and added corresponding helper functions (see documentation). This means previous versions made of a ClusterExperiment object will no longer be valid objects! Old, saved objects from previous versions must be manually adapted to have these slots (with NULL or NA values as appropriate).

• Add function plotClustersWorkflow, see documentation

• Add function plotDimReduce for plotting low-dim pca with points labeled by cluster.

• Add function plotContrastHeatmap to plot the significant genes that are result of getBestFeatures

• getBestFeatures: can now be run on result of mergeClusters without having to call makeDendrogram again for the merged clusters.

• Change argument to plotClusters and plotBarplot from clusters to object

• makeDendrogram: default in is now dimReduce="mad" to avoid accidentally calling it with dimReduce="none" (previous default), which can kill interactive R sessions.

• Changes to plotHeatmap: - default in plotHeatmap to clusterSamplesData="dendrogramValue". - Changed handling of clusterSamplesData argument in plotHeatmap so that if argument equals dendrogramValue or primaryCluster and gives bad results / errors, will give warning and change argument appropriately. - Added arguments to plotHeatmap allowing more user control regarding making blank lines for when have gene groupings.

• mergeClusters now aligns the colors from mergeClusters and combineMany internally.

• mergeClusters now suppresses warnings created by the estimation of the percentage non-null unless showWarnings=TRUE.

• plotDendrogram: - has new argument clusterLabelAngle allowing user to change the angle of the clusterLabel printed on top (when plot is of type “colorblock”) - argument labelType has been changed to plotType

Bugs

• Arguments passed to mergeClusters, ClusterExperiment version, via the ... command will now go first to the mergeClusters matrix version and then onto the plotting, as stated in documentation (plotting arguments were being ignored on the clusterExperiment version of the function).

Changes in version 1.3.4 (2017-09-28):

Changes

• Add argument clusterLabels to plotClusters to allow user to set clusterLabels without changing the object.

• Added data object of run of RSEC. Changed lazyLoad to false because loading this object on installation was creating errors.

• Updated vignette to more completely cover RSEC.

• Change default clusterFunction argument to RSEC to be “hierarchical01” rather than all 01 methods (previous default). This reduces load of making simple call.

• Updated validity checks to reduce memory load, and dropped validObject calls.

• Added function getClusterManyParams to parse the parameter values in the clusterLabels from clusterMany

• Removed old dependency on diagram (from previous vignette, no longer needed)

Bugs

• Fixed error in subsetting of clusterExperiment object when dendrogram is attached (previously didn’t reset dendro_outbranch to NA)

Changes in version 1.3.3 (2017-09-07):

Changes

• Bug fix in clusterContrasts – missing match.arg option for outputType argument

Changes in version 1.3.2 (2017-07-05):

Changes

• Default for top.can in seqCluster are changed to be top.can=5.

• makeDendrogram now has the default argument ignoreUnassignedVar=TRUE like in RSEC

• add ClusterFunction class and update all functions to work on this. All built in cluster functions are now given ClusterFunction Objects, so all built in clustering functions can now work for either subsampleClustering or mainClustering. This will also make it easier for a user to define their own ClusterFunction object and have it be used by functions like clusterSingle. This is a major change in how some of the underlying functions work, but should not impact common functions like clusterMany and RSEC. Some of the more notable changes in the arguments for programmers are: - clusterD and clusterDArgs have been changed to mainClustering and mainClusterArgs. This change was made to make these arguments more clear as to their role in the clustering workflow (and because the clusterD refered to clustering a dissimilarity but it has clustered either x or D for many versions now. ) - seqCluster and clusterSingle no longer take the argument clusterFunction. clusterFunction must be given via mainClusterArgs and subsampleArgs to be passed to mainClustering or subsamplingCluster, respectively. Now only the upper-level function clusterMany takes clusterFunction directly as an argument. - mainClustering (previously clusterD) and subsampleClustering no longer take k nor alpha as a direct argument. These arguments, like all arguments used directly by the cluster function, now need to be passed to the clustering function in a list via clusterArgs. - The list of available built-in clustering routines provided by the package can now be accessed via listBuiltInFunctions(). The functions that are used for these functions are now available to the user via their ClusterFunction object that the user can access with the function getBuiltInFunction. (see ?listBuiltInFunctions)

• hiearchical01 clustering now has a different default, namely to apply as.dist to the input diss in order to get a dist object, rather than dist(1-diss) which was previously the default for historical reasons. This is controlled by argument whichHierDist, and can be set to the previous version by passing whichHierDist="dist" to the clusterArgs argument in either subsampleArgs or mainClusterArgs, depending on where hierarchical01 is being used.

• Spectral clustering is now available ("spectral") via the specc function of kernlab.

• clusterSingle now only returns the dissimilarity matrix in the coClustering slot if subsample=TRUE in the call. Furthermore, for the resulting dissimilarity to replace an existing coClustering slot value, the user must request it by setting replaceCoClustering=TRUE in the call to clusterSingle.

• Removed default value for argument proportion in combineMany. The previous default was proportion=1 but didn’t match most common use cases and was accidentally called by upper functions like RSEC.

• If the clusterFunction argument is not given to subsampleArgs by the user explicitly, and the clusterFunction of mainClusterArgs is appropriate, it will be used for subsampleClustering; if the clusterFunction in mainClusterArgs is not appropriate (e.g. subsampleClustering needs a type K because sequential=TRUE), then the default for the subsampleClustering will be 'pam'. This changes the previous behavior of subsampleClustering where the default was ‘pam’ in all cases where not explicitly given by the user. This change should have no impact on RSEC: since the clusterFunction for the mainClustering terms is a '01' type in RSEC and the subsampleClustering has to be type 'K' when sequential=TRUE, it will revert to the default "pam" as before.

Bugs

• Fixed error so where if clusterSingle was called on existing clusterExperiment object it would overwrite the information of the existing clusterExperiment object.

• Fixed RSEC so now if rerun on existing clusterExperiment object, it will grab defaults from the matrix version (previously defaults were those of the underlying function, which were not always the same, e.g. combineProportion default was previously 1)

• Fixed clusterMany so now it explicitly sets dimReduce="none" in call to clusterSingle. Before, might have been calling all of the dimReduce defaults (i.e. all of them!).

• Fixed so gives error if whichClusters in plotBarplot doesn’t match anything.

Changes in version 1.3.1 (2017-06-14):

Changes

• change how plotHeatmap handles visualizeData argument, so not required to have same number of genes as original, only same number of samples.

• Now if color of vectors given in clusterLegend does not have names, plotHeatmap will give them names matching the variable so that they will be used by aheatmap (previously would have left all colors white because do not have matching names).

• Large changes to how dendrograms are plotted by plotDendrogram and mergeClusters. This includes the ability to see the before and after clusterings along side the mergeClusters result, as well as a new slot added to the clusterExperiment class (dendro_outbranch). The names of several arguments to mergeClusters and plotDendrogram were changed for clarity: - leaves is now leafType in plotDendrogram. - plotType is now plotInfo in mergeClusters - doPlot is now plot in mergeClusters - leafType is now an option for mergeClusters as well. - Now when plotInfo (previously plotType) is set to none, the plot is still drawn, but just no information about the merging is added to the plot. To not plot the dendrogram at all, set plot=FALSE. - The option labelType in either plotDendrogram or mergeClusters controls whether names (name) or rectangular color blocks corresponding to the cluster (colorblock) are put at the tips of the dendrogram to label the clusters/samples.

• added dendroClusterIndex that behaves similarly to primaryClusterIndex

• added ability to give dendro as charater option to whichClusters argument

• added transformation<- to be able to assign manually the transformation slot

• Move MAST into ‘suggests’ pacakge so that not need R 3.4 to run the package.

• Change calculation of PCA dimensionality reduction to use svds from RSpectra package to improve speed

Bugs

• Fixed bug in RSEC where combineProportion argument was being ignored (set to 1)

• Fixed bug in definition of transform so that extends existing generic rather than masking it.

Changes in version 1.3.0 (2017-05-24):

Changes

• plotHeatmap accepts data.frame or ExpressionSet objects for the data argument (calls data.matrix or exprs on object and sends to matrix version)

• Added plotBarplot to plot a barplot for 1 cluster or comparison of 2 clusters along with tests.

• Added whichClusters argument to clusterMatrix to return only clusters corresponding to certain clusters. Mainly relevant for using arguments like workflow that are used by other commands (otherwise could just index the complete matrix manually…)

Bug fixes

• plotHeatmap now goes through the clusterLegend input and removes levels that do not exist in the sampleData; this was causing incorrect coloring when the clusterLegend had more (or less) levels that it assigned color to than the sampleData did (e.g. if sampleData was a subset of larger dataset upon which the original colors were assigned.) NOTE: that this now has the effect of NOT plotting all values in the clusterLegend if they are not represented in the data, thus changing the previous behavior of plotHeatmap legend.

• fixed bug in how plotHeatmap checked that the dimensions of user-supplied dendrogram match that of data (matrix version).

• fixed convertClusterLegend so when output is matrixNames or matrixColors, the resulting matrix has the colnames equal to cluster labels, like clusterMatrix.

• internal function .convertToNum now preserves names of input vector.

• fixed bug in plotting with merge clusters; previously if plotType=”all”, might not have been correctly plotted with the right internal node of the dendrogram.

ClusterJudge

Changes in version 0.99:

USER VISIBLE CHANGES

• added an Introductory vignette

clusterProfiler

Changes in version 3.5.6:

• fixed R check <2017-09-28, Thu>

Changes in version 3.5.5:

• ko2name <2017-08-14, Mon>

• bioc git transition <2017-07-18, Tue>

Changes in version 3.5.4:

• change keytype parameter in enrichGO to keyType for consistent <2017-06-28, Wed> + https://github.com/GuangchuangYu/clusterProfiler/issues/91#issuecomment-311657933

• bug fixed of simplify for compareCluster result <2017-06-19, Mon> + https://github.com/GuangchuangYu/clusterProfiler/issues/67#issuecomment-307815402

Changes in version 3.5.3:

• fixed https://github.com/GuangchuangYu/clusterProfiler/issues/88 <2017-05-24, Wed>

• accept background gene list via universe parameter in enrichDAVID <2017-05-16, Tue> + https://github.com/GuangchuangYu/clusterProfiler/issues/87

Changes in version 3.5.2:

• support keyType in enrichMKEGG <2017-05-10, Wed>

• bug fixed of maintaining input list order in plotting compareCluster result <2017-05-02, Tue> + https://support.bioconductor.org/p/95400/#95426

Changes in version 3.5.1:

• bug fixed of converting KEGG PATH ID to NAME using KEGG.db <2017-04-28, Fri> + https://github.com/GuangchuangYu/clusterProfiler/issues/85

ClusterSignificance

Changes in version 1.5.3:

• Fixed bug in pcp 2D projection plot where colors did not match classification plot.

Changes in version 1.5.2:

• Fixed typo in vignette.

CNEr

Changes in version 3.5:

NEW FEATURES

• Add function orgKEGGIds2EntrezIDs to fetch the mapping between KEGG IDs and Entrez IDs

• Add function makeAxtTracks

• Add function addAncestorGO

Changes in version 3.4:

NEW FEATURES

• Updated CNE class for storing all the information about running the pipeline.

• Add read.rmMask.GRanges to read RepeatMasker .out file.

• Add read.rmskFasta to read soft repeat masked fasta file.

• Add the distribution plot of axt alignment matches.

• Add the distribution plot of CNE length.

• Add the syntenicDotplot for axt alignment and GRangePairs.

• When readAxt and readBed, seqinfo is kept when available.

• New fixCoordinates function makes the coordinates of Axt alignments always relative to positive strands.

• Add parallel subAxt for Axt alignment.

• Add the plot of genomic distribution of CNE.

• Add the function to make bed and bigwig files of CNEs.

BUG FIXES

• Instead of an error, an empty GRangePairs is returned when no CNEs identified.

Changes in version 3.3:

BUG FIXES

• Fix a bug caused by “format” in the blat step.

NEW FEATURES

• Add the pairwise whole genome alignment pipeline

• Add a new class “GRangePairs”

• “Axt” class is now based on “GRangePairs” class.

• readAncora for reading Ancora format CNE files.

coexnet

Version: 0.1.0 Category: NEW FEATURES Text: 18/04/17 –> changing the CCP function. 23/06/17 –> Released in Biocondonductor-devel 12/10/17 –> geneSymbol error test fixed.

COMPASS

Changes in version 1.15.1:

• Exported SimpleCOMPASS interface for use with count matrices

• Previous versions - added translate_marker_names API for use with SimpleCOMPASS

ComplexHeatmap

Changes in version 1.15.1:

• random colors are generated by new rand_color() function in circlize package.

• add density_param in densityHeatmap() function

• annotations with duplicated names have no legends any more

• re-implement grid.xaxis() to draw axis labels rotated 90 degrees

• grids in discrete legend are arranged by rows if ncol > 1

• raster image is generated in an independent R session

• empty string in annotation or heatmap is mapped to NA

• annotation and heatmap legends can be merged into one column.

• change the default value of row_names_max_width and column_names_max_height

• default legend style for continuous values is changed to “continuous”

• add grid.dendrogram2() which draws dendrograms with uneven position for leaves

• move dendextend to Suggests field because it depends/imports rlang indirectly which has a print.frame() function and it will affect to print a frame object returned by frameGrob().

• decorate_*() functions return to the viewport where they are called.

• fixed a bug that annotation names are drawn for all row slices.

• construct a valid path under Windows

cosmiq

Changes in version 1.11.3 (2017-06-19):

• added vignettes/poster.Rmd for 13th Annual Conference of the Metabolomics Society <URL: metabolomics2017.org> (in portrait).

CountClust

Changes in version 1.5.1:

• Release We have added a FitGoMpool() function that automatically performs GoM model with multiple starting points and outputs the one run with the most optimal BIC. Besides, removed switch_axis_position() as a dependency from cowplot as the function has been deprecated. r

CrispRVariants

Changes in version 1.5.9:

• More comprehensive input checking in readsToTarget, removed redundant checking from CrisprSet initializer.

• Fix bug where sequences falsely called no variant if target is on the negative strand but positive strand reference given.

• Changed default SNV calling to 6 bases downstream instead of 5 to cover PAM

• Added tests for mismatched reference and target

Changes in version 1.5.8:

• Adds an option to filter variants by name when counting or plotting

Changes in version 1.5.7:

• Fixes major bug preventing filtering in plotFreqHeatmap

• Fixes bug in mergeChimeras if no chimeras mergeable

Changes in version 1.5.6:

• Autogenerate bam index for readsToTarget option chimeras = “ignore”

Changes in version 1.5.3:

• plotAlignments now accepts the same filtering arguments as variantCounts

Changes in version 1.5.1:

• New argument alleles in plotAlignments and plotFreqHeatmap for selecting which alleles to display or specifiying a plotting order

• Removed unnecessary fields from CrisprRun class

• New accessor function alns to get alignments from a CrisprSet

• Improvements to plotAlignments to avoid unnecessary symbols in legend

• Fix to header of plotFreqHeatmap when using type = “proportions” and providing sample order

• consensusSeqs now returns cigars as metadata by default

• Started indenting with four spaces at the start

csaw

Changes in version 1.11.4:

• Removed support for paramList objects.

• Added option for normOffsets() to return SummarizedExperiment objects containing normalization data.

• Deprecated normalize() to avoid S4 method clashes.

• Moved scaling prior to control-based filtering into a new function, scaleControlFilter(), for greater modularity.

• Updated user’s guide.

cydar

Changes in version 1.1.4:

• Added labelSpheres() function for labelling unannotated hyperspheres.

• Exported multiIntHist() for plotting multiple intensity histograms.

• Slight fix to spatialFDR(), which now computes the correct n-th nearest neighbour.

cytofkit

Changes in version 1.9.5 (2017-10-23):

MODIFICATIONS

• Standardise plot scales across samples in shiny App

BUG FIXES

• Fixed an issue with Phenograph failing if sampling with replacement was done. Now cytofkit tests if any FCS files have less events than specified in fixedNum argument.

Changes in version 1.9.4 (2017-09-27):

MODIFICATIONS

• Added function, cytof_clustermtrx(), to obtain marker expression values for cells in a given cluster.

• Included cytof_clustermtrx() into main cytofkit function.

• Cluster ID integers saved to fcs files as additional channels.

BUG FIXES

• Quick fix on FCS saving.

Changes in version 1.9.3 (2017-09-27):

MODIFICATIONS

• Added arguments to cytofkit() and cytof_cluster() to allow user to set a seed, for reproducible results.

BUG FIXES

• Users can now save .fcs from shiny output after renaming samples.

Changes in version 1.9.2 (2017-09-11):

MODIFICATIONS

• Added save data options for shiny app. Now you can select any combination of .fcs, .csv, and .rdata outputs.

• cytofkitShinyAPP() uses code from cytofkit_shinyAPP.R for visualisation on local machines, while ui.R and server.R can be used separately to host the app on servers.

BUG FIXES

• Fixed some issues with viewing and downloading the marker heatmap in the shiny app

• Fixed an inconsistency where expression data used for clustering was not selective for markers used for dimension reduction

Changes in version 1.8.3 (2017-09-06):

BUG FIXES

• cytofkitShinyAPP file size cap consistently set to 100mb

Changes in version 1.8.2 (2017-07-24):

NEW FEATURES

• cytofkitShinyAPP function now takes RData as argument to skip reuploading RData

• While choosing selected markers for dimension reduction and clustering, all markers can be visualised in the shiny app

• Added a “reset” button to ShinyApp to clear the session and start over

• Added Server file select button to allow browsing server files

MODIFICATIONS

• Combined both cytofkitShinyAPP functions into one

• ShinyApp uses actionButton for download instead of a downloadHandler

• ShinyApp displays what .RData is loaded into its reactive data

• ShinyApp lists markers in alphabetical order

• Marker selection done at dimensionality reduction stage rather than at raw data transformation, to allow all expression data to be visualised at later stages

• Updated examples and vignettes to account for updates done

• Updated maintainer email address

Changes in version 1.8.1 (2017-04-26):

NEW FEATURES

• fixed documentation warning for function cytofkitShinyAPP2

• updated my maintainer email address

DAPAR

Changes in version 1.9.15:

BUG FIXES

• When the aggregation step has been performed, the interface switches to the first tab of the ‘Descriptive Statistics’ in order to view informations aout the new dataset (the protein one).

• A new package (readxl) is used to read xls or xlxs files. In certain circumstances, the functions of the previsous package openxlsx is not able to decode properly Excel files.

• When converting a new (text or Excel) file in Prostar : the missing values were not registered as expected. Especially, they did not appear in blue in the table above the volcanoplot. Bug fixed

NEW FEATURES

• Implementation of a parallel version of the function which saves the (new) protein dataset after the aggregation step.

• Enhancement of the string-based filtering UI

• The automatic generation of an analysis report has been integrated in the Dataset Manager (menu ‘Export’). It allows the user to download plots and parameters used in Prostar ont their dataset.

• Implementation of a parallel version of the function which saves the (new) protein dataset after the aggregation step.

• Added a Gene Ontology (GO) analysis module in Data Processing. This module allows to perform GO grouping and GO Enrichment

• Several plots are now based on the package highcharter which is a wrapper to the highcharts graphical library. It provides interactivity with the user.

DASC

Changes in version 0.1.0:

• Requirements: Please install NMF, cvxclustr, Biobase R package before the installation of DASC package.

• Workflow: The function convexBatch() performs all steps for the detction of the batches in the dataset.

DChIPRep

Changes in version 1.7.2:

• added betaPrior = TRUE to nbinomWaldTest in order to keep the shrinkage of the log2 fold changes. (The shrinkage is now disabled by default in DESeq2)

• Changed R dependency to R 3.4

• Added WholeGenome Bioc View

Changes in version 1.7.1:

• extended the importing section in the vignette a little bit

• fixed the robust mean function so that now plotting also works without replicates

• new function robust_mean that is used in plotting

• when importing matrices, it is now checked that their column names correspond to the sample IDs given

debrowser

Changes in version 1.5.4:

• heatmap redblue fix

Changes in version 1.5.3:

• Figure caption fix

• Menu fix

Changes in version 1.5.2:

• img path build fix

deepSNV

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

Updates

• A few changes to shearwater vignette

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

Bugfixes

• Fixed bug in bf2Vcf() when no variant is called

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

Updates

• Updated CITATION

• Added verbose option to bam2R to suppress output

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

Bugfixes

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

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

Updates

• Using knitr for prettier vignettes

• Including shearwater vignette

Bugfixes

• fixed issues with deletions in bf2Vcf()

• makePrior() adds background on all sites

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

Updates

• New shearwater algorithm

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

DEGreport

Version: 1.13.12 Text: 2017-10-11 Lorena Pantano lorena.pantano@gmail.com Feature: Return scatter plots between PCs and metadata in degCovariates. Feature: Use ConsensusClusterPlus to cluster genes with degPatterns.

Version: 1.13.11 Text: 2017-09-22 Lorena Pantano lorena.pantano@gmail.com Feature: significant works with DESeqResults class. Fix: log2 in degPlot wasn’t active. Feature: Allow plot samples together or not in degCheckFactor. Feature: Migrate vignette to new BiocStyle. Fix: Automatic QC report. Reduce final report with most important figures.

Version: 1.13.10 Text: 2017-09-07 Lorena Pantano lorena.pantano@gmail.com Fix: Complete vignette with new functions. Feature: Add DEGSet construct to accept other sources. Feature: Adapt degQC to accept DEGSet object. Feature: Allow multiple group for degMB and degVB. Feature: Add optional log2 for gene plotting. Feature: Plot correlation of shrunken vs unshruken log2fc. Feature: Allow to plot original MA plot. Feature: Adapt summary of DESeq2Results to data.frame and compatible with markdown output, and multiple alpha values. Fix: links in man pages. Feature: Pass options to Heatmap in degCorCov.@vbarrera. Feature: Add parameter to select top rows from DEGset. Fix: Change method names to short words. Feature: degVolcano accepts DESeq2Results class. Fix: degPCA print the correct PC number on x/ylabels. Fix: Move NEWS to parent folder. Feature: Add method to get significant genes from DEGSet class. Feature: Add plotMA method to show shrunken effect. @vbarrera Fix: Move to testthat for examples. Feature: Adding main class and methods to handle DEG output. Fix: axis in degPCA now show the values. Feature: Handle multiple contrasts/coefficient for DESeq2 results.

Version: 1.13.7 Text: 2017-08-08 Lorena Pantano lorena.pantano@gmail.com Feature: new function to analyze the correlation among covaritaes in metatdata Deprecation: all functions related to foldchange accuraty are removed. Using lfcShrink much better now Style: Add more unit tests Feature: Accept SE like objects to degPlot and use better gene names if rowData has it Feature: Use plot_grid for degPattern and save plot Feature: Use text or point in degPCA Feature: Fix labels of degPlot Feature: Accept matrix in degPlot Fix: correctly handling rowData in SE objects for degPlot Fix: plot only legend if group > 1 Feature: More output for degPattern Style: change to lower-cases inside degCovariates function

Version: 1.13.6 Text: 2017-05-30 Lorena Pantano lorena.pantano@gmail.com Feature: Add degPCA plot from Rory Kirchner

Version: 1.13.5 Text: 2017-05-30 Lorena Pantano lorena.pantano@gmail.com Feature: Accept matrix for degWidePlot

Version: 1.13.4 Text: 2017-05-22 Lorena Pantano lorena.pantano@gmail.com Feature: Add degCovariates to calculate correlations between PCs from count data and covariates from metadata

Version: 1.13.3 Text: 2017-05-19 Lorena Pantano lorena.pantano@gmail.com Feature: Add degMDS for PCA like clustering figures Feature: Add labels parameters to degPlot

Version: 1.13.2 Text: 2017-05-05 Lorena Pantano lorena.pantano@gmail.com Feature: add degFilter to filter genes by group

Version: 1.13.1 Text: 2017-04-27 Lorena Pantano lorena.pantano@gmail.com Feature: change arrange for plotQC plots with cowplot Feature: Use theme_minimal inside degResults Feature: Change title for some sections in degResults

DEP

Changes in version 1.0.0:

• First release of the DEP package for differential enrichment analysis of proteomics data.

derfinder

Changes in version 1.11.8:

BUG FIXES

• Improved the documentation regarding an error when coverageInfo$position is NULL when running analyzeChr() [and indirectly running preprocessCoverage()]. See https://support.bioconductor.org/p/99400/ for details.

Changes in version 1.11.7:

SIGNIFICANT USER-VISIBLE CHANGES

• Vignette now uses the new BiocStyle::html_document that was recently released.

Changes in version 1.11.4:

BUG FIXES

• regionMatrix() will now pass the hidden arguments ‘species’ and ‘currentStyle’ to getRegionCoverage() so they can be used by extendedMapSeqlevels(). Related to https://support.bioconductor.org/p/95721/.

Changes in version 1.11.2:

BUG FIXES

• Improved documentation of extendedMapSeqlevels(). Related to https://support.bioconductor.org/p/95521/.

• Improved filterData() based on https://github.com/lcolladotor/derfinder/issues/38

derfinderHelper

Changes in version 1.11.2:

SIGNIFICANT USER-VISIBLE CHANGES

• Vignette now uses the new BiocStyle::html_document that was recently released.

derfinderPlot

Changes in version 1.11.2:

SIGNIFICANT USER-VISIBLE CHANGES

• Vignette now uses the new BiocStyle::html_document that was recently released.

DESeq2

Changes in version 1.18.0:

• lfcShrink() offers alternative estimators type=”apeglm” and type=”ashr”, making use of shrinkage estimators in the ‘apeglm’ and ‘ashr’ packages, respectively. See ?lfcShrink for more details and appropriate references. The integration of these alternative shrinkage estimators is still in development. Additionally, the DESeqResults object gains priorInfo(res), which passes along details of the fitted prior on LFC.

• Factor levels using characters other than letters, numbers, ‘_’ and ‘.’ will print a message (not a warning or error) that it is recommended to restrict to these “safe characters”. This follows a suggestion from the Bioconductor support site to avoid user errors.

DEsubs

Version: 1.3.4 Text: the package and the output in the landing page.

Version: 1.3.3 Text: Placed external figure importing within chunks.

Version: 1.3.2 Text:

Version: 1.3.1 Text:

DiffBind

Changes in version 2.6.0:

• Feature changes

  • Change sortFun parameter in dba.plotHeatmap to default sd, with FALSE as option for no sorting

  • Change sortFun parameter in dba.plotHeatmap to default sd, with FALSE as option for no sorting

  • Sort peaks when adding directly via dba.peakset

  • don’t add _ if no initString in dba.report

  • Internal feature: alternate peak counts: pv.resetCounts

• Bug Fixes

  • Fix bug in dba.plotHeatmap is all values in a row are zero

  • Change authors in vignette to conform to new standard

  • Fix single peak boundary conditions

  • Subset config$fragmentSize when masking

  • Update example peaks to match data objects

  • Fix bug in dba.plotHeatmap if all values in a row are zero

  • Bugfix when returning report as GRanges with only one site

  • Bugfix when plotting venns of consensus peaksets

  • Fix buffer overrun causing segfault on MacOS

diffHic

Changes in version 1.9.9:

• Added extractPatch() function to count bin pairs in a specified area of the interaction space.

• Modified connectCounts() to eliminate warnings upon stranded entries, unknown chromosomes. All entries of input regions are now retained, though not necessarily in the input order. Also switched original metadata to NA when second.regions is an integer.

• Modified preparePairs() to be more generous when considering inward-facing reads if they overlap past each other.

• Fixed bug in savePairs() involving failure to swap other information when enforcing index ordering.

• Added mergeCMs() function to allow entry into the pipeline from ContactMatrix objects.

• Moved pre-processing scripts out of the package to the repository for the user’s guide.

• Updated presplit_map.py to use new samtools API for sorting.

• Updated user’s guide.

diffuStats

Changes in version 1.0.0:

• Five diffusion kernels available, they can be computed from an ‘igraph’ object.

• Diffusion implementations divided between ‘diffuse_raw’ for deterministic scores and ‘diffuse_mc’ for permutation analysis, which is parallelised. In total, seven diffusion scores are accessible through the ‘diffuse’ function.

• Performance evaluation wrapped in the ‘perf’ function.

• Helper functions in helpers.R (to plot diffusion scores, to check if a kernel matrix is actually a kernel, to extract largest CC from a graph)

Director

Changes in version 1.3.1:

• Improved notice of discovered feedback loops.

• Added example input with feedback loop to manual.

DMCHMM

Changes in version 0.99.10:

CHANGES SINCE LAST TIME

• Several issues are fixed.

• Some modification are done to expedise the process.

• Instead of the parallel package, the BioParallel package is used.

Changes in version 0.99.9:

CHANGES SINCE LAST TIME

• Some parameters in examples are changed to make the running time faster.

• The BSData-method is changed to cBSData-method.

• The BSDMCs-method is changed to cBSDMCs-method. BUG FIXES

• None reported.

Changes in version 0.99.0:

IMPROVEMENTS SINCE LAST TIME

• We have refined some of the codes to speed up the running the package.

FUTURE DEVELOPMENT

• Some functions will be rewitten in C.

BUG FIXES

• None reported so far.

DOSE

Changes in version 3.3.2:

• new project site using blogdown <2017-09-28, Thu>

• ridgeplot for gseaResult <2017-08-17, Thu>

Changes in version 3.3.1:

• throw warning instead of error when fail to setReadable. <2017-06-28, Wed> + https://github.com/GuangchuangYu/clusterProfiler/issues/91

• better msg when using wrong ID types in GSEA <2017-06-01, Thu> + https://support.bioconductor.org/p/96512/#96516

EBImage

Changes in version 4.20.0:

NEW FEATURES

• ‘abind()’ method for combining Image arrays

• ‘floodFill()’ has been vectorized over its arguments ‘pt’ and ‘col’ allowing to specify multiple start points and different fill colors

SIGNIFICANT USER-VISIBLE CHANGES

• ‘display()’ “browser” mode has been updated to use the htmlwidgets infrastructure

• ‘filter2()’ does not require filter dimensions to be odd numbers when filter size equals image size

BUG FIXES

• fixed issues with ‘normalize()’ (https://github.com/aoles/EBImage/issues/25)

• various improvements to the ‘clahe()’ function

edgeR

Changes in version 3.20.0:

• DGEList() sets genes and counts to have same row.names.

• topTags() preserves row.names.

• estimateDisp() uses ‘y$design’ if it exists.

• estimateDisp() doesn’t use average log-CPM in the prior.df calculation if ‘trend.method’ is ‘none’.

• estimateDisp() doesn’t return trended.dispersion if ‘trend.method’ is ‘none’.

• Design matrix defaults to ‘y$design’ before ‘y$samples$group’ in all the gene set testing functions.

• New arg ‘group’ for mglmOneWay(). Results in slight speed improvement for glmFit().

• ‘design’ arg for predFC() is now compulsory.

• Switched ‘coef.start’ back to a vector in mglmOneGroup().

• New functions cpmByGroup() and rpkmByGroup().

• Renamed arg ‘x’ to ‘y’ in cpm() and rpkm().

• Restored null dispersion check in glmFit().

• Removed ‘offset’ arg from glmQLFit() to be consistent with glmFit().

• Exported CompressedMatrix subset operator.

• Refactored C++ code with greater C++11 support to use Rcpp.

• Streamlined input dimension checks in C++ code.

• Supported zero-row input to addPriorCounts() C++ code.

• Added cbind and rbind S3 methods for DGEList objects.

• Added ‘Dims’ as part of the compressedMatrix class.

• Added common methods for the compressedMatrix class.

• Register S3 methods for compressedMatrix.

• Added a case study of differential methylation analysis to the user’s guide.

EGSEA

Changes in version 1.5.6 (2017-09-11):

• modified: GSVA invokation due to changes from GSVA developers on the return value and arguments

Changes in version 1.5.5 (2017-08-24):

• fixed: bug in egsea.ora where interpret files not generated correctly.

• fixed: summary plot based on ranking when using egsea.ora

• Renamed: entrezIDs in egsea.ora into geneIDs

• fixed: bug in egsea.ora when ‘title’ includes white spaces or special characters

• fixed: several minor bugs

Changes in version 1.5.4 (2017-08-10):

• changed: entrezIDs into geneIDs in buildCustomIdx and buildGMTIdx.

Changes in version 1.5.3 (2017-07-20):

• Replaced: underscore characters and dots with dashes in vignette, gsaplots.R and htmlUtils.R

Changes in version 1.5.2 (2017-07-18):

• changed: method name from getlogFCFromLMFit to runStandardLimmaDEA

• fixed: a minor bugin buildKEGGIdx

• Added: votep to combining p-values

• Changed: egsea.dir into report.dir

• Replaced: print statements with message, warning, stop where appropriate.

• Added: interactive stats table and interactive summary plots.

• Added: parameter ‘interactive’ to egsea main functions, generateReport and plotSummary

• Modified: vignette so that images that are not generated are replaced with a warning message

Changes in version 1.5.1 (2017-04-11):

• Merged: the documentation of relevenat functions into one help page

• Added: a function buildGMTIdx to build gene set collection index from a GMT file

• Added: a new function named egsea.ma to work with Microarray dataset

• Modified: egsea functions to generate all the pairwise comparisons (contrasts) when the contrast parameter is NULL. This is mainly done based on the primary factor of the design matrix that is defined by ‘group’ parameter or column in voom.results$targets$group.

ENmix

Changes in version 1.13.9:

• getBeta: bugfix for handling large dataset

Changes in version 1.13.7:

• updated User’s guide

Changes in version 1.13.6:

• corrected User’s guide

Changes in version 1.13.4:

• bug fix

Changes in version 1.13.3:

• add pipeline function mpreprocess

• bug fix

Changes in version 1.12.1:

• bug fix

• bug fix

EnrichedHeatmap

Changes in version 1.7.1:

• show_row_names is put in the function argument list

• we don’t use a position with 0 (either +1 or -1)

• add dist_by_closeness()

• add extract_anno_enriched()

• add ticks on axes

• add a new vignette (compare row ordering methods)

EnrichmentBrowser

Changes in version 2.8.0:

• Major migration from ExpressionSet to SummarizedExperiment

ensembldb

Changes in version 2.1.12:

BUG FIXES

• Use new defaults from the IRanges package for arguments maxgap = -1L, minoverlap = 0L in transcriptsByOverlaps and exonsByOverlaps methods.

• Remove RSQLite warnings (issue #54).

Changes in version 2.1.11:

BUG FIXES

• ensDbFromGtf failed to parse header for GTF files with more than one white space.

Changes in version 2.1.10:

USER VISIBLE CHANGES

• supportedFilters returns a data frame with the filter class name and corresponding field (column) name.

Changes in version 2.1.9:

NEW FEATURES

• Support for global filters in an EnsDb object.

• Add filter function.

Changes in version 2.1.8:

NEW FEATURES

• New annotations available in EnsDb objects: gene.description and tx.tx_support_level.

• New TxSupportLevelFilter object.

EpiDISH

Changes in version 0.99.0:

• Initial submission to Bioconductor.

• Added NEWS file.

• Added constraint mode parameter in CP mode.

epiNEM

Version: 2017.01 Category: Github made public and submitted to Bioconductor Text:

epivizrChart

Changes in version 0.99.0:

• Bioc Devel Release

epivizrData

Changes in version 999.999:

• This NEWS file is only a placeholder. The version 999.999 does not really exist. Please read the NEWS on Github: <URL: https://github.com/epiviz/epivizrData>

epivizrServer

Changes in version 999.999:

• This NEWS file is only a placeholder. The version 999.999 does not really exist. Please read the NEWS on Github: <URL: https://github.com/epiviz/epivizrServer>

epivizrStandalone

Changes in version 999.999:

• This NEWS file is only a placeholder. The version 999.999 does not really exist. Please read the NEWS on Github: <URL: https://github.com/epiviz/epivizrStandalone>

esATAC

Version: 1.0.0 Category: INITIAL RELEASE Text:

Version: 1.0.0 Category: Preset pipelines are available for case study and case-control study Text:

Version: 1.0.0 Category: All basic elements in preset pipeline are available for building customized pipeline. Text:

ExperimentHub

Changes in version 1.4.0:

NEW FEATURES

• ExperimentHub will now work offline utilizing argument ‘localHub’; will also use this option automatically if no internet connection is detected.

• Add new vignette for creating ExperimentHub packages

MODIFICATIONS

• Update AnnotationHub dependency; new resource class RDSResource

• move listResources and loadResources from AnnotationHub to here

BUG FIXES

• Fix typo in createHubAccessors with hard coded value

ExperimentHubData

Changes in version 1.4.0:

MODIFICATIONS

• Moved vignette to ExperimentHub as more practical use there; created new vignette

• Allow specification of metadata file in inst/extdata to be used

BUG FIXES

• updated addResources

FamAgg

Changes in version 1.5.3:

SIGNIFICANT USER-VISIBLE CHANGES

• plotPed with haplopaint plotting supports device = “txt” that just writes the data.frame for haplopaint and returns the file name, does however not call Haplopaint.

Changes in version 1.5.2:

NEW FEATURES

• New binomial test implemented (binomialTest and FABinTestResults object).

GA4GHclient

Changes in version 1.2:

BUG FIXES

• Fix bug due to changes in dplyr package

gage

Changes in version 2.27.3:

• fixed bug in kegg.gsets function, which cause error when species=”ko” (KEGG Orthology).

Changes in version 2.27.1:

• major expansion in korg, which now include both KEGG and NCBI taxonomy IDs, two more gene ID types, i.e. NCBI protein and uniprot IDs. In addition, Entrez or NCBI Gene IDs are discontinued for most prokaryotes.

• korg now include 4800 KEGG species, in the meantime, an updated version of korg is now checked out from Pathview Web server each R session when kegg.gsets function is called the first time. version 2.20.1

• updated RNA-seq workflow vignette, especially step 1 summarizeOverlaps, and correct tophat web link. version 2.19.1

• updated gage main vignette and RNA-seq workflow vignette. Add reminder on species and gene ID data consistence check to the former, and correct Cufflinks output format and web link. version 2.17.2

• updated khier to included newly added reference pathways. kegg.gsets can work with 397 pathways now. version 2.15.5

• updated korg to included over 80 newly added species, such as sheep, apple, mandarin orange etc. Pathview can work with 3050 species now. version 2.14.3

• revised the internal function gs.heatmap as to allow margin sizes ajustment for gene set heatmaps directly or through sigGeneSet. version 2.14.1

• revised “RNA-Seq Data Pathway and Gene-set Analysis Workflows” to reflect summarizeOverlaps() migration to GenomicAlignments package for Bioc 2.14. version 2.13.5

• add function go.gsets, which generates up-to-date GO gene sets for 19 common species annotated in Bioconductor and more others by the users. version 2.13.3 (2.12.3)

• updated korg to included over 600 newly added species. kegg.gsets can work with 2970 species now.

• fixed typos in joint workflows with Cufflinks (page 13): range(exp.fc) to range(cuff.fc) version 2.12.2

• fixed typos in joint workflows with DESeq2 (page 11): cnts.kegg.p should be fc.kegg.p

gdsfmt

Changes in version 1.14.0:

• tweak error message

GeneNetworkBuilder

Changes in version 1.19.1:

• Fix the problem when STRINGdb not work.

GENESIS

Changes in version 2.7.4:

• In fitNullMM, for Binomial and Poisson GLM families, the variance of the fixed effects will not be multiplied by the dispersion parameter RSS.

Changes in version 2.7.3:

• Change defaults in assocTestSeq*: Davies method for SKAT p-values, flat weights.

geneXtendeR

Changes in version 1.3.5:

• Remove deprecated README.

Changes in version 1.3.4:

• Update citation.

Changes in version 1.3.3:

• New peaksMerge() function.

Changes in version 1.3.2:

• New allPeakLengths() function.

Changes in version 1.3.1:

• New cumulative line plot (cumlinePlot()) function.

• Output to distinct() function is a lot more visually appealing now (no more tab delimiter signs), yay!

• New differential gene ontology (diffGO()) function.

• New gene-GO network (makeNetwork()) function.

• New GO word cloud (makeWordCloud()) function.

• New barplot function for plotting word frequencies found within GO terms (plotWordFreq()).

• New significant/total peaks (hotspotPlot()) function.

• Add new meanPeakLength(), meanPeakLengthPlot(), and peakLengthBoxplot() functions.

GENIE3

Version: 0.99.4 Text: Removed argument “seed”, use set.seed instead Minor improvemtents

Version: 0.99.2 Category: INTERFACE CHANGES Text: Functions and parameters renamed to CamelCase rather than containing dots (e.g. get.link.list into getLinkList)

Version: 0.99.2 Category: NEW FEATURES Text: GENIE3 now accepts ExpressionSet, SummarizedExperiment and SCESet as input

genomation

Version: 1.9.7 Category: IMPROVEMENTS AND BUG FIXES Text: bug fix relating to calculation of the last bin in scoreMatrixBin function for bin.op = “max” (https://github.com/BIMSBbioinfo/genomation/issues/166)

Version: 1.9.7 Category: Implemented by Bozena Mika-Gospodorz Text:

Version: 1.9.6 Category: IMPROVEMENTS AND BUG FIXES Text: bug fix relating to calculation of the last bin in scoreMatrixBin function (https://github.com/BIMSBbioinfo/genomation/issues/166)

Version: 1.9.6 Category: Implemented by Bozena Mika-Gospodorz Text:

Version: 1.9.5 Category: NEW FUNCTIONS AND FEATURES Text: enrichmentMatrix() function computes an enrichment of IP sample over IgG or input DNA control sample (issue: https://github.com/BIMSBbioinfo/genomation/issues/138)

Version: 1.9.5 Category: IMPROVEMENTS AND BUG FIXES Text: removed a requirement of having a ‘chr’ string in chromosome names in checkBedValidity() function (issue: https://github.com/BIMSBbioinfo/genomation/issues/160)

Version: 1.9.5 Category: Implemented by Bozena Mika-Gospodorz Text:

Version: 1.9.4 Category: NEW FUNCTIONS AND FEATURES Text: C++ functions that create a matrix storing data with desirable number of bins for each window: - listSliceMean() - calls the binMean() function, - listSliceMedian() - calls the binMedian(), - listSliceMax() - calls the binMax(), - listSliceMin() - calls the binMin(), - listSliceSum() - calls the binSum().

Version: 1.9.4 Category: NEW FUNCTIONS AND FEATURES Text: C++ functions that compute the value for each bin: - binMean() - computes a mean value, - binMedian() - computes a median value, - binMax() - computes a maximum values, - binMin() - computes a minumum values, - binSum() - computes a sum value.

Version: 1.9.4 Category: NEW FUNCTIONS AND FEATURES Text: C++ function Median_c() - computes a median value from a vector.

Version: 1.9.4 Category: Implemented by Bozena Mika-Gospodorz Text:

Version: 1.9.3 Category: IMPROVEMENTS AND BUG FIXES Text: tests for different parameter combinations for ScoreMatrixBin

Version: 1.9.2 Category: NEW FUNCTIONS AND FEATURES Text: c() function to append a ScoreMatrix as well as a ScoreMatrixList to an existing ScoreMatrixList (issue: https://github.com/BIMSBbioinfo/genomation/issues/151). Implemented by Bozena Mika-Gospodorz.

Version: 1.9.2 Category: IMPROVEMENTS AND BUG FIXES Text: added a slot “names” to a ScoreMatrixList class

Version: 1.9.1 Category: IMPROVEMENTS AND BUG FIXES Text: The knitrBootstrap dependecy is removed and following issues are fixed - https://github.com/BIMSBbioinfo/genomation/issues/135 - https://github.com/BIMSBbioinfo/genomation/issues/146 - https://github.com/BIMSBbioinfo/genomation/issues/147

GenomeInfoDb

Version: 1.14.0 Category: NEW FEATURES Text:

Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text:

Version: 1.14.0 Category: DEPRECATED AND DEFUNCT Text: Remove ‘force’ argument from seqinfo() and seqlevels() setters (the argument got deprecated in BioC 3.5 in favor of new and more flexible ‘pruning.mode’ argument).

Version: 1.14.0 Category: BUG FIXES Text: Add missing Y/chrY entry in seqlevel style db for Drosophila melanogaster and Rattus norvegicus.

GenomicAlignments

Changes in version 1.14.0:

SIGNIFICANT USER-LEVEL CHANGES

• makeGAlignmentPairs() no more drops pairs with discordant seqnames.

• Change ‘maxgap’ and ‘minoverlap’ argument defaults in methods of the findOverlaps() so they adhere to the new argument defaults of the generic defined in IRanges 2.12.0. See NEWS file in the IRanges package for more information about this change.

DEPRECATED AND DEFUNCT

• Remove ‘force’ argument from seqinfo() and seqlevels() setters (the argument got deprecated in BioC 3.5 in favor of new and more flexible ‘pruning.mode’ argument).

BUG FIXES

• Fix bug in pairing code of readGAlignmentPairs() when one mate in a pair is lost because of user-supplied filtering (e.g. mapqFilter=10).

GenomicFeatures

Changes in version 1.30:

NEW FEATURES

• Add makeTxDbFromEnsembl() for creating a TxDb object by querying directly an Ensembl MySQL server. This seems to be faster and more reliable than makeTxDbFromBiomart().

• Improve makeTxDbFromBiomart() support for EnsemblGenomes marts fungal_mart, metazoa_mart, plants_mart, and protist_mart.

• makeTxDbFromGFF() and makeTxDbFromGRanges() now import the CDS phase. This required a change in the schema of the underlying SQLite db of TxDb objects. This is still a work-in-progress e.g. cdsBy(txdb, by=”tx”) still needs to be modified to return the phase info.

SIGNIFICANT USER-VISIBLE CHANGES

• The *ByOverlaps() functions now use the same ‘maxgap’ and ‘minoverlap’ defaults as subsetByOverlaps().

DEPRECATED AND DEFUNCT

• Remove ‘force’ argument from seqinfo() and seqlevels() setters (the argument got deprecated in BioC 3.5 in favor of new and more flexible ‘pruning.mode’ argument).

BUG FIXES

• exonicParts() and intronicParts() are now documented.

• Address a couple of issues pointed out by Matt Chambers in internal helpers get_organism_from_Ensembl_Mart_dataset() and .extractEnsemblReleaseFromDbVersion() used by makeTxDbFromBiomart().

• Fix internal utility .Ensembl_getMySQLCoreDir(). Was failing for some of the 69 datasets from the Ensembl mart, causing makeTxDbFromBiomart() to fail loopking up the organism scientific name and the chromosome lengths. Thanks to Matt Chambers for reporting this.

• Some tweaks and fixes needed to support RSQLite 2.0.

GenomicRanges

Changes in version 1.30.0:

NEW FEATURES

• Support GPos-based GRangesList objects.

• Add ‘na.rm’ argument to binnedAverage().

SIGNIFICANT USER-LEVEL CHANGES

• Change ‘maxgap’ and ‘minoverlap’ defaults for findOverlaps() and family (i.e. countOverlaps(), overlapsAny(), and subsetByOverlaps()). This change addresses 2 long-standing issues: (1) by default zero-width ranges are not excluded anymore, and (2) control of zero-width ranges and adjacent ranges is finally decoupled (only partially though). New default for ‘minoverlap’ is 0 instead of 1. New default for ‘maxgap’ is -1 instead of 0. See ?findOverlaps for more information about ‘maxgap’ and the meaning of -1. For example, if ‘type’ is “any”, you need to set ‘maxgap’ to 0 if you want adjacent ranges to be considered as overlapping.

• GPos now extends GRanges but with a ranges slot that must be an IPos object. Update “old” GPos objects with updateObject().

• Move pos() generic to IRanges package.

• Move rglist() generic to IRanges package.

• Rename GenomicRangesORmissing and GenomicRangesORGRangesList classes -> GenomicRanges_OR_missing and GenomicRanges_OR_GRangesList, respectively.

• Remove “seqinfo” method for RangesList objects.

• Remove “stack” method for GenomicRangesList objects.

DEPRECATED AND DEFUNCT

• Remove ‘force’ argument from seqinfo() and seqlevels() setters (the argument got deprecated in BioC 3.5 in favor of new and more flexible ‘pruning.mode’ argument).

BUG FIXES

• nearest() and distanceToNearest() now call findOverlaps() internally with maxgap=0 and minoverlap=0. This fixes incorrect results obtained in some situations e.g. in the situation reported here: https://support.bioconductor.org/p/99369/ (zero-width ranges) but also in this situation: nearest(GRanges(“chr1”, IRanges(5, 10)), GRanges(“chr1”, IRanges(1, 4:5)), select=”all”) where the 2 ranges in the subject are both nearest to the 5-10 range.

• ’$’ completion on GenomicRanges works in RStudio.

• Minor tweaks to conversion from character to GRanges and reverse conversion.

GenomicScores

Changes in version 1.2.0:

USER VISIBLE CHANGES

• Added methods ‘name()’ and ‘type()’ for GScores objects.

• Enabled the retrieval of multiple score values per genomic position (e.g., as in CADD or M-CAP scores).

• Added method ‘citation()’ to fetch citation information for genomic scores.

• Added function ‘makeGScoresPackage()’ to create an annotation package from an AnnotationHub genomic scores resource.

• Added ‘qfun()’ and ‘dqfun()’ methods to fetch the quantization and dequantization functions from used to store and retrieved genomic scores.

• Added ‘quantized’ argument to the ‘scores()’ method to obtain quantized values if the user wants to dequantize the values him or herself.

• Fallback to local AnnotationHub when there is no internet connection to fetch genomic scores through AnnotationHub resources.

• Added ‘MafDb’ class, derived from ‘GScores’ to store and access minor allele frequency values. This was originally defined in the ‘VariantFiltering’ package.

• The vignette has been updated to illustrate the use of some of the previous changes.

GEOquery

Version: 2.45.2 Text: Improvements: * GPL parsing 4-5x faster * GSM parsing 3x faster * GSEMatrix parsing is much smarter with respect to sample characteristics. In short, for GSEs where sample characteristics are actually used, the pData should have nice, neat column headers with the phenodata keys and values in the columns, including correct handling of missing values, etc.

Version: 2.45.1 Text: Bug fixes * getDirectoryListing fixed to deal with changes to NCBI server listing formats

Version: 2.45 Text: Improvements: * GDS parsing is 2-3x faster * GSEMatrix parsing is 2-3x faster

ggcyto

Version: 1.5.5 Category: add data replacement feature through %+% operator Text:

ggtree

Changes in version 1.9.4:

• geom_hilight_encircle and geom_cladelabel2 <2017-09-12, Tue> + https://github.com/GuangchuangYu/ggtree/pull/152

• set_hilight_legend <2017-08-30, Wed>

• geom_motif for aligned motif <2017-08-22, Tue> + https://github.com/GuangchuangYu/ggtree/issues/148

• fixed R CMD build error: cannot stat ‘ggtree/site_src/themes’: No such file or directory <2017-08-22, Tue>

Changes in version 1.9.3:

• update to using !! in tidyr::gather for compatible with tidyr 0.7.0 <2017-08-03, Thu>

• now geom_text2, geom_label2, geom_point2 and geom_segment2 work with ggplot2 <2017-08-01, Tue>

• update fortify.jplace to support number of placement (nplace) <2017-07-27, Thu>

Changes in version 1.9.2:

• add bg_line and height parameter in msaplot <2017-07-26, Wed> + use can set bg_line = FALSE and height = 1 to plot more beautiful alignment

• extend parameter in geom_cladebar <2017-07-26, Wed> + https://github.com/GuangchuangYu/ggtree/issues/142#issuecomment-317817995

• scaleClade works after calling viewClade <2017-07-20, Thu> + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/bioc-ggtree/QVSryszPaFY

• gheatmap support handling collapsed tree <2017-06-29, Thu> + https://github.com/GuangchuangYu/ggtree/issues/137

Changes in version 1.9.1:

• now mapping parameter will passed to segment layer in geom_tiplab(align=T) <2017-06-19, Mon>

• geom_cladelabel support angle="auto" for circular layout tree <2017-05-05, Fri>

Glimma

Changes in version 1.6.0:

• Added table to MDS plot.

• Changed encoding of javascript data to be more compact

• Fixed handling of top and gene.selection parameters in glMDSPlot

GoogleGenomics

Changes in version 2.0.0:

gRPC support and more authentication options

• Can use gRPC to access the entire method set in v1 API.

• Support for application default credentials.

• Support for GCE service account credentials.

GOSemSim

Changes in version 2.3.1:

• new project site using blogdown <2017-09-28, Thu>

• speed up by pre-calculating GO similarities <2017-05-22, Mon> + contributed by Lluís Revilla Sancho + https://github.com/GuangchuangYu/GOSemSim/pull/13

graphite

Changes in version 1.23.7 (2017-10-19):

• Provide the URL of each pathway in its original database.

• New vignette describing pathway analysis of metabolic activities.

Changes in version 1.23.6 (2017-10-18):

• Removed DEGraph support.

Changes in version 1.23.5 (2017-10-13):

• runClipper gains an option to set the seed for random number generation.

Changes in version 1.23.3 (2017-10-12):

• Metabolites in pathways.

• Multiple views of each pathway: proteins only, metabolites only or both.

• New databases: SMPDB and PharmGKB.

• Removed support for RCytoscape (by default, use RCy3).

• Conversion of metabolite identifiers.

• Faster conversion of idenfiers on multicore systems.

GraphPAC

Changes in version 1.19.1:

• Url corrections for new pdb.org website file structure.

GRmetrics

Changes in version 1.3.3:

• Renamed column “GR” to “GRvalue” for GR value table to match other code.

• Fixed erroneous error message in division rate GR value calculation

Changes in version 1.3.2:

• Renamed some curve parameters for the relative cell count curve

• changed “IC” to “rel_cell”.

• Changed GRdrawDRC function parameter option for dose response curves based on relative cell counts from ‘metric = “IC”’ to ‘metric = “rel_cell”’.

• Changed GRinf (and Einf) value to the minimum of the mean GR values (relative cell count) at the two highest concentrations tested for the case of horizontal line fits (same as GRmax).

• Changed GRmax (and Emax) so that in the case of averaging over multiple conditions, the value taken is the minimum of the mean of GR values (relative cell count) at the two highest concentrations instead of the absolute minimum GR value at these concentrations.

• “duration” column in input changed to “treatment_duration” to match the nomenclature in other code.

• Added calculation of GR values from division rates for Case “C”

Changes in version 1.3.1:

• Added calculation of GR values from division rates for Case “A”

• now accepts columns “duration” and “division_time” instead of “cell_count__time0”

• Added a few parameters to calculation

• “control_cell_doublings” is the number of cell doublings that occur in the control population over the assay, calculated either from initial and final cell counts or given division rate and time of assay.

• “concentration_points” is the number of different concentrations used in an experiment

GSEABase

Changes in version 1.39:

BUG FIXES

• goSlim() did not correctly count duplicate identifiers. (https://support.bioconductor.org/p/100403/)

GSVA

Changes in version 1.26:

USER VISIBLE CHANGES

• Updated implementation of the option ‘abs.ranking=TRUE’ to use the original Kuiper statistic.

• Arguments ‘rnaseq’ and ‘kernel’ have been deprecated and replaced by a new argument ‘kcdf’.

• Arguments ‘no.bootstraps’ and ‘bootstrap.percent’ have been deprecated.

• The return value with the default argument ‘method=”gsva”’ has been simplified and it is not a list object anymore. Now the ‘gsva()’ function return always a matrix or an ‘ExpressionSet’ object, when the input expression data is also an ‘ExpressionSet’ object.

• The ‘gsva()’ function can now be used through a shiny app that runs through the function ‘igsva()’.

gtrellis

Changes in version 1.9.1:

• Functions in GenomicRanges are imported

GWASTools

Changes in version 1.23.2:

• Add a function to coerce a GenotypeData object to a VCF object for use with VariantAnnotation.

Changes in version 1.23.1:

• Move ncdf4 from Imports to Suggests. Users who wish to use NetCDF files instead of GDS will have to install the ncdf4 package separately. This change eliminates the requirement to install the NetCDF library on Linux machines for users who plan to use GDS only.

Heatplus

Changes in version 2.23.1:

• Resolved issue with inconsistent plotting on the same device

hiAnnotator

Changes in version 1.11.1:

• GenomicRanges package update adjustments & improved tests

HIBAG

Changes in version 1.14.0:

• modify the kernel to support the GPU extension

• add matching proportion to measure the similarity of SNP haplotypes between training and test datasets

• new function hlaReportPlot()

• the argument ‘cl’ in predict.hlaAttrBagClass(), hlaPredict() and hlaParallelAttrBagging() allows a numeric value for the number of cores

HiTC

Changes in version 1.21.0:

BUG FIXES

• Fix bug in getExpectedCountsMean for non-symmetrical data

• Deal with NA in getPearson function

• Fix bug in normLGF leading to non symmetrical matrices

hpar

Changes in version 1.19.1:

• Re-generate data sets from scripts/getHpaData.R, as discrepancies with the data downloaded form the hpa site were documented by Martin Bush <2017-07-19 Wed>

Changes in version 1.19.0:

• new Bioconductor devel

iCOBRA

Changes in version 1.5.5:

• The default selection of the measure to use for ROC and FP curves have been changed to improve consistency. Now, the preferred order is pval, padj, score. The behaviour of previous versions can be obtained by setting prefer_pval = FALSE in calculate_performance(). Note that the type of measure that is used to calculate a certain performance value can be retrieved from the respective slots of the COBRAPerformance and COBRAPlot objects.

• Improved robustness in selection of measure to use for FDR/TPR and FDR/NBR curves, especially for methods where both p-values and scores are available.

• Additional validity checks for pval and padj slots

Changes in version 1.5.1:

• Added support for false sign rate calculations

immunoClust

Version: 1.9.2 Text: CHANGES * Optional label parameter in meta-clustering to continue the meta-clustering with an initial cluster to meta-cluster assignment

Version: 1.9.1 Text: CHANGES * Minor improvements and additional option in plot and splom methods * Introduce of ALPHA option also for normalization precedures

intansv

Changes in version 1.17.1:

Notes

• Fix a small bug in function methodsMerge.

Changes in version 1.17.0:

Notes

• Update to the latest version of different tools.

InteractionSet

Changes in version 1.5.7:

• Removed c() method for InteractionSet, rbind method for GInteractions.

• Generalized ContactMatrix to allow any type of matrix-like object.

• Supported inflate() for GInteractions without specifying fill. Changed default fill for InteractionSet to missing.

• Separated subsetting and combining documentation into two different pages.

• Added convenience wrappers for resize(), narrow() and shift() on the GenomicRanges slot in all objects.

• Modified anchors() to return a list rather than GRangesList.

• Modified width() for GInteractions to return a list() rather than a DataFrame(). Also changed names of list element.

• Added the anchorIds() function for rapid extraction of anchor IDs.

• Removed the requirement for identical regions in pcompare() and match().

IntEREst

Changes in version 1.2.0:

NEW FEATURES

• DEXSeqIntEREst() runs DEXSeq differential exon usage or intron retention test on the SummarizedExperiment objects (resulted from interest() or interest.sequential() analysis).

• unionRefTr() performs union on the genes in reference data frame with overlapping introns/exons. The resulted data frame features from each repeating exon or intron a single copy only.

• deseqInterest() runs differential intron retention test adapted from the DESeq2 package.

• interestResultIntEx() builds a SummarizedExperiment object from an intron retention and an exon-exon junction object (resulted from interest(), interest.sequential() and/or InterestResult() functions). The average of the junction levels of the flanking exons are added to the SummerizedExperiment with the intron retention values.

SIGNIFICANT USER-VISIBLE CHANGES

• u12Index() supports intronExon parameter that provides the possibility to extract either the rows that represent the U12-type introns or the exons flanking to the U12-type introns from a SummerizedExperiment object.

BUG FIXES

• Correcting interestAnalyse.R and interestAnalyse.sequential.R so that interest() and interest.sequential() support bam files with single (unpaired) reads.

• Correct bpparam setting in interest().

iPAC

Changes in version 1.20.1:

• Url corrections for new pdb.org website file structure.

IPO

Changes in version 1.7.5:

• added usage of clustering method FORK on unix-systems (thanks to Pablo Moreno)

• fixed bug in parallelization to prevent conflicts with package ‘snow’

Changes in version 1.7.4:

• preceded parallel-functions with ‘parallel::’ to use right package

• fixed bug in function writeRScript using ‘loess’ retention time cor.

• decreased runtime for R CMD check IPO

Changes in version 1.7.3:

• added runnable examples

• decreased size of pictures in vignettes/rsmDirectory

• decreased runtime for unit-tests

• replaces expand.grid with expand.grid.subset (in utils.R)

Changes in version 1.7.2:

• bugfix: try to prevent error in calcPPS possibly caused by NAs

• replaced cat() and print() calls with message()

Changes in version 1.7.1:

• checking correlation of peak-shape with sinus curve (-pi/2 to pi*1.5), normal distribution or checkBorderIntensity

• findIsotopes.IPO renamed parameter checkBorderIntensity to checkPeakShape

• performance improvement calcPPS for checkPeakShape=FALSE

• calculating xcmsSet-object and respective PPS for each DoE. (PPS is not estimated from rsm anymore)

• additionally forwarding nSlaves for xcmsSet-function (also see getDefaultXcmsSetStartingParams())

Changes in version 1.7.0:

• added support for XCMS-method retcor.loess

• updated help files

• changed return value of getRGTVValues

• adapted unit tests

• parameter scanrange for XCMS-methods findPeaks can be set but not optimized

Changes in version 1.6.2:

• Updated the function getNormalizedResponse() to prevent NAs

Changes in version 1.6.1:

• Added installation script and installation description in vignette

Changes in version 1.6:

• Added support of CAMERA isotope identification (findIsotopes.CAMERA)

• selectivity of findIsotopes.IPO may be increased if checkBorderIntensity is set to TRUE: ‘maxo’ of each peak of an isotopologue must be three times higher than the intensities at ‘rtmin’ and ‘rtmax’

• simplified return value of calcPPS() to vector with meaningful names

• changed getDefaultXcmsSetStartingParams() for min_peakdwidth = c(12, 28) and for ppm to c(17, 32)

Changes in version 1.5.7.1:

• using predict() to identify best levels and expand.grid to generate testdata for model

Changes in version 1.5.7:

• supporting single parameter optimization. Only basic version with redundant levels in consecutive DoEs

• removed integer-rounding in maximum focusing for all findPeaks parameters except prefilter(I) and steps

• Update documentation to match code

• Remove use of getwd() preventing absolute subdir paths

Changes in version 1.5.6:

• updated vignette

• generally using Central-Composite design instead of Box-Behnken design

• fixed bug when defining subdir=NULL in functions optimizeXcmsSet and optimizeRetGroup

• modified unit tests to handle versions > 1.5.6

• added function writeRScript to NAMESPACE export

• updated man for optimizeXcmsSet and optimizeRetGroup

Changes in version 1.5.5:

• increased recall of reliable peaks in calcPPS. Changed exponent for PPS calculation from 1.5 to 2

Changes in version 1.5.4.8:

• remove file lookup in optimizeXcmsSet, and leave that to xcmsSet()

Changes in version 1.5.4.7:

• explicitely use serial evaluation if nSlaves=1, to help debugging

Changes in version 1.5.4.6:

• remove dependency on Rmpi

Changes in version 1.5.4.5:

• added examples from msdata

• fix Depends, imports and library() and require() calls

Changes in version 1.5.4.4:

USER VISIBLE CHANGES

• packaged script

• changed method name attachparams to attachList

• changed method name calculateRGTV to getRGTVValues

• changed method name getDefaultStartingXcmsParams to getDefaultXcmsSetStartingParams

• changed method name typeCastFactor to typeCastParams

• changed method name writeRSkript to writeRScript

• changed the parameter name n_slaves to nSlaves

• resultIncreased: if last optimization score was 0, no isotopes have been found hence the dataset is not optimizable with IPO.

• added man files for attachList, calcPPS, combineParams, createModel, decode, decodeAll, encode, getBbdParameter, getCcdParameter, getDefaultRetCorCenterSample, getDefaultRetGroupStartingParams, getDefaultXcmsSetStartingParams, getNormalizedResponse, getRGTVValues, IPO-package, optimizeRetGroup, optimizeXcmsSet, startSlaves, toMatrix, typeCastParams

• removed xcmsSetsettingsAsString.R

• getResponses: now able to handle NULL value for slices parameter

• calcPPS: peaks with NA values are removed before isotopes identification

• if subdir is NULL, no rsm’s are saved

• optimizeXcmsSet: lowere minimum value for min_peakwith from 5 to 3 #IPO_V1.5.4.3: * LIP calculation in calcPPS fixed #IPO_V1.5.4.2: * added initial parameter check # * renamed all factor-variables to params # * in optimizeXcmsSet: - also look for mzML-files # - check if files were found # * bug in optimization for matchedFilter fixed; sigma and mzdiff have to be # definded later (combineFactors()) when sigma and step as well as steps are already known #IPO_V1.5.4.1: changes in calcPPS: # rt_window <- rt * 0.005 # rt_lower <- part_peaks[,”rt”] - rt_window # rt_upper <- part_peaks[,”rt”] + rt_window #IPO_V1.5.4: if bad_group == 0; bad_group = 1 && good_group += 1 #IPO_V1.5.3: no parameter for isotope detection. # c13_peak[,”mz”] has to be within (mzmin + isotope_mass) and (mzmax + isotope_mass) # c13_peak[,”rt”] has to be within (rtmin + isotope_mass) and (rtmax + isotope_mass) #IPO_V1.5.: in RCSandGSIncreased: also used good_groups ^ 2 #IPO_V1.4.: vectorized isotope identification; # no intensity window, between intensity of max carbon and 1 #IPO_V1.3.: good_groups ^ 2 to increase recall

Changes in version 1.3.3:

User visible

• new plot-parameter for optimizeXcmsSet and optimizeRetGroup to control plotting (#51)

Changes in version 1.3.2:

• bug fix #50: correct peaks-matrix, to handle xcms bug (sneumann/xcms#220) for older xcms-versions

• test order of parameters to optimize

Changes in version 1.3.1:

• bug fix regarding conflict of BPPARAM and nSlaves arguments (thx to @lauzikaite)

IRanges

Changes in version 2.12.0:

NEW FEATURES

• Add IPos objects for storing a set of integer positions where most of the positions are typically (but not necessarily) adjacent.

• Add coercion of a character vector or factor representing ranges (e.g. “22-155”) to an IRanges object, as well as “as.character” and “as.factor” methods for Ranges objects.

• Introduce overlapsRanges() as a replacement for “ranges” methods for Hits and HitsList objects, and deprecate the latter.

• Add “is.unsorted” method for Ranges objects.

• Add “ranges” method for Ranges objects (downgrade the object to an IRanges instance and drop its metadata columns).

• Add ‘use.names’ and ‘use.mcols’ args to ranges() generic.

SIGNIFICANT USER-VISIBLE CHANGES

• Change ‘maxgap’ and ‘minoverlap’ defaults for findOverlaps() and family (i.e. countOverlaps(), overlapsAny(), and subsetByOverlaps()). This change addresses 2 long-standing issues: (1) by default zero-width ranges are not excluded anymore, and (2) control of zero-width ranges and adjacent ranges is finally decoupled (only partially though). New default for ‘minoverlap’ is 0 instead of 1. New default for ‘maxgap’ is -1 instead of 0. See ?findOverlaps for more information about ‘maxgap’ and the meaning of -1. For example, if ‘type’ is “any”, you need to set ‘maxgap’ to 0 if you want adjacent ranges to be considered as overlapping. Note that poverlaps() still uses the old ‘maxgap’ and ‘minoverlap’ defaults.

• subsetByOverlaps() first 2 arguments are now named ‘x’ and ‘ranges’ (instead of ‘query’ and ‘subject’) for consistency with the transcriptsByOverlaps(), exonsByOverlaps(), and cdsByOverlaps() functions from the GenomicFeatures package and with the snpsByOverlaps() function from the BSgenome package.

• Replace ifelse() generic and methods with ifelse2() (eager semantics).

• Coercion from Ranges to IRanges now propagates the metadata columns.

• Move rglist() generic from GenomicRanges to IRanges package.

• The “union”, “intersect”, and “setdiff” methods for Ranges objects don’t act like endomorphisms anymore: now they always return an IRanges instance whatever Ranges derivatives are passed to them (e.g. NCList or NormalIRanges).

DEPRECATED AND DEFUNCT

• Deprecate “ranges” methods for Hits and HitsList objects (replaced with overlapsRanges()).

• Deprecate the “overlapsAny”, “subsetByOverlaps”, “coverage” and “range” methods for RangedData objects.

• Deprecate the universe() getter and setter as well as the ‘universe’ argument of the RangesList(), IRangesList(), RleViewsList(), and RangedData() constructor functions.

• Default “togroup” method is now defunct (was deprecated in BioC 3.3).

• Remove grouplength() (was deprecated in BioC 3.3 and replaced with grouplengths, then defunct in BioC 3.4).

BUG FIXES

• nearest() and distanceToNearest() now call findOverlaps() internally with maxgap=0 and minoverlap=0. This fixes incorrect results obtained in some situations e.g. in the situation reported here: https://support.bioconductor.org/p/99369/ (zero-width ranges) but also in this situation: nearest(IRanges(5, 10), IRanges(1, 4:5), select=”all”) where the 2 ranges in the subject are both nearest to the 5-10 range.

• Fix restrict() and reverse() on IRanges objects with metadata columns.

• Fix table() on Ranges objects.

• Various other minor fixes.

IrisSpatialFeatures

Changes in version 0.99.3 (2017-08-10):

• First version

IsoformSwitchAnalyzeR

Version: 2017-10-25 Text: Fixed a small mistake in the documentation causing build warnings

Version: 2017-10-22 Text: isoformSwitchTestDRIMSeq() was updated to per default use dmFilter()

Version: 2017-10-22 Text: Small updates to documentation better explaining the functionalities from udate 0.99.12

Version: 2017-10-19 Text: Version bump for Bioconductor to keep up

Version: 2017-10-12 Text: importIsoformExpression() have been completely redesigned to utilize the tximport package as well as implementing the option for inter-library normalization of abundance (TxPM) values.

Version: 2017-10-12 Text: The vignette got a thorough workover - huge shoutout to Maria Dalby for the help!

Version: 2017-10-12 Text: isoformSwitchTestDRIMSeq() was extended to also include the dmFilter() functionality as part of the workflow.

Version: 2017-10-12 Text: The internal process calculating gene expression from isoform expression was cast as its own function: isoformToGeneExp().

Version: 2017-10-12 Text: Fixed an error that could cause problems when importing CDSs from a GTF file

Version: 2017-10-12 Text: Updated descriptions and other minor style issues.

Version: 2017-06-01 Text: Fixes some issue raised in the Bioconductor review To adhere to Bioconductor conventions the subset() method was removed and replaced by the subsetSwitchAnalyzeRlist() function.

Version: 2017-06-01 Text: The importIsoformExpression() function was updated to support import of Transcript Per Million (TxPM) as the relative abundance measure (Instead of TPM and RPKM/FPKM, which are discontinued) when importing data from Kallisto, Salmon and RSEM.

Version: 2017-06-01 Text: The isoformSwitchTestDRIMSeq() function was updated to make one linear model (one dmFit) instead of one model per pairwise comparison.

Version: 2017-06-01 Text: Small update to the switchPlot() functions to make it robust to NA annotation in non-essential data.

Version: 2017-06-01 Text: Added citation information since the article describing the R package was published: Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).

Version: 2017-05-24 Text: Fixes some issue raised in the Bioconductor review

Version: 2017-05-24 Text: Fixes a but introdued during the recent update in how pfam results were integrated.

Version: 2017-05-24 Text: Updates of the vignette for inproved readability.

Version: 2017-05-19 Text: MAJOR update which: 1) Introduces the iso_ref and gene_ref handles to all entires in the switchAnalyzeRlist which allows for easy integration of data across the different enteries. 2) Now offers full integration with the DRIMSeq tool which utilizises advanced linear models to identify significant changes in isoform usage at isoform level enabling robust analysis of more complex designs including batch effects. The integraiton is availabe via the isoformSwitchTestDRIMSeq() function. 3) Updates IsoformSwitchAnalyzeR to handle EBI’s new server for running Pfam. 4) To enable the integration with DRIMSeq switchAnalyzeRlist object have been extended with: a) Isoform replciate count matrix. b) A design matrix. 5) The preFilter function have been updated with new functionalities and default cutoffs that are more suitable for use with DRIMSeq. See function documentation for details. 6) Implements suggested updates from Bioconductor reviewer This update is so large backward compatability is unfortunatly not feasiblie so all existing switchAnalyzeRlists will have to be remade. The extention of the switchAnalyzeRlist have also made a few changes in how to import data nessesary. Specifically: - The importRdata() function now take a replicate count matrix as it’s main input and the replicate FPKM matrix is optional. - The importBallgownData() function and it’s accompanying “exampleRdata.RData” have been decapitated since it does not contain count information. - The importIsoformExpression() function have been introduced to help with importing data from Kallisto, Salmon and RSEM. This function generates a isoform count matrix from the parent directory of the Kallisto/Salmon/RSEM analysis - which can easily be used with the importRdata() function to generate a switchAnalyzeRlist. Lastly the vignette have naturally been updated and improved accordingly.

Version: 2017-04 Text: Small incremental updates to ensure IsoformSwitchAnalyzeR lives up to all Bioconductor standards mostly consering how namespaces are organised and imported.

Version: 2017-04-18 Text: The following functionalities were added: - Enable filtering for significant switches in the preFilter() function. - The extractGenomeWideAnalysis() function was extended with the “annotationToAnalyze” parameter enabling specification of which annotation types to analyze. - The analyzeSwitchConsequences() function was extended to enable analysis of truncated protein (by supplying ‘domain_length’ to the ‘consequencesToAnalyze’ argument). - The analyzeSwitchConsequences() function was extended so the ‘ntCutoff’ also applies to TSS and TTS analysis. The following bugs were corrected: - A bug where importCufflinksCummeRbund() imported all genomic features of isoforms, including CDS etc, resulting in duplicated regions which caused problems for the intron retention analysis. This is only a problem for Cufflinks/Cuffdiff analysis where the refrence transcriptome contaied non-exon annotation (as defined in the type columns (column 3)) of the gtf file. - A bug in the analyzePFAM() function that sometimes prevented IsoformSwitchAnalyzeR in correctly format the result file whereby the function could not run. - The multi-threading option was removed since it was not supported by windows computers. We plan to bring it back in a later update. - The option of manually supplying the start and stop codon sequences that the annotateORF() function should scan for in transcripts. Furthermorethe vignette was extended for enhanced usability.

isomiRs

Changes in version 1.5.5:

FIX

• Migrate vignette to new BiocStyle

• Remove unused function join_all

• Use parameter not integer number

• Using testthat for unit test

Changes in version 1.5.4:

FEATURES

• Better documentation for isoCorrection function. Add proper authors and citation.

Changes in version 1.5.3:

FEATURES

• Better colors for polar plot of isomiRs

FIX

• Fix notes during R CHECK for variables inside dplyr/ggplot functions

• Use roxygen2 for NAMESPACE

Changes in version 1.5.2:

FIX

• Remove TMB dependency

Changes in version 1.5.1:

FEATURES

• Add new polar figure to plot all isomiRs at the same time

• Add NLQO distribution to correct expression knowing sequencing bias [Argyropoulos et al, 2017]

• Improve data documentation

IWTomics

Version: 1.1.1 Text:

Version: 1.1.2 Text:

Version: 1.1.3 Text:

JASPAR2018

Changes in version 3.6:

NEW FEATURES

• JASPAR2018 data package

JunctionSeq

Changes in version 1.7.5:

Structural revamp

• Changes to DESeq2 have made it necessary to copy C++ code from DESeq2. As a result: JunctionSeq once again requires compilation.

• Minor bugfixes.

• Added more useful error messages when encountering incompatible GFF / count files.

KEGGprofile

Changes in version 1.19.3:

• Fix bugs in download_KEGGfile function, which was caused by the updates of KEGG web site.

Changes in version 1.19.1:

• Fix a bug in download_KEGGfile function, which was caused by the updates of KEGG web site.

limma

Changes in version 3.34.0:

• read.idat() can now handle idat files in SNP format.

• New argument ‘sort.by’ for topSplice().

• diffSplice() now treats any NA geneid as a separate gene with one exon. Previously all NA geneids were treated as the same gene.

• Bug fixes for plotSplice() which, in some circumstances, was not highlight significant exons.

• Default value for ‘style’ in volcanoplot() changed to “p-value” instead of “p”. This doesn’t change the behavior of the function.

• volcanoplot() didn’t work with MArrayLM objects produced by treat(). Now fixed.

• The gene.info.file argument of alias2SymbolUsingNCBI() will now optionally accept a data.frame instead of a file name.

• alias2SymbolUsingNCBI() now always produces a data.frame. Previously a single-column data.frame was returned as a vector.

• Bug fixes to camera() and cameraPR() when ‘index’ contains character row names.

• New argument ‘restrict.universe’ for the default kegga() method. The default is now not to the restrict the universe to genes with KEGG annotation.

• goana.default() code is rewritten to more closely match kegga.default. Slight speed improvement. Prior probabilities are now computed using the restricted universe with GO annotation instead of the whole universe.

• Bug fix for kegga() when trend=TRUE or a prior.prob or covariate is specified. Previously the Down p-values were substantially too small and the Up p-values were too large.

• plotWithHighlights() checks whether ‘status’ is a factor and converts to character.

• Bug fixes for beadCountWeights(). Default is now set correct for ‘design’ and the function now works correctly when ‘y’ is an EList object contain bead standard errors but not standard deviations.

LymphoSeq

Changes in version 1.4.1:

• Fixed bug in topSeqPlot

maftools

Changes in version 1.4.00:

NEW FUNCTIONS

• plotApobecDiff - plots differences between APOBEC enriched and non APOBEC enriched samples

• gisticOncoplot, gisticBubblePlot and gisticChromPlot to visualize GISTIC results

• somaticInteractions - to identify mutually exclusive/co-occuring gene sets

• genotypeMatrix - function to create genotype matrix

• mutCountMatrix - generate count matrix

SIGNIFICANT USER-LEVEL IMPROVEMENT

• Changes to MAF object: It now includes clinical data slot similar to PhenoData of expressionset objects.

• Changes to MAF object: Silent variants will be stored seperately in MAF object and won’t be mixed with non-syn variants.

• Changes to MAF object: Oncomatrix is built on the fly whenever required, its no longer stored in MAF object.

• You can specify a manual list of variant classifications to be considered as non-synonymous via argument vc_nonSyn in read.maf

• Dropped mutExclusive function - Use somaticInteractions instead.

• Many sorting options and plotting improvements to oncplots.

• One can include q values from mutsig (or any similar program) as a side barplot in oncoplot

• rainfallPlot can detect hyper mutated genomic segments via ChangePoint detection method

• plotSignatures includes cosine similarity score and aetiology of detected signature

• readGistic has argument cnLevel to choose deep or shallow CN variants

• inferHeterogeneity includes MATH score in the plot

• Tumor_Sample_Barcodes remains as is; earlier ‘-‘ were converted to ‘.’ in sample names

NON SIGNIFICANT CHANGES

• mafCompare output includes adjusted p-values

• trinucleotideMatrix output includes adjusted p-values for APOBEC enrichment

• added plot arguments to control title size and point size in lollipopPlot

BUG FIXES

• Major bug fix in signature analysis

• minor bug fixes in oncostrip

matter

Changes in version 1.3.8 (2017-10-26):

NEW FEATURES

• Added ‘matter_fc’ class for on-disk factors

SIGNIFICANT USER-VISIBLE CHANGES

• Added character encodings to ‘matter_str’ on-disk strings

BUG FIXES

• Fixed bug in ‘matter_df’ when subsetting by columns

• Fixed bug when coercing ‘data.frame’s to ‘matter_df’

Changes in version 1.3.7 (2017-10-25):

BUG FIXES

• Fixed bug where default ‘matter_df’ chunksize was tiny

• Changed ‘datamode’ for ‘matter_df’ from ‘list’ to ‘virtual’

Changes in version 1.3.6 (2017-10-20):

SIGNIFICANT USER-VISIBLE CHANGES

• Lists (ragged arrays) may now be heterogenous (elements must still be vectors)

• More memory-efficient initialization of data on disk when length(data) is 1

• Files are now created by default in constructors if they do not already exist

• When coercing with ‘as.matter’, names and/or dimnames are now retained

Changes in version 1.3.5 (2017-10-18):

SIGNIFICANT USER-VISIBLE CHANGES

• Improved length/dim defaults when data is given to constructors

BUG FIXES

• Trying to write to a read-only dataset now fails gracefully

• Fixed integer overflow when subsetting via subsetMatterMatrix

Changes in version 1.3.4:

BUG FIXES

• Fixed bug where NAs did not propogate correctly for integers

• It is now an error when ‘matter()’ cannot infer data structure

Changes in version 1.3.3:

SIGNIFICANT USER-VISIBLE CHANGES

• Added new vignettes with benchmarks and examples on real data

BUG FIXES

• Fixed bug in delayed arithmetic operations with vectors

Changes in version 1.3.2:

NEW FEATURES

• Added class ‘matter_list’ for homogenous lists (ragged arrays)

• Added class ‘matter_str’ for on-disk strings

• Added class ‘matter_df’ for on-disk data frames

• Added ‘as.matter’ for function coercing to matter objects

Changes in version 1.3.1:

NEW FEATURES

• Updated base matter classes (matter_vec, matter_mat, matter_arr) to support ‘Arith’ and ‘Compare’ group generics

MEAL

Version: 1.8.0 Category: MAJOR CHANGES Text:

Version: 1.8.0 Category: o Substitute AnalysisResults and AnalysisRegionResults by ResultSet Text:

Version: 1.8.0 Category: o Substitute MethylationSet by GenomicRatioSet Text:

Version: 1.8.0 Category: USER-VISIBLE CHANGES Text:

Version: 1.8.0 Category: o Rename analysis functions Text:

Version: 1.8.0 Category: o Create wrappers for each DMR methd Text:

Version: 1.8.0 Category: NEW FEATURES Text:

Version: 1.8.0 Category: o Add differences of variances analysis Text:

Version: 1.8.0 Category: o Add new plot to simultaneously show all results of the same region Text:

meshes

Changes in version 1.3.1:

• new project site <2017-09-30, Fri>

metabomxtr

Changes in version 1.11.1:

• *corrected bugs that occur when mixture models include at most 1 predictor

MetaboSignal

Changes in version 1.7.12:

• MetaboSignal integrates KEGG metabolic and signaling networks with regulatory interactions reported in OmniPath and TRRUST.

• New functions: “MS2_ppiNetwork( )” and “MS2_mergeNetworks( )”.

Changes in version 1.7.8:

• MetaboSignal includes a new function: “MS_getPathIds()” which allows retrieving the identifiers (IDs) of all metabolic and signaling KEGG pathways of a given organism.

• “MS_keggNetwork()” can now transform KEGG IDs into Entrez gene IDs (use expand_genes = TRUE, convert_entrez = TRUE).

• “MS_filterNetwork()” has been renamed as “MS_topologyFilter”.

Changes in version 1.7.2:

• Major changes in function names:

• “MetaboSignal_matrix()” renamed as “MS_keggNetwork”

• “MetaboSignal_distances()” renamed as “MS_distances”

• “MetaboSignal_NetworkCytoscape()” renamed as “MS_shortestPathsNetwork”

• “MS_ToCytoscape()” renamed as “MS_exportCytoscape”

• “MS_ChangeNames()” renamed as “MS_changeNames”

• “MS_FilterNetwork()” renamed as “MS_filterNetwork”

• “MS_FindKEGG()” renamed as “MS_keggFinder”

• “MS_GetKEGG_GeneID” renamed as “MS_convertGene”

• “MS_NodeBW()” renamed as “MS_nodeBW”

• “MS_ReplaceNode()” renamed as “MS_replaceNode”

• “MS_RemoveNode()” renamed as “MS_removeNode”

• “MS_FindMappedNodes()” renamed as “MS_findMappedNodes”

• New functions:

• “MS_tissueFilter()”: allows filtering a network based on tissue expression data.

• Functions removed:

• “MS_interactionType()”: interactions can be now retrieved directly from MS_keggNetwork.

• Functionality changes:

• “MS_keggNetwork()”: output networks are now formatted as 3-column matrices, where the third column indicates interaction type. Unlike, MetaboSignal_matrix, “MS_keggNetwork()” does not perform network filtering by tissue expression data. Tissue filtering is now done with “MS_tissueFilter()”. Also, the compound nodes of the networks are not only metabolites, but also drugs and glycans.

• “MS_distances()”, “MS_shortestPathNetworks()”: use network nodes (i.e. KEGG IDs) as source nodes, not entrez IDs or gene symbols. However, the function “MS_convertGene()” allows to easily convert entrez IDs or gene symbols into KEGG IDs.

Changes in version 1.7.1:

• Significant improvements in the tissue-filtering option from “MetaboSignal_matrix()”.

• Cytoscape .txt files are now exported with a header.

metaseqR

Changes in version 1.17.4 (2017-10-06):

NEW FEATURES

• New option: utr.flank for counting reads in 3’ UTR flank regions when analyzing Quant-Seq data.

• New gene filter: genes where x samples present less than y counts are excluded from statistical testing. x is determined as a fraction of available samples.

BUG FIXES

• Fixed bug in problematic backwards compatibility of strandedness in targets files which caused strandedness to be ignored (thans to Martin Reczko, BSRC ‘Alexander Fleming’).

metavizr

Changes in version 1.3.20:

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

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

Changes in version 1.3.11:

• Add NEWS file

• Update documentation on ‘slideshow’ function

Changes in version 1.3.10:

• Changed default on ‘slideshow’ to show all ranges

Changes in version 1.3.9:

• Added ‘heatmapChart’ convenience function

Changes in version 1.3.8:

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

Changes in version 1.3.7:

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

Changes in version 1.3.6:

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

Changes in version 1.3.5:

• Fails gracefully on daemonization request on Windows

• Deprecates the ‘proxy’ argument to ‘startEpiviz’

Changes in version 1.3.4:

• Upgrading to Epiviz v2 webapp

MetCirc

Changes in version 1.5.0:

• no changes, check if package passes R CMD build and R CMD check without any error messages and vignette can be run without any errors [2017-10-20 Fri]

methimpute

Version: 1.0.0 Category: INITIAL RELEASE Text:

methylInheritance

Changes in version 1.1.1:

SIGNIFICANT USER-VISIBLE CHANGES

• Functions runObservation() and runPermutation() don’t return the result anymore. The results are saved in RDS files. The results can be loaded through the loadAllRDSResults() function.

• New plotConvergence() function enable visualization of convergence

• New “saveInfoByGeneration” parameter which generates RDS files containing information about each generation for each permutation

BUG FIXES AND IMPROVEMENTS

• Major changes in parallel processing to limit memory consumption

methylKit

Changes in version 1.3.8:

IMPROVEMENTS AND BUG FIXES

• changes to methCall(): more verbose output, reduce -Wunsigned warnings, check for fragmented chromosome order, write conversion stats to extra file

• add Tests to check for chromosome disorder

Changes in version 1.3.7:

IMPROVEMENTS AND BUG FIXES

• if methylDiff object contains NA in a qvalue/meth.diff column the getMethylDiff function returns an error. This is now fixed: https://github.com/al2na/methylKit/issues/83

• Changed how the methylBase version of regionCounts handle missing values. Before, a missing value made the whole region/tile missing. Now, a missing value is treated as a site with zero coverage. Contributed by Karl Nordström: https://github.com/al2na/methylKit/pull/77

Changes in version 1.3.6:

• changes to methSeg() function: update function description by beeing more explicit about the sorting, sort(x,ignore.strand=TRUE) is now called once if needed, update tests

Changes in version 1.3.5:

IMPROVEMENTS AND BUG FIXES

• fix problem with methSeg() error occurring when GRanges is not sorted by position

Changes in version 1.3.4:

IMPROVEMENTS AND BUG FIXES

• fix problem with assocComp() on methylBaseDB

Changes in version 1.3.3:

IMPROVEMENTS AND BUG FIXES

• changes to calculateDiffMeth() function: add a message explaining the calculation procedure based on either two or more treatment groups, fixed bugs that prohibited the use of treatment groups other than 0/1 in two group case, allow for more than two groups, update tests

• changes in methSeg() function: update function documentation to inform that provided Granges has to be sorted, add check if granges is sorted and contains at least one meta.col

Changes in version 1.3.2:

IMPROVEMENTS AND BUG FIXES

• quick fix for long filename issue: in unite() and calculateMethylDiff() instead of concatenated sample_ids, filename will be “methylBase” concatenated with either 13-char random string or provided suffix

• updated vignette: added two short FAQs

Changes in version 1.3.1:

IMPROVEMENTS AND BUG FIXES

• fix conversion rate error in methCall()

microbiome

Changes in version 0.99.8 (2017-08-21):

• Added sample names in divergence output

• coreset option added in divergence

• plot_taxa_prevalence argument “detection” added

• transform argument removed from plot_composition for simplicity

• data/DynamicsIBD data set and associated documentation removed to shrink the package

• inst/extdata/qiita data sets and associated documentation removed to shrink the package

• Baxter data removed to save space

• Utilities that do not belong to the package moved to maintenance branch

Changes in version 0.99.6 (2017-07-21):

• Fixed bug in transform option “clr”

• “lineplot” option added in plot_composition

Changes in version 0.99.5 (2017-07-07):

• fixed vignette headers

• heat function now takes also labels as input for order.rows and order.cols

• added age_group and bmi_group for easy access to standard groupings of these variables

• package homepage host location changed to master:docs/

Changes in version 0.99.3 (2017-06-05):

• Reduced the number of dependencies

• Removed marginal functionality

Changes in version 0.99.1 (2017-05-15):

• Major rewrite of the package

• Switched to support the phyloseq class

• HTML vignette added

• A separate online tutorial added

• Removed less essential functionality and dependencies

Changes in version 0.99.0 (2014-09-14):

• First draft of the BioC release version

Changes in version 0.12.14 (2012-05-10):

• added pitchipdb in PITChip array name list in profiling.R

Changes in version 0.12.12 (2012-05-02):

• added MITChip level 0

• added separate get.phylogeny.MITChip function to include level 0 for MITChip

Changes in version 0.12.10 (2012-04-17):

• automatized the levels and methods output within run.profiling.script

• now providing also non-logarithmized data matrices in the run.profiling.script output

• added in run.profiling.script save.image(paste(params$wdir, “/tmp.RData”, sep = “”)) to enable the use of data from the current workspace during a session

• multcomp replaced by parallel in dependencies

• Removed “Use existing data from the workspace” (useDB) option. Problems when called from within a function. More clear and modular when the run.profiling.script is used for preprocessing, and any new plots are performed as separate steps based on the profiling output files if needed.

• Moved run.profiling.script plots to their own functions and added usage examples to vignette.

Changes in version 0.12.08 (2012-04-05):

• detailed protocol added to the vignette

• hierarchical clustering method moved from complete to ward in profiling script as it was in some of the previous versions

• ‘level 0’ added in MITChip profiling

• removed featureprofile from output files to save disk space, typically not needed

• added remove.nonspecific.oligos option to run.profiling.script and FetchHITChipAtlas functions (through get.phylogeny)

• summarize.probesets modified to include levels both in the form of “level.1” and “level 1”

Changes in version 0.12.06 (2012-04-04):

• fixed PITChip-specific issues

• removed parallel from dependencies to allow compatibility with R-2.12.2

Changes in version 0.12.05 (2012-03-29):

• removed background correction from profiling script (run.profiling.script)

• kept standard normalizations: none, minmax, quantile - others removed

• now using 16S phylogeny in profiling script. Other option removed

• polishing of the functions

• merged funcions from the phyloarray package

• removed minmax, quantnorm from profiling.R functions

Changes in version 0.12.04 (2012-03-28):

• removed the additional background correction step which resulted in considerable information loss based on external validations

Changes in version 0.12.01 (2012-03-23):

• PlotMatrix updates

Changes in version 0.3.63 (2012-12-24):

• separated MySQL/preprocessing functions into a distinct package, HITChipDB

Changes in version 0.3.43 (2012-09-28):

• added relative.abundance function

• polished estimate.diversity function

• added functions: richness, evenness, diversity

Changes in version 0.3.15 (2012-08-31):

• FetchHITChipAtlas and run.profiling.script validated against each other

• default imputation removed from run.profiling.script; this had considerable effect on normalized data

Changes in version 0.3.13 (2012-08-30):

• standardized the pipeline; output validated against previous atlas version

Changes in version 0.3.05 (2012-08-22):

• added MDS.classical and MDS.isometric to project.data

Changes in version 0.3.02 (2012-06-20):

• calculate.stability function added

• added L2->species option to levelmap function

• estimate.diversity function updated. Detection thresholds applied with richness and evenness

• estimate.min.threshold mode detection improved

• cross.correlate function added

Changes in version 0.3.01 (2012-06-19):

• draft version for GitHub

Changes in version 0.2.04 (2012-06-15):

• RMySQL removed from explicit dependencies

Changes in version 0.2.03 (2012-06-06):

• hitchip.phylodistance added

• cross-hyb control functions added

Changes in version 0.2.02 (2012-06-03):

• annotation functions added

Changes in version 0.2.01 (2012-05-31):

• removed absolute scale matrices from run.profiling.script output. The idea is that just one log10 file for each phylogenetic level is outputted, and the user can then use other reading/analysis routines to read the data, convert to original non-log domain if necessary, etc. This is to provide a unique output format to avoid mistakes.

• save.data and tree.display removed from run.profiling.script arguments

• combined get.phylogeny and get.phylogeny.MITChip

• moved plotting functions from run.profiling.script into a separate function profiling.hclust;

• removed the option to read profiling parameters from R file in ReadParameters function

• output file name phylogenyinfo.tab changed into phylogenyinfo-nspecies.tab

• made run.profiling.script modular with respect to preprocessing, plotting, data storage, and logging

• added instructions in the vignette on reading the final data

Changes in version 0.0.12 (2012-03-15):

• multicore removed from dependencies

• vignette updated

• R-2.12.1 required

Changes in version 0.0.10 (2012-03-06):

• standard profiling script included

• added selected.samples in fetch.sample.info

Changes in version 0.0.08 (2012-02-25):

• Atlas preprocessing finalized. For usage examples, see vignette.

Changes in version 0.0.05 (2012-02-22):

• atlas functions added and polished

Changes in version 0.0.02 (2012-02-06):

• profiling_010.r script functions and dependencies added

Changes in version 0.0.01 (2012-01-12):

• First version based on profiling script version 010

minfi

Changes in version 1.23:

• Fixed as() (coercion) from RGChannelSetExtended to RGChannelSet, to support the argument extended=TRUE in read.matharray(). The core issue is the new(“RChannelSetExtended”) is an invalid object because it does not have correct elements of the assay slot. Instead of addressing this, I used a check for ncol=0, nrow=0 in the coercion function which asssumes the presence of correctly named assays. Original issue report by Stewart Morris swmorris@exseed.ed.ac.uk.

• Improved (made prettier) the printing of messages in read.metharray() and friends.

• Changed seqlevels(…, force = TRUE) to seqlevel(…, pruning.mode = “coarse”).

miRmine

Version: 0.99.8 Text:

Version: 0.99.1 Text:

Version: 0.99.0 Text:

miRsponge

Version: 1.1.1 Category: Update miRsponge.R <2017-10-01, Sun Text:

Version: 1.1.0 Category: Update netModule function <2017-09-07, Thur Text:

Version: 0.99.17 Category: Update DESCRIPTION <2017-08-23, Wed Text:

Version: 0.99.16 Category: Update moduleSurvival function <2017-08-08, Tues Text:

Version: 0.99.15 Category: Update test_miRsponge.R <2017-07-22, Sat Text:

Version: 0.99.14 Category: Update test_miRsponge.R <2017-07-22, Sat Text:

Version: 0.99.13 Category: Improve the code of miRsponge.R <2017-07-22, Sat Text:

Version: 0.99.12 Category: Update related references in man folder <2017-07-20, Thur Text:

Version: 0.99.11 Category: Improve the code of miRsponge.R <2017-07-20, Thur Text:

Version: 0.99.10 Category: Update README.md and miRsponge.Rmd <2017-07-18, Tues Text:

Version: 0.99.9 Category: Update moduleSurvival function <2017-07-14, Fri Text:

Version: 0.99.8 Category: Update cernia.Rd and hermes.Rd <2017-07-13, Thur Text:

Version: 0.99.7 Category: Update dtHybrid function <2017-07-13, Thur Text:

Version: 0.99.6 Category: VERSION BUMP REQUIRED <2017-07-13, Thur Text:

Version: 0.99.5 Category: Update DESCRIPTION file <2017-07-13, Thur Text:

Version: 0.99.4 Category: Rename functions in R folder <2017-07-13, Thur Text:

Version: 0.99.3 Category: Update LICENSE file <2017-07-13, Mon Text:

Version: 0.99.2 Category: Improve the code format of miRsponge.R <2017-07-13, Mon>. Text:

Version: 0.99.1 Category: Improve the code format of miRsponge.R <2017-07-13, Mon>. Text:

Version: 0.99.0 Category: This is the first version of miRsponge package. If any bugs, please let me know. Contact Email: zhangjunpeng_411@yahoo.com Text:

monocle

Changes in version 2.5.0:

• Various plot utilities for visualizing complex developmental trajectory (plot_complex_cell_trajectory), multi-way kinetic curve and multi-way heatmap (plot_multiple_branches_pseudotime, plot_multiple_branches_heatmap).

• ClusterCells now in principle supports clustering for 100 k+ cells which depends on a procedure of kNN based density peak clustering algorithm. densityClust package version 0.3 are required for users to use this functionality.

• New functions supporting importing scater or Seurat cds into monocle or vice versa (importCDS, exportCDS).

motifcounter

Changes in version 1.1.9:

• Removed compiler warnings

• Changes to the vignette

Changes in version 1.1.8:

• Internal refactoring

• Changed citation information

MotifDb

Changes in version 1.20:

NEW FEATURES

• Now 13 sources, 52 organisms and 8369 motifs

• New sources: HOCOMOCOv10, HOMER, jaspar2016, SwissRegulon

• New methods: motifToGene, geneToMotif, associateTranscriptionFactors

SIGNIFICANT USER-VISIBLE CHANGES

• The new methods mentioned above provide both strict and permissive mapping from motifs to their cognate transcription factors, thus supporting reproducible regulatory network construction.

motifStack

Changes in version 1.21.7:

• add newline at the end of RUNX1.pfm

Changes in version 1.21.6:

• update the documentations

Changes in version 1.21.5:

• add class psam

• add function plotAffinityLogo

Changes in version 1.21.4:

• add function importMatrix

Changes in version 1.21.3:

• add one more option for motifPiles and motifCircos

Changes in version 1.21.2:

• fix a bug in plotMotifLogo for pcm

Changes in version 1.21.1:

• update the vignettes.

mpra

Changes in version 0.99:

• Initial release to Bioconductor.

MSnbase

Changes in version 2.3.14:

• Use normalizePath to force absolute file paths in readMSData.

Changes in version 2.3.13:

• Add write support for MSnExp and OnDiskMSnExp objects allowing to save the MS data to mzML or mzXML files. <2017-09-15 Fri>

Changes in version 2.3.12:

• Keep protocolData in isobaric quantification; fixes #265

Changes in version 2.3.11:

• Amend addIdentificationData when sourceInfo reports multiple files and when scores are missing from the identification results (closes #261).

• Don’t overwrite processingData slot when creating an MSnSet object (closes #264).

Changes in version 2.3.10:

• New isCentroidedFromFile function <2017-08-11 Fri>

• Add msLevel slot to Chromatogram object <2017-08-16 Wed>

• Add msLevel argument to chromatogram,MSnExp method <2017-08-16 Wed>

• calculateFragments now just calculate fragments for all n - 1L bonds (before it incorrectly adds an additional bond; fixes #248) <2017-08-20 Sun>

• Add isEmpty methods for Chromatogram and Chromatograms objects <2017-09-05 Tue>

• plot,Chromatogram[s] creates an empty plot and returns a warning if the Chromatogram[s] object is empty (issue #249) <2017-09-05 Tue>

Changes in version 2.3.9:

• Using new mzR::openIdfile backend to add identifcation data to raw and quantitative data (see issue #232) <2017-07-28 Fri>

• New utils functions: factorsAsStrings, makeCamelCase and reduce,data.frame <2017-07-29 Sat>

• Coerce mzRident to data.frames <2017-07-29 Sat>

• Add phenoData slot to Chromatograms class<2017-08-02 Wed>

• new readMzIdData function to read mzId files as data.frames (uses the new coerce,mzRident,data.frame method) <2017-08-03 Thu>

• new filterIdentificationDataFrame function to filter PSM data.frames as produced by readMzIdData. Also used in the addIdentificationData methods. <2017-08-03 Thu>

• readMSData has a new mode argument to set onDisk or inMemory (default) mode <2017-08-10 Thu>

Changes in version 2.3.8:

• New infrastructure for chromatogram data <2017-06-24 Sat>

• Change naming scheme for spectra: FFILEID.SSPECTRUMID, e.g. F01.S0001. Before it has been XSPECTRUMID.FILEID. The new naming scheme changes the order of the spectra. See #255 (and PR #256) for details <2017-06-25 Sun>.

Changes in version 2.3.7:

• export filterEmptySpectra

Changes in version 2.3.6:

• Brutally remove xic and chromatogram functions/methods, to be replaced by the Chromatogram[s] infrastructure <2017-06-15 Thu>

Changes in version 2.3.5:

• Fix superscript syntax in demo vignette <2017-06-14 Wed>

Changes in version 2.3.4:

• Use the injection time from mzR (see PR #109) which in now in seconds (was in milliseconds) <2017-06-13 Tue>

Changes in version 2.3.3:

• Rewrite getColsFromPattern and getRowsFromPattern and add unit tests <2017-05-11 Thu>.

• Add .filterNA and rewrite filterNA for matrix and MSnSet <2017-05-11 Thu>.

• Convert main MSnbase-demo vignette to Rmd/html <2017-05-27 Sat>

• naplot gains a reorderRows and reorderColumns argument <2017-06-05 Mon>.

Changes in version 2.3.2:

• Rewrite utils.clean. It now keeps just the zeros in the direct neighbourhood (see #210) <2017-05-04 Thu>.

Changes in version 2.3.1:

• Introduce “NTR” method for combineFeatures <2017-04-26 Wed>.

• Rewrite nQuants and featureCV to avoid returning of rows for empty factors; see PR #208 for details <2017-04-28 Fri>.

• Add $,pSet method to easily access columns in the phenoData (see #203)

Changes in version 2.3.0:

• Version bump for new Bioc devel.

MSnID

Changes in version 1.11.1:

• Switch from mclapply to parLapply in filter optimizaition. This fixes a bug “Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.” Also allows to run parallel on Window OS

msPurity

Changes in version 1.3.9:

• Added very basic SIMS stitch compatibility

• pcalc can handle NAs

• Update of purityX to handle obiwarp RT correction (requires recording the RT RAW at an earlier step)

• bug fix for when library spectra is bigger than target spectra (thanks Martin)

Changes in version 1.3.1:

• Add spectral matching functionality for LC-MS/MS

MSstats

Version: 3.9.7 Text: NEW FEATURES - cluster (default=1) is no longer available for groupComparison function, due to memory issue.

Version: 3.8.6 Text: NEW FEATURES - can cluster (default=1) for dataProcess and groupComparison function (Thanks John!!)

Version: 3.8.5 Text: BUG FIXES - PDtoMSstatsFormat : three options are added for outputs from different versions of PD. (Thanks to Felipe!) - which.quantification - which.proteinid - which.sequence

Version: 3.8.4 Date: 2017-08-28 Text: BUG FIXES - SkylinetoMSstatsFormat : DDA case lost ‘StandardType’ column after summing peaks. Fixed. (Thanks, Nick)

Version: 3.8.3 Date: 2017-07-13 Text: NEW FEATURES - SpectronauttoMSstatsFormat : if PG.Qvalue is available, filter out the data with greater than 0.01. - dataProcessPlots, groupComparisonPlots, modelBasedPlots : with address=FALSE option, one plot a time can be drawn in the panel and won’t be saved as in pdf. BUG FIXES - designSampleSize : fix the calculation of variance (Thanks, Tsung-Heng) - SkylinetoMSstatsFormat : when Condition and BioReplicate columns are NA, there was issue for merge with annotation. - SkylinetoMSstatsFormat : fix the bug to recognize the protein with one peptide only for the option: ‘removeProtein_with1Peptide = TRUE’ - dataProcess : when cutoff.lower is negative, with maxQuantileforCensored option + censoredInt=’0’, zero log2 endogenous intensity should be censored. - ProgenesistoMSstatsFormat : handle inputs with some limited columns. such as no Spectral.counts columns.

Version: 3.8.2 Date: 2017-04-21 Text: NEW FEATURES - required ‘Fraction’ information in annotation for pre-processing - dataProcess function is updated for merge fractions BUG FIXES - warning message during dataProcessPlots for profile plot is not shown anymore.

multiClust

Changes in version 6-19-16:

• -Package version pushed to 1.0.3 -Updated package title and abstract to reflect that of publication in Cancer Informatics DOI: 10.4137/CIN.S38000.

Changes in version 3-2-16:

• -Package version pushed to 0.99.6 -Added Biobase, GEOquery, and preprocessCore to package suggests -Minor revisions in the package vignette

Changes in version 2-13-16:

• -Package version changed to 0.99.5 -Added option to specify FDR cutoff when using the Adaptive GMM method in the number_probes function. -Updated documentation in the vignette

Changes in version 2-11-16:

• -Packaged changed to version 0.99.4 -Revised the code in the vignette -Added explanation of using RNA-seq data with package in vignette -Revised code documentation for probe_ranking function

MWASTools

Changes in version 1.1.1:

• MWASTools includes new functions: “MWAS_heatmap()”, “MWAS_KEGG_pathways()”, “MWAS_KEGG_network()”, and “MWAS_KEGG_shortestpaths()”.

mzR

Changes in version 2.11.11:

• Fix problem in writeMSData: ensure precursor data is saved even if precursor scan is not available (see MSnbase issue #245).

Changes in version 2.11.10:

• Fix problem that can cause a SEGFAULT in writeMSData/copyWriteMSData when MS data with spectra linking to missing precursor scans is saved (issue #129).

Changes in version 2.11.9:

• Update peaks man page with details about spectrumId, acquisitionNum and seqNum

Changes in version 2.11.8:

• Add contributions guide with code of conduct.

• Update installation instructions for Mac.

• Report the spectrum ID in the header data.frame (column spectrumId).

• Fix in copyWriteMSData and writeMSData ensuring that MSn data is correctly

• Import pwiz r11174 fix for mzML without <componentList> (see #113).

Changes in version 2.11.7:

• Nothing yet.

• Import fix by Brian Pratt (pwiz r11174) for mzML without <componentList> Another way to fix #113

• Removing mz5 support from manual page, as currently unsupported.

Changes in version 2.11.6:

• runInfo returns the run start time stamp from files providing this information (mzML files).

Changes in version 2.11.5:

• writeMSData and copyWriteMSData functions enabling to export MS data to mzML or mzXML files.

Changes in version 2.11.4:

• Use full TMT file pattern to select a single file

Changes in version 2.11.3:

• Read ion injection time from mzML files and add it to the data.frame returned by the header function.

Changes in version 2.11.2:

• New getScanHeaderInfo and getAllScanHeaderInfo implementations for the pwiz backend. Fixes issue #106 and issue #216 in MSnbase.

Changes in version 2.11.1:

• Change default I/O backend from Ramp to pwiz.

Changes in version 2.11.0:

• Bioc devel 3.6

NanoStringQCPro

Changes in version 1.9.1 (2017-10-11):

• Fixed vignette build issues following recent overhaul of BiocStyle (cf. https://github.com/Bioconductor/BiocStyle/blob/master/announcement.md (91e6565 on Aug 9)).

ndexr

Changes in version 0.99.10:

• Breaking changes of the function names!

• Changed the naming of the functions: dots are replaced by underscores, so that the functions may not be confused with S3 methods. The naming convention itself doesn’t change! E.g. the new name of the function “ndex.network.update.aspect” is now “ndex_network_update_aspect”

• Moved packages httr, jsonlite, plyr and tidyr from “Depends” field to “Imports” (Import into NAMESPACE not necessary, because external package function names are always explicitly qualified)

• Fixed a bug in ngraph_fromRCX, which prevented the resulting ngraph object from node attributes to be set correctly. This also lead the following warnings: “Warning in vattrs[[name]][index] <- value : number of items to replace is not a multiple of replacement length”

• Changed functions from passing a quoted string (e.g. host = “ndexConf$connection$host”) as default parameter to using the actual object (e.g. host = ndexConf$connection$host)

• Made some minor changes to NDExConnection object; removed an undesired warning.

• Implement a print method for the classes “NDExConnection” and “RCX” to provide the user with a useful summary of this complicated object

• changed to the usage of message() rather than cat() for verbose outputs, where it wasn’t already done

• Specified a single ‘Maintainer’ representing the primary contact for maintenance issues related to this package.

• Removed the .gitignore file from this directory

• Changed installation instructions in the vignette to Bioconductor

Changes in version 0.99.0:

• Pushing version number to 0.99.0 according to Bioconductor checklist

• Initial submission to Bioconductor

normr

Version: 1.3.1 Category: FEATURES Text: summary() output more concise

Version: 1.3.1 Category: FEATURES Text: getEnrichment() takes F for specifying a desired foreground component for standardization of the enrichment

Version: 1.3.1 Category: FEATURES Text: iterations argument allows running multiple fits with different starting values

Version: 1.3.1 Category: FEATURES Text: T Filter threshold can now be specified with minP argument for less stringent filtering

Version: 1.3.1 Category: FEATURES Text: Added a normR overview scheme to the vignette

Version: 1.3.1 Category: FEATURES Text: Qvalue computation improvement by specifying range for prop. of H_0

Version: 1.3.1 Category: BUGFIXES Text: Fixed the erroneous tiling of supplied GR objects in char,char,GRanges

Version: 1.3.1 Category: BUGFIXES Text: diffR() is more robust by doing a label-switched fit also

Version: 1.3.0 Text:

Version: 3.6 Text:

Version: 3.5 Text:

Version: 3.4 Text:

Onassis

Changes in version 0.99.8:

• SRAdbHandler

• GEOHandler

• EntityFinder-methods

• similarity-methods

• AllGenerics

• AllClasses

• AllFunctions

• CMdict-methods

• Init_methods

• onLoad

• SupportingFunctions

• CMoptions-methods

oncomix

Changes in version 0.99.0:

• First version (0.99.0) of oncomix is available.

• Paper to follow soon!

OncoSimulR

Changes in version 2.7.2 (2017-09-27):

• genot_to_adj_mat in C++.

• fast_peaks (for no backmutation cases).

• Better explanation and testing of peaks and valleys.

• Clarified simOGraph transitive reduction.

• Better handling of ti corner cases.

• Magellan reading fuctions adapted to output of newer (as of 2017-07) version of Magellan.

• sorting gene names in allGenotypes_to_matrix.

• sampledGenotypes: genotype names with sorted gene names.

oneSENSE

Changes in version 0.99.1 (2017-07-04):

MODIFICATION

• Formatting changes

• Added Vignette

• Removed assignments to global variables

Changes in version 0.99.0:

MODIFICATION

• renamed package name from onesense to oneSENSE

ontoProc

Version: 1.0.1 Text:

oposSOM

Version: 1.15.1 Text:

OPWeight

Changes in version 1.0.0:

• First stable release with Bioconductor (2017-06)

pathview

Changes in version 1.17.7:

• updated combineKEGGnodes.R, i.e. changed the stop error to a warning message when a group node include different node types, i.e. both gene and compound. This problematic KEGG node definition does exist in pathway 04136 Autophagy - other, and caused error when calling pathview with kegg.native = F.

• fixed bug in mol.sum introduced at 1.15.1, i.e. indexing using which(eff.idx). This problem only affect direct call of mol.sum with sum.method other than “sum” and “mean”.

Changes in version 1.17.1:

• major expansion in korg, which now include both KEGG and NCBI taxonomy IDs, two more gene ID types, i.e. NCBI protein and uniprot IDs. In addition, Entrez or NCBI Gene IDs are discontinued for most prokaryotes.

• korg now include 4800 KEGG species, in the meantime, an updated version of korg is now checked out from Pathview Web server each time pathview package is loaded.

PathwaySplice

Changes in version 0.99.0:

• Initial version(2016-12-09)

philr

Changes in version 1.3.1:

USER-VISIBLE CHANGES

• Squashed Bug in philr and philrInv handling of vector input

piano

Changes in version 1.18.0:

DOCUMENTATION

• Switched to accommodate documentation in r-files using roxygen

BUG FIXES

• Fix print addInfo for GSC bug

Changes in version 1.16.4:

BUG FIXES

• Fix R CMD check NOTE on calling require(snowfall)

Changes in version 1.16.3:

BUG FIXES

• Fix BiocGenerics::sd and stats::sd collision when loading

Changes in version 1.16.2:

BUG FIXES

• Fix error: “Error in if (maxP > -minP) { : missing value where TRUE/FALSE needed” that appeared occasionally during runGSA for method gsea. This happened when the running sum was only positive or only negative, leading to that the if-statement broke due to missing values.

Changes in version 1.16.1:

BUG FIXES

• Fix biomaRt Rchunk in vignette to avoid build error

Pigengene

Changes in version 1.3.8 (2017-09-13):

Changes in existing functions

• Order of conditions in pheatmap.type can now be determined by the user.

Changes in version 1.3.6 (2017-08-20):

Changes in existing functions

• A bug in gene.mapping () function fixed to better map probe IDs.

Changes in version 1.3.4 (2017-07-31):

Changes in existing functions

• The doTranspose argument added to the heatmap.type() function.

polyester

Version: 1.99.3 Text: NB function now exported

Version: 1.99.3 Text: note that version 1.99.3 on GitHub was version 1.1.0 on Bioconductor.

Version: 1.99.2 Text: bug fix in fragment generation (last 2 bases of transcript were never sequenced)

Version: 1.99.1 Text:

pRoloc

Changes in version 1.17.5:

• Filtering for unique features when running plot2D with t-SNE method <2017-10-15 Sun>

Changes in version 1.17.4:

• Added new (private) dimred function that computes dimensionality reduction <2017-06-05 Mon>

• Add F1000research workflow to citations <2017-06-22 Thu>

• Classification functions now return the classification score matrix for all classes as a single column in fData, rather that each class as its own fData column. <2017-09-01 Fri>

Changes in version 1.17.3:

• Convert vignettes to Rmd with html output <2017-05-25 Thu>

• Import, rather than suggest Rtsne <2017-05-25 Thu>

Changes in version 1.17.2:

• phenoDisco speed improvements and added support for t-SNE <2017-05-19 Fri>

Changes in version 1.17.1:

• Support Rtsne’s new pca_center and pca_scale arguments <2017-05-02 Tue>

Changes in version 1.17.0:

• Version bump for Bioc devel 3.6

pRolocGUI

Changes in version 1.11.2:

• Fix links in vignette to point to new html pRoloc vignettes <2017-05-30 Tue>

Changes in version 1.11.1:

• Avoid computing dimensionality reduction at every reactive rendering, assuring that other, slower methods, in particular t-SNE, can be used <2017-05-20 Sat>

Changes in version 1.11.0:

• New version for Bioc devel 3.6

Prostar

Changes in version 1.9.15:

BUG FIXES

• When the aggregation step has been performed, the interface switches to the first tab of the ‘Descriptive Statistics’ in order to view informations aout the new dataset (the protein one).

• Implementation of a parallel version of the function which saves the (new) protein dataset after the aggregation step.

• Disable the extra row appearing in the metadata table when convertinga text file to a MSnSet file.

• Disable the extra row appearing in the metadata table when convertinga text file to a MSnSet file.

• A new package (readxl) is used to read xls or xlxs files. In certain circumstances, the functions of the previsous package openxlsx is not able to decode properly Excel files.

• When converting a new (text or Excel) file in Prostar : the missing values were not registered as expected. Especially, they did not appear in blue in the table above the volcanoplot. Bug fixed

• A bug occured when the user load successively several datasets in Prostar. The previous ones were note correctly erased and this has lead to side effects. This bug is now fixed

NEW FEATURES

• Enhancement of the string-based filtering UI

• The automatic generation of an analysis report has been integrated in the Dataset Manager (menu ‘Export’). It allows the user to download plots and parameters used in Prostar ont their dataset.

• Added a Gene Ontology (GO) analysis module in Data Processing. This module allows to perform GO grouping and GO Enrichment.

• Several plots are now based on the package highcharter which is a wrapper to the highcharts graphical library. It provides interactivity with the user.

ProtGenerics

Changes in version 1.9.1:

• add writeMSData <2017-09-20 Wed>

PSEA

Changes in version 1.11.1 (2017-06-09):

• A new vignette shows how we applied PSEA to deconvolute expression from RNA mixtures (originally presented in the Nature Methods paper).

PureCN

Changes in version 1.8.0:

NEW FEATURES

• Support for off-target reads in copy number normalization and segmentation

• Added mutation burden calculation

• More robust mapping bias estimation

• Added support for CNVkit coverage files (*.cnn, *.cnr)

• IntervalFile.R can annotate targets with gene symbols and automatically convert chromosome naming styles

• Better artifact filtering by using normalDB more efficiently

• Support for mappability scores

• Coverage calculation can now include duplicates

• calculateBamCoverageByInterval now provides fragment counts and duplication rates

• findBestNormal pooling now fragment count based, not coverage based

• Experimental support for GATK4

• predictSomatic now reports posterior probabilites of minor segment copy numbers, flags segments if copy numbers are unreliable

• Targets can be annotated with multiple gene symbols (comma separated)

• Code cleanups (switch to GRanges where possible, switch to optparse in command line tools)

API CHANGES

• Due to novel optimizations of provided bait intervals, we highly recommend to regenerate the interval files and normal databases and recalculate all coverages from BAM files

• New functions: annotateTargets, callMutationBurden

• Defunct functions: createSNPBlacklist, getDiploid, autoCurateResults, readCoverageGatk

• min.normals defaults to 2 (changed from 4) in setMappingBiasVcf

• normalDB.min.coverage defaults to 0.25 (changed from 0.2) in filterTargets

• log.ratio.calibration defaults to 0.1 (from 0.25) in runAbsoluteCN; now relative to purity, not log-ratio noise

• Removed gc.data from filterTargets since gc_bias is now added to tumor coverage

• dropped purecn.output from correctCoverageBias (no two-pass anymore)

• Coverage.R argument –gatkcoverage renamed to –coverage

• Dropped GC-normalization functionality in NormalDB, since this is now conveniently done in Coverage.R

• Renamed PureCN.R –outdir argument to –out. Can now specify a file prefix as in GATK. Filenames are thus not forced to sample id anymore. If –out is a directory, it will behave like before and will use out/sampleid_suffix as filename.

qcmetrics

Changes in version 1.15.2:

• Merge PR by aoles to re-use BiocStyle (see commit 381d01d1c4dcced040f77a447962cd7865cb7417 for details) <2017-10-27 Fri>

Changes in version 1.15.1:

• Don’t user BiocStyle for vignette to allow to knit documents from within the vignette. This was needed to fix the error at build time. <2017-10-25 Wed>

Changes in version 1.15.0:

• Bioconductor devel

qpgraph

Changes in version 2.12:

USER VISIBLE CHANGES

• Updated citation data to include the published work in Castelo and Roverato (2017) on path weights.

qsea

Changes in version 1.3.2:

New feature

• select active BSgenome masks for pattern density estimation

Bugfix

• adaptions to changed behavior of GenomicRanges

Changes in version 1.3.1:

• transition to Github

QuartPAC

Changes in version 1.8.1:

• Bug fix to support new pdb file locations.

Rbowtie2

Changes in version 1.0.0:

INITIAL RELEASE

• bowtie2 version 2.3.2

• AdapterRemoval version 2.2.1a

RCyjs

Changes in version 1.9.8:

BUG FIXES

• Significant (3x) speedup. A 5000-node, 6000-edge graph transmits to Cytoscape from R in about 20 seconds.

ReactomePA

Changes in version 1.21.3:

• new project site using blogdown <2017-09-30, Fri>

Changes in version 1.21.2:

• correct typo in vignette <2017-05-18, Thu>

Changes in version 1.21.1:

• update vignette according to the change of reactome.db (pathway ID was changed) <2017-04-28, Fri>

recount

Changes in version 1.3.13:

BUG FIXES

• Changed reproduce_ranges() since disjoint exons are more useful than reduced exons for downstream analyses.

Changes in version 1.3.12:

NEW FEATURES

• Added the function read_counts().

Changes in version 1.3.9:

SIGNIFICANT USER-VISIBLE CHANGES

• Added citations for https://www.biorxiv.org/content/early/2017/06/03/145656 and https://f1000research.com/articles/6-1558/v1 as well as mentions to them in the vignette.

Changes in version 1.3.7:

SIGNIFICANT USER-VISIBLE CHANGES

• add_predictions() was bumped to version 0.0.05

Changes in version 1.3.5:

SIGNIFICANT USER-VISIBLE CHANGES

• Vignette now uses the new BiocStyle::html_document that was recently released.

Changes in version 1.3.2:

NEW FEATURES

• coverage_matrix() now has two new arguments: scale and round. Use scale = FALSE to get raw coverage counts, which you can then scale with scale_counts(). scale is set to TRUE by default, so the counts are scaled to a library size of 40 million reads. round is set to FALSE by default, but can be set to TRUE if you want to get integer counts, just as in the default of scale_counts().

Changes in version 1.3.1:

SIGNIFICANT USER-VISIBLE CHANGES

• Changed the default version argument of add_predictions() to ‘latest’. Internally, that’s still 0.0.03.

RedeR

Changes in version 1.26.0:

• Regular maintenance, stable release.

regioneR

Changes in version 1.9.2:

NEW FEATURES

• Simplified the interface of toGRanges for simpler use when manually creating GRanges. Now toGRanges(“chr1”, 10, 20) is valid.

BUG FIXES

• Multiple minor bug fixes

regionReport

Changes in version 1.11.6:

SIGNIFICANT USER-VISIBLE CHANGES

• Changed the default style to BiocStyle::html_document to mirror recent changes in BiocStyle.

Changes in version 1.11.4:

SIGNIFICANT USER-VISIBLE CHANGES

• Vignette now uses the new BiocStyle::html_document that was recently released.

Changes in version 1.11.2:

BUG FIXES

• Fixed the citations.

• Fixed DESeq2Report() for limma-results so that it will properly cite limma.

Changes in version 1.11.1:

SIGNIFICANT USER-VISIBLE CHANGES

• DESeq2Report() can now be used with other software if their results are made to look like DESeq2 results. For example, with limma-voom results.

BUG FIXES

• Made the DESeq2Report() more robust in case rlog() fails initially.

rGREAT

Changes in version 1.9.1:

• change url according to changes on GREAT website

Rhdf5lib

Changes in version 1.0:

New features

• Updated internal version of HDF5 to 1.8.19

Bug fixes

• Switched Windows compilation script to use CMake rather than configure. This seems to have solved problems in opening multiple files using different access modes.

Changes in version 0.99:

• Package submitted

RnaSeqSampleSize

Changes in version 1.9.1 (2017-08-03):

BUG FIXES

• Fix a bug about estimating genes in pathway power in est_power_distribution function, which was caused by update of KEGG web site.

RnBeads

Changes in version 1.9.4:

• You can now retrieve custom region sets from the RnBeads resource using the rnb.load.annotation.from.db function

• improved import from GEO

• bigff disk dump is now the default option for dealing with disk-based big matrices

• Several bugfixes and performance improvements in Greedycut, normalization, Bisulfite data loading and others

• Added differential variability analysis in addition to differential methylation

Changes in version 1.9.3:

• LOLA support for differentially methylated regions

• various LOLA utitility functions

• What used to be the “differential.enrichment” option is now called “differential.enrichment.go” to reflect the distinction between GO and LOLA enrichment analyses

• Missing methylation data can now be imputed (using mean, random or nearest-neighbor imputation)

• Gender prediction now supports sequencing and EPIC data

• Added a function for combining two array-based datasets from (potentially) different platforms.

• Several bugfixes and performance improvements

rols

Changes in version 2.5.6:

• bump version

Changes in version 2.5.5:

• Fix failing test do to different order <2017-10-23 Mon>

Changes in version 2.5.4:

• Fix bug in pagesize limit when reporting children, ancestors, … (see issue #25) <2017-10-17 Tue>

• New term(s) to data.frame coersion methods <2017-10-14 Sat>

Changes in version 2.5.3:

• Add import Ontology in NAMESPACE

Changes in version 2.5.2:

• Update to latest BiocStyle <2017-09-01 Fri>

• Quick fix for issue #24 (reported upsteams) <2017-09-02 Sat>

• Use Ontology generic from BiocGenerics <2017-09-03 Sun>

Changes in version 2.5.1:

• Fix unit test <2017-06-20 Tue>

Changes in version 2.5.0:

• Bioconductor devel 3.6

ROTS

Changes in version 1.6.0:

• Added support for testing multiple groups

• Bug fixes

rpx

Changes in version 1.13.4:

• Restore reference unit test

Changes in version 1.13.3:

• No commit

Changes in version 1.13.2:

• Fix errors due to changes on PX side. PXD000001 reference remains untested - see https://twitter.com/lgatt0/status/885091284142239744 for details. <2017-07-12 Wed>

Changes in version 1.13.1:

• Using xml2 <2017-06-13 Tue>

• Use functions instead of methods <2017-06-13 Tue>

Changes in version 1.13.0:

• Bioc devel 3.6

Changes in version 1.12.1:

• Using xml2 (backported from devel) <2017-06-13 Tue>

• Use functions instead of methods (backported from devel) <2017-06-13 Tue>

Rqc

Changes in version 1.12:

BUG FIXES

• Fix bug when generating report on Windows system

• Using default graphic device for report generation

rSFFreader

Version: 0.99.0 Category: Seattle time Text:

Version: 0.99.0 Category: Marc will contact you off-tracker for the follow-up Text:

Version: 0.99.0 Category: MS: If the version is set to 0.5, the package still goes to the release branch, or stays in devel Text:

Version: 0.99.0 Category: If it goes to release, I’m cool with that, it is still under construction, but functional Text:

Rsubread

Version: 1.28.0 Category: NEW FEATURES Text:

Version: 1.28.0 Category: o New functions: promoterRegions() and txUnique Text:

Version: 1.28.0 Category: o New parameter in featureCounts() for counting long reads - ‘isLongRead Text:

Version: 1.28.0 Category: o New parameter in featureCounts() for counting reads by read groups - ‘byReadGroup Text:

Version: 1.28.0 Category: o New parameter in featureCounts() for requiring minimum fraction of overlapping bases in each feature - ‘fracOverlapFeature Text:

Version: 1.28.0 Category: o Assignment results for each read can be added to the provided SAM/BAM files by featureCounts (‘reportReads’ option Text:

Version: 1.28.0 Category: o Align() and subjunc() produce a mapping summary including percentages of uniquely mapped reads, multi-mapping reads and unmapped reads Text:

RTCA

Changes in version 2009-07-13:

• combineRTCA(list): Additional column is renamed into Plate. The vlues is evaluated from list item names. When the list has no name, an integer index beginning from 1 is used. Special attentions to list partially with names is noted in the documentation.

• parseRTCA(file, dec=”.”,phenoData, skipWell,…): Example is added in the documentation how to import pre-configured phenoData. Details section in the documentation is re-written to describe the process of parsing.

• RTCA-class: Experiment ID added to RTCA class

• Makefile: add Makefile to simplify common tasks like check and install

• plotGridEffect: takes ‘column’ instead of ‘col’ as mode parameter, and renders the mode as the title of the legend. Documentation updated.

• plotRTCA: is removed from the package and is substituted by the plot function.

RTN

Changes in version 1.16.0:

• Improved annotation slots for TNA/TNI classes.

RTNduals

Changes in version 1.2.0:

• Improved workflow integration with derivative packages (RTN / RTNsurvival).

RTNsurvival

Changes in version 1.0.0:

• 1st Bioconductor release of RTNsurvival [2017-03-01].

runibic

Version: 0.99.14 Category: Updating tutorial, adding citation Text:

Version: 0.99.13 Category: Documentation to the package was updated. Text:

Version: 0.99.9 Category: Including required biocViews. Refactoring R code Text:

Version: 0.99.8 Category: Code optimizations Text:

Version: 0.99.6 Category: Parallel version using OpenMP Text:

Version: 0.99.5 Category: Fixing discretize() function bug Text:

Version: 0.99.2 Category: Improved performance of functions in package Text:

Version: 0.99.2 Category: Removing some errors and warnings Text:

Version: 0.99.1 Category: Compatibility with SummarizedExperiment Text:

Version: 0.99.1 Category: Providing documentation and examples Text:

Version: 0.99.0 Category: Development of the runibic package prototype completed Text:

Version: 0.99.0 Category: First upload to Bioconductor Text:

Version: 0.90.1 Category: Working version of UniBic algorithm Text:

S4Vectors

Changes in version 0.16.0:

NEW FEATURES

• Introduce FilterResults as generic parent of FilterMatrix.

• Optimized subsetting of an Rle object by an integer vector. Speed up is about 3x or more for big objects with respect to BioC 3.5.

SIGNIFICANT USER-VISIBLE CHANGES

• coerce,list,DataFrame generates “valid” names when list has none. This ends up introducing an inconsistency between DataFrame and data.frame but it is arguably a good one. We shouldn’t rely on DataFrame() to generate variable names from scratch anyway.

BUG FIXES

• Fix showAsCell() on data-frame-like and array-like objects with a single column, and on SplitDataFrameList objects.

• Calling DataFrame() with explict ‘row.names=NULL’ should block rownames inference.

• cbind.DataFrame() ensures every argument is a DataFrame, not just first.

• rbind_mcols() now is robust to missing ‘x’.

• Fix extractROWS() for arrays when subscript is a RangeNSBS.

• Temporary workaround to make the “union” method for Hits objects work even in the presence of another “union” generic in the cache (which is the case e.g. if the user loads the lubridate package).

• A couple of (long-time due) tweaks and fixes to “unlist” method for List objects so that it behaves consistently with “unlist” method for CompressedList objects.

• Modify Mini radix C code to accomodate a bug in Apple LLVM version 6.1.0 optimizer. [commit 241150d2b043e8fcf6721005422891baff018586]

• Fix match,Pairs,Pairs() [commit a08c12bf4c31b7304d25122c411d882ec52b360c]

• Various other minor fixes.

SC3

Changes in version 1.5.5 (2017-10-19):

• scater now works based on SingleCellExperiment class

• sc3 slot has moved to the metadata slot of SingleCellExperiment class

• scater class is completely deprecated from SC3

• All scater functionality can work on SingleCellExperiment class

• Clustering logic hasn’t been changed at all

Scale4C

Version: 1.0.0 Category: First release of Scale4C Text:

scater

Changes in version 1.5.11:

• Complete refactoring of the package to use the SingleCellExperiment class

scfind

Changes in version 0.99.0:

• The first version of scmap is submitted to Bioconductor.

scmap

Changes in version 0.99.2 (2017-07-05):

• Fixed issues for the first round of reviews at Bioconductor.

Changes in version 0.99.0 (2017-06-28):

• The first version of scmap is submitted to Bioconductor.

scone

Changes in version 1.1.3 (2018-10-19):

• Modified COR scores to reflect R^2 for regression on UV/WV/QC rather than max correlation.

• Bug fix for shiny report.

• Updated vignette.

Changes in version 1.1.2:

• Moved many Imports: packages to Suggests: to reduce impact of loading scone

Changes in version 1.1.1:

• Added fast ziber imputation method

scPipe

Changes in version 0.99.20 (2017-09-22):

• scPipe now supports SingleCellExperiment class and use it as the base class

• add two functions plot_demultiplex and plot_UMI_dup

• scPipe support the offical bam tags for cell barcode and UMI

Changes in version 0.99.0 (2017-07-28):

• Package prepared for Bioconductor submission.

scran

Changes in version 1.5.13:

• Supported parallelization in buildSNNGraph(), overlapExprs() with BPPARAM options.

• Forced zero-derived residuals to a constant value in correlatePairs(), overlapExprs().

• Allowed findMarkers() to return IUT p-values, to identify uniquely expressed genes in each cluster. Added options to specify the direction of the log-fold changes, to focus on upregulated genes in each cluster.

• Fixed bug in correlatePairs() when per.gene=TRUE and no spike-ins are available. Added block.size argument to control caching.

• Switched all C++ code to use the beachmat API. Modified several functions to accept ANY matrix-like object, rather than only base matrix objects.

• quickCluster() with method=”igraph” will now merge based on modularity to satisfy min.size requirements. Added max.size option to restrict the size of the output clusters.

• Updated the trendVar() interface with parametric, method arguments. Deprecated the trend=”semiloess” option in favour of parametric=TRUE and method=”loess”. Modified the NLS equation to guarantee non-negative coefficients of the parametric trend. Slightly modified the estimation of NLS starting parameters. Second d.f. of the fitted F-distribution is now reported as df2 in the output.

• Modified decomposeVar() to automatically use the second d.f. when test=”f”.

• Added option in denoisePCA() to return the number of components or the low-rank approximation. The proportion of variance explained is also stored as an attribute in all return values.

• Fixed a variety of bugs in mnnCorrect().

SeqArray

Changes in version 1.18.0:

NEW FEATURES

• progress information: showing overall running time when completed

• new variable names “$ref” and “$alt” can be used in seqGetData() and seqBlockApply()

• new argument ‘.progress’ in seqDigest()

• new argument ‘ref.allele’ in seqAlleleCount()

• new variable name “$chrom_pos_allele” can be used in seqGetData() and seqBlockApply()

UTILITIES

• move VariantAnnotation to the suggest field from the import field

• remove an unused argument ‘.list_dup’ in seqBlockApply()

• slightly improve the computational efficiency of seqAlleleFreq() and seqAlleleCount() when ‘ref.allele=0’

• seqGetData(f, "$chrom_pos") outputs characters with the format ‘chromosome:position’ instead of ‘chromosome_position’

BUG FIXES

• fix the unexpected behaviors in seqSetFilter(, action="push") and seqSetFilter(, action="push+intersect")

• fix a bug in seqGetData(f, "$dosage") when the number of unique alleles at a site greater than 3 (https://github.com/zhengxwen/SeqArray/issues/21)

• fix a bug in seqSNP2GDS() for inverted genotypes during importing data from SNP GDS files (https://github.com/zhengxwen/SeqArray/issues/22)

• fix an issue of no phase data in seqExport()

seqCAT

Changes in version 1.0.0:

FEATURES

• Create single nucleotide variant (SNV) profiles from RNA/DNA-seq samples

• Characterise the biological equivalency and difference between samples

• Evaluate putative impacts of SNVs differing between samples

• Investigate and validate known variants and specific genomic regions

• Authenticate cell lines with a known SNV profile or the COSMIC database

seqcombo

Changes in version 0.99.11:

• geom_genotype <2017-08-29, Tue>

Changes in version 0.99.10:

• geom_hybrid <2017-08-17, Thu>

Changes in version 0.99.9:

• hybrid_plot <2017-06-30, Fri>

Changes in version 0.0.3:

• more parameters for plot, by, xlab, color, fill etc.

Changes in version 0.0.2:

• add vignette

Changes in version 0.0.1:

• initial version with plot method for nucleotide differences between twwo aligned sequences <2016-11-16, Wed>

SeqSQC

Version: 0.99.10 Text: – updated the man for sampleQC and LoadVfile.

Version: 0.99.9 Text: Updated the output argument in function of sampleQC and LoadVfile, by using the default value of sampleqc in working directory. In vignette and the example code of these 2 functions, temporary directory is used for the directory to save the QC results.

Version: 0.99.8 Text: vignette, using a tempdir() for vignette output.

Version: 0.99.8 Text: Vignette: Additional explanation added for the option to do a wrapper all-inclusive QC or specific QC steps.

Version: 0.99.8 Text: documentation for argument “output” in “LoadVfile” and “sampleQC”, to indicate that the dirname(output) would be used as the directory to save the other QC results in .txt and plots in .pdf. The default value is added as file.path(tempdir(), "sampleqc").

Version: 0.99.8 Text: sampleQC.R: Arguments of plotting=TRUE, results=TRUE added and documented, giving the option for users to whether or not output the QC results and plots. The problem list will always in output for the simplest sample QC result and summary.

Version: 0.99.8 Text: the package documentation updated, by adding a @seealso for links of main functions of SeqSQC.

Version: 0.99.7 Text: Added checking for input in subsetGDS.

Version: 0.99.7 Text: Removed commented code for subsetGDS.

Version: 0.99.7 Text: SeqSQCclass renamed as SeqSQC.

Version: 0.99.7 Text: mergeGDS.R. using lapply for some repeated functions like “read.gdsn(index.gdsn())”. In SexCheck, Inbreeding, IBDCheck, PCACheck.

Version: 0.99.7 Text: sampleQC: 1. check the class of vfile for SeqSQC file or vcf/plink file, instead of using vfile / sfile.

Version: 0.99.7 Text: plotting function writing separately (not export), wrapper with plotQC().

Version: 0.99.7 Text: Removed IBDRemoveAll.R. Will check IBD for all sample pairs (including benchmark samples) by adding argument “all” in “IBDRemove.R”.

Version: 0.99.7 Text: debugged warning messages from “LoadVfile” and using “rbokeh”.

Version: 0.99.6 Text: modified SeqSQCclass to SeqSQC (not in vignette..).

Version: 0.99.5 Text: Installed BiocGenerics locally.

Version: 0.99.4 Category: Load benchmark data from ExperimentHub Text:

Version: 0.99.4 Category: o added in the R script, will download only once with first time running of the LoadVfile() or sampleQC Text:

Version: 0.99.4 Category: Bioconductor submission check: Text:

Version: 0.99.4 Category: o Added unit test Text:

Version: 0.99.4 Category: o Added a NEWS file to keep track of changes Text:

Version: 0.99.4 Category: o Added zzz.R to fix the no visible binding for global functions or variables. Text:

Version: 0.99.4 Category: o Added the “example_sub.vcf” for 1000 lines of variants to run as example in the package vignette Text:

Version: 0.99.4 Category: o Added accessor methods for SeqSQCclass data structure to get the slots of “gdsfile” and “QCresult Text:

Version: 0.99.4 Category: Vignettes: Text:

Version: 0.99.4 Category: o Added bioconductor installation and library load section in the vignette. Text:

Version: 0.99.4 Category: o Added runnable example vcf file added in “inst/extdata/example_sub.vcf”, with 1000 lines of variants. Text:

Version: 0.99.4 Category: MAN: Text:

Version: 0.99.4 Category: o added package documentation for dataset, class, methods and constructor Text:

SeqVarTools

Changes in version 1.15.3:

• alleleFrequency method accounts for sex when computing frequency for X and Y chromosomes.

Changes in version 1.15.2:

• Added iterator classes: SeqVarBlockIterator, SeqVarRangeIterator, SeqVarWindowIterator, SeqVarListIterator.

• Creating a SeqVarData object with missing sample or variant annotation will store 0-column data frames in sampleData or variantData, instead of duplicating sample.id and variant.id.

• Added methods to return variant data in expanded form, with one row per alternate allele.

Changes in version 1.15.1:

• Following SeqArray, remove dependency on VariantAnnotation

• Add generic isSNV (replacing previous import of this generic from VariantAnnotation)

ShortRead

Changes in version 1.35:

SIGNIFICANT USER-VISIBLE CHANGES

• Reads up to 2M bases can be parsed

SIMLR

Changes in version 1.3.1 (2017-09-15):

• Implemented estimation of number of clusters from data

Changes in version 1.2.1 (2017-05-29):

• Fix Windows memory usage

SingleCellExperiment

Changes in version 0.99.4:

• New package SingleCellExperiment, for representation of single-cell genomics data.

slalom

Changes in version 0.99.0:

• R/C++ package implementing f-scLVM model submitted to Bioconductor

SNPRelate

Changes in version 1.12.0:

• new arguments ‘with.sample.id’ and ‘with.snp.id’ in snpgdsSNPRateFreq()

Changes in version 1.10.2:

• progress information: showing overall running time when completed

• An unexpected exception in a thread could result in deadlock: the current implementation shows error information and exits the R session

splatter

Changes in version 1.1.8 (2017-10-13):

• Now published in Genome Biology!

• Converted to the SingleCellExperiment object

• Added new simulations: BASiCS, mfa, PhenoPath, ZINB-WaVE

• Added batch effects to the Splat simulation. This required a change to the SplatParams object.

• Improved scDD estimation

• Added and improved comparison functions

• Improved default Splat parameters and estimation

• Improvements to the Lun2Params object

• Added addGeneLength function

• Updated simulation references

• Various other minor updates and bug fixes

SPONGE

Changes in version 0.99.1:

• Support for ExpressionSet

• Extensive unit testing

• Simplified dependencies

• Code improvements

• Methods return data frames by default

• Default log level is now ERROR

SummarizedExperiment

Version: 1.8.0 Category: NEW FEATURES Text: Add ‘chunk_dim’ and ‘level’ arguments to saveHDF5SummarizedExperiment().

Version: 1.8.0 Category: NEW FEATURES Text: Add coercion from ExpressionSet to SummarizedExperiment.

Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text:

Version: 1.8.0 Category: DEPRECATED AND DEFUNCT Text: Remove ‘force’ argument from seqinfo() and seqlevels() setters (the argument got deprecated in BioC 3.5 in favor of new and more flexible ‘pruning.mode’ argument).

Version: 1.8.0 Category: BUG FIXES Text: Coercion from SummarizedExperiment to RangedSummarizedExperiment was losing the metadata columns. Fixed now.

Version: 1.8.0 Category: BUG FIXES Text: Fix cbind() and rbind() of SummarizedExperiment objects when some of the assays are DataFrame or data.frame objects.

Version: 1.8.0 Category: BUG FIXES Text: ‘$’ completion on SummarizedExperiment works in RStudio and on RangedSummarizedExperiment.

SWATH2stats

Changes in version 1.7.7:

BUG FIXES

• update vignette to prevent misunderstanding what data to load

Changes in version 1.7.6:

BUG FIXES

• manual convert4PECA

Changes in version 1.7.5:

BUG FIXES

• library not recognized in vignette

Changes in version 1.7.4:

NEW FEATURES

• add function convert4PECA

Changes in version 1.7.3:

NEW FEATURES

• add option to keep all columns to disaggregate function

Changes in version 1.7.2:

NEW FEATURES

• add option to no not remove decoys to filter_proteotypic_peptides(), filter_on_max_peptides(), and filter_on_min_peptides()

Changes in version 1.7.1:

NEW FEATURES

• SWATH2stats in BioC 3.6 development release

Changes in version 1.6.1:

NEW FEATURES

• SWATH2stats in BioC 3.5 release

TarSeqQC

Changes in version 1.7.1:

• CITATION file was added to include the new publication describing TarSeqQC application on real datasets

TFARM

Changes in version 0.99.8:

MAJOR CORRECTIONS

• two datasets were renamed (from I to TF_Imp and from p to p_TFs)

• some loops were vectorized in the vignettes

TFBSTools

Changes in version 3.5:

NEW FEATURES

• Add function to parse MEME output.

• Add parallel computing of searchSeq.

Changes in version 3.4:

BUG FIXES

• Fix a bug in PFMSimilarity.

• Fix an error when there are multiple classes for motif matrx.

NEW FEATURES

• readJASPARMatrix function to add the JASPAR format file.

Changes in version 3.3:

BUG FIXES

• Adapt the runMEME to work with meme 4.10.x version.

• Fix the scientific notation in run_MEME

• Better error handling of MEME wrappe

tofsims

Version: 099.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: changed function behvaiour in the whole package from call-by-ref to call-by value. Adjusted accordingly all examples and the vignette.

Version: 099.1 Category: INTERNALS Text: depends now on ProtGenerics from which it uses ‘mz’

Version: 099.1 Category: INTERNALS Text: exchanged various print() with message()

Version: 099.1 Category: BUGFIXES Text:

topdownr

Changes in version 0.99.0 (2017-10-05):

• First public release.

TPP

Changes in version 3.5.0:

• New Bioconductor release candidate! Chenges in version 3.5.xx (May-xx-2017):

• Importing the whole tidyverse instead of ggplot2, dplyr etc. individually

• Shift tidyverse and Biobase to “depends” so that they are automatically availabe for downstream analyses.

trackViewer

Changes in version 1.13.11:

• fix the bug maxgap could not be less than 0 in findOverlaps

Changes in version 1.13.10:

• fix the bug documentation of ideogramPlot is different from the codes.

Changes in version 1.13.9:

• fix the bug when using findOverlaps, when ‘type’ is “any”, at least one of ‘maxgap’ and ‘minoverlap’ must be set to its default value

Changes in version 1.13.8:

• automatic set the font size in ideogramPlot

Changes in version 1.13.7:

• fix the bug in ideogramPlot when data range is identical for heatmap layout.

Changes in version 1.13.6:

• add draggable tracks in browseTracks function

Changes in version 1.13.5:

• add arrow tools in browseTracks function

Changes in version 1.13.4:

• add label tools in browseTracks function

Changes in version 1.13.3:

• fix bugs in browseTracks function

Changes in version 1.13.2:

• add more columns to GRoperator function

• add browseTracks function

transcriptogramer

Changes in version 1.0.0:

• Release of the transcriptogramer package at Bioconductor [YYYY-MM-DD].

treeio

Changes in version 1.1.2:

• new project site using blogdown <2017-09-28, Thu>

Changes in version 1.1.1:

• parse mlc file without dNdS <2017-08-31, Thu> + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/bioc-ggtree/hTRj-uldgAg

• better implementation of merge_tree <2017-08-31, Thu>

TRONCO

Changes in version 2.8.1:

• Minor fix on documentation

TVTB

Changes in version 1.3.2 (2017-09-02):

Bug fix

• Updated vignette output format for compatibility with BiocStyle (>= 2.5.19); one vignette turned to PDF to respect the package size limit in the new context.

Changes in version 1.3.1 (2017-05-30):

Bug fix

• Fixed VCF import from multiple files in Shiny application.

VariantFiltering

Changes in version 1.14:

USER VISIBLE CHANGES

• The ‘MafDb’ class and methods have been moved to the ‘GenomicScores’ package.

• ‘VariantFilteringResults’ objects also store now a ‘GenomeDescription’ object that can be fetched using the method ‘referenceGenome()’.

• Changes in the internal storage of ‘VariantFilteringResults’ objects that allow one to serialize this type of object with ‘saveRDS()’.

wiggleplotr

Changes in version 1.1.2:

• New makeManhattanPlot() function makes it easier visualise association p-values together with read coverage and transcript structure plots.

xcms

Changes in version 2.99.10:

BUG FIXES

• Fix #230: Failing vignettes on Windows.

Changes in version 2.99.9:

USER VISIBLE CHANGES

• Chromatographic peak detection uses adjusted retention times on an aligned XCMSnExp object (issue #213, #208).

• New parameter msLevel for processHistory,XCMSnExp.

• New parameter keepAdjustedRtime for filterMsLevel,XCMSnExp, dropChromPeaks, XCMSnExp and dropFeatureDefinitions,XCMSnExp.

• Add parameter msLevel to chromatogram,XCMSnExp method (issue #205).

• Obiwarp alignment is now performed on one MS level and adjustment is applied to all MS levels (issue #214).

• Add function plotMsData to plot intensity against retention time and m/z against retention time for a MS slice in one sample.

• Add argument msLevel = 1L to extractMsData method (issue #223).

• New applyAdjustedRtime function to consolidate the alignment results, i.e. replace the raw retention times in the XCMSnExp with the adjusted retention times.

• [,XCMSnExp method gains argument keepAdjustedRtime to allow keeping adjusted retention times in the sub-setting.

• Implement spectrapply,XCMSnExp to ensure returned results use adjusted retention times (if present).

• [[,XCMSnExp method returns a Spectrum object with adjusted retention time, if the XCMSnExp contains adjusted retention times.

• Argument ‘sampleGroups’ is mandatory for ‘PeakDensityParam’ (issue #228).

BUG FIXES

• Fix #191: Excessive memory use in fillPeaks.

• Fix #220: peaks matrix is missing column “sample” if no peaks were found in the first sample.

• Fix #222: findChromPeaks does not return an XCMSnExp object filtered to a single MS level despite peak detection is performed on a single level.

• Fix problem in plotMsData causing wrong colors to be used to label the data points.

Changes in version 2.99.8:

BUG FIXES

• Replace xcmsMSn Rnw with Rmd vignette to fix Windows build errors.

Changes in version 2.99.7:

BUG FIXES

• Fix #201: Warnings: ‘readMSData2’ is deprecated, thanks to L. Gatto.

• Merge with BioC git after transition

Changes in version 2.99.6:

NEW FEATURES

• calibrate,XCMSnExp method that allows to calibrate chromatographic peaks.

USER VISIBLE CHANGES

• Export phenoDataFromPaths function (issue $195).

• Add arguments mz and rt to featureDefinitions method allowing to extract features within the specified ranges.

• Increase n for the density function call in group density-based correspondence by 2.

• Replace xcmsDirect.Rnw with rmarkdown-based vignette using the new user interface.

BUG FIXES

• issue #196: removed the unnecessary requirement for same-dimension profile matrices in adjustRtime,XCMSnExp,ObiwarpParam.

• issue #194: fixes in retcor.obiwarp: 1) subset raw data if scanrange != NULL. 2) if the mz range of the two files to be aligned differ, expand them correctly. Depending on the profStep and the mz values/ranges the matrices were not expanded correctly.

• Potential problems in the plotChromPeakDensity function.

Changes in version 2.99.5:

USER VISIBLE CHANGES

• Re-enable sleep parameter in findPeaks.centWave and findPeaks.matchedFilter.

Changes in version 2.99.4:

NEW FEATURES

• Add plotChromPeaks function to plot the definition (rt and mz range) of detected chromatographic peaks of one file into the mz-rt plane.

• Add plotChromPeakImage function to plot the number of detected peaks along the retention time axis per file as an image plot.

USER VISIBLE CHANGES

• Move Chromatogram class and functionality to the MSnbase package

• Add argument msLevel to the findChromPeaks method to allow (chromatographic) peak detection also on MS level > 1.

BUG FIXES

• Polarity information was not read from mzXML files (issue #192).

Changes in version 2.99.3:

BUG FIXES

• issue #188: determine file type from file content if file ending not known.

Changes in version 2.99.2:

BUG FIXES

• issue #181: problem when isCentroided,Spectrum method returns NA because of too few peaks in a spectrum. Fixed by checking in such cases all spectra in the file.

• issue #184: add parameter sleep to do_groupChromPeaks_density function to be backwards compatible with the old group.density code.

Changes in version 2.99.1:

NEW FEATURES

• extractMsData to extract raw MS data as a data.frame (issue #120).

BUG FIXES

• issue #175: an error is now thrown if no peak group was identified for peak group retention time correction.

• issue #178: scanrange was collapsed when the adjusted range was reported (pull request by Jan Stanstrup).

• issue #180: error when both parameters method and smooth are provided in the retcor method.

Changes in version 2.99.0:

NEW FEATURES

• plotChromatogram and highlightChromPeaks functions.

• plotChromPeakDensity function.

• clean method for Chromatogram classes.

USER VISIBLE CHANGES

• Change default for ppm parameter in chromPeaks method to 0.

• extractChromatograms supports extraction of multiple rt and mz ranges.

• New parameter missing for extractChromatograms allowing to specify the intensity value to be used for rts for which no signal is available within the mz range.

• extractChromatograms returns Chromatograms of length equal to the number of scans within the specified rt range, even if no signals are measured (intensity values are NA).

Changes in version 1.53.1:

BUG FIXES

• Increase parameter n for the density call in the peak density correspondence method. This enables to separate neighboring peaks using small n (issue #161). Thanks to Jan Stanstrup.

xps

Changes in version 3.4:

VERSION xps-1.37.2

• configure.in file - unix line endings

VERSION xps-1.37.1

• update INSTALL and README file

yamss

Changes in version 1.3:

• Updating citation information.

• Changes related to moving Bioconductor from SVN to GIT.

zFPKM

Changes in version 0.99.18:

• initial release

• Methods adapted from primary manuscript

zinbwave

Changes in version 0.99.10 (2017-10-23):

• Added AIC and BIC to decide number of factors

• Added function to compute observational weights for DE

Changes in version 0.99.7 (2017-07-17):

• zinbwave() now returns a SingleCellExperiment object.

Changes in version 0.99.6 (2017-07-05):

• Fixed bug in zinb.loglik.matrix to avoid Inf values

Changes in version 0.99.5 (2017-07-03):

• Added function computeDevianceResiduals() to compute residuals

• Added function imputeZeros() to use the model to impute technical zeros

• Added function zinbwave() to perform dimensionality reduction

• Changed vignette to illustrate new functions

Changes in version 0.99.4 (2017-06-08):

• Switch from parallel to BiocParallel

• Improvements to code efficiency, e.g., avoid copying ZinbModel objects

Changes in version 0.99.3 (2017-05-31):

• More informative Description: field

• Improved documentation

• Added getAlpha, getBeta, and getGamma accessor functions

• Improved show() method

• Vectorized code in zinbSim()

• Fixed bug that introduced an error when initializing an object with empty X or V

• Added tests on numerical correctness

Changes in version 0.99.2 (2017-05-12):

• New formula interface for SummarizedExperiment

• Add t-SNE example to vignette

Changes in version 0.99.0 (2017-05-09):

• Bumped version for submission to Bioconductor

• Minor changes to compile vignette

• Required R version 3.4

Changes in version 0.1.4 (2017-04-10):

• Improved documentation

• zinbSim now produces matrix of J x n dimension

• Removed unnecessary dependency on clusterExperiment

• Additional tests

• Better default for epsilon

Changes in version 0.1.2 (2017-03-29):

• New vignette

• Change name to zinbwave

Changes in version 0.1.0 (2016-09-23):

• Introducing S4 class zinbModel

• Major restructuring of the initialization and optimization (see vignette)

• Method zinbFit to fit a model

• Many other methods, including zinbInitialize, zinbOptimize, zinbSim

Deprecated and Defunct Packages

Nine software packages were removed from this release (after being deprecated in BioC 3.5): pdmclass, coRNAi, GENE.E, mmnet, AtlasRDF, CopyNumber450k, saps, MeSHSim, GEOsearch.

Nine software packages (BioMedR, ddgraph, EWCE, HCsnip, stepwiseCM, domainsignatures, iontree, oneChannelGUI, RCytoscape ) are deprecated in this release and will be removed in BioC 3.7.

One experimental data package (CopyNumber450kData) was removed from this release (after being deprecated in BioC 3.5).

No experimental data packages are deprecated in this release.