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• Bioconductor 3.18 Released

October 25, 2023

Bioconductors:

We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books.

There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows, 1 new book, and many updates and improvements to existing packages.

Bioconductor 3.18 is compatible with R 4.3, and is supported on Linux, 64-bit Windows, Intel 64-bit macOS 11 (Big Sur) or higher and macOS arm64. This release will also include updated Bioconductor Docker containers.

Thank you to everyone for your contribution to Bioconductor

Visit Bioconductor BiocViews for details and downloads.

Contents

• Getting Started with Bioconductor 3.18
• New Software Packages
• New Data Experiment Packages
• New Annotation Packages
• New Workflow
• New Books
• NEWS from existing software packages
• NEWS from existing data experiment packages
• NEWS from existing workflows
• Deprecated and Defunct Packages

Getting Started with Bioconductor 3.18

To update to or install Bioconductor 3.18:

1. Install R 4.3. Bioconductor 3.18 has been designed expressly for this version of R.

2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 69 new software packages in this release of Bioconductor.

• adverSCarial adverSCarial is an R Package designed for generating and analyzing the vulnerability of scRNA-seq classifiers to adversarial attacks. The package is versatile and provides a format for integrating any type of classifier. It offers functions for studying and generating two types of attacks, single gene attack and max change attack. The single gene attack involves making a small modification to the input to alter the classification. The max change attack involves making a large modification to the input without changing its classification. The package provides a comprehensive solution for evaluating the robustness of scRNA-seq classifiers against adversarial attacks.

• alabaster.files Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.

• beachmat.hdf5 Extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.

• BioCartaImage The core functionality of the package is to provide coordinates of genes on the BioCarta pathway images and to provide methods to add self-defined graphics to the genes of interest.

• BiocBook A BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, …) who wish to 1) write (compile a body of biological and/or bioinformatics knowledge), 2) containerize (provide Docker images to reproduce the examples illustrated in the compendium), 3) publish (deploy an online book to disseminate the compendium), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases).

• CaDrA Performs both stepwise and backward heuristic search for candidate (epi)genetic drivers based on a binary multi-omics dataset. CaDrA’s main objective is to identify features which, together, are significantly skewed or enriched pertaining to a given vector of continuous scores (e.g. sample-specific scores representing a phenotypic readout of interest, such as protein expression, pathway activity, etc.), based on the union occurence (i.e. logical OR) of the events.

• CardinalIO Fast and efficient reading and writing of mass spectrometry imaging data files. Supports imzML and Analyze 7.5 formats. Provides ontologies for mass spectrometry imaging.

• CCPlotR CCPlotR is an R package for visualising results from tools that predict cell-cell interactions from single-cell RNA-seq data. These plots are generic and can be used to visualise results from multiple tools such as Liana, CellPhoneDB, NATMI etc.

• CDI Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be accurate. However, there have not been unsupervised metric designed for scRNA-seq to evaluate clustering performance. Hence, we propose clustering deviation index (CDI), an unsupervised metric based on the modeling of scRNA-seq UMI counts to evaluate clustering of cells.

• cfdnakit This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).

• ClustIRR ClustIRR is a quantitative method for clustering of immune receptor repertoires (IRRs). The algorithm identifies groups of T or B cell receptors (TCRs or BCRs) with similar specificity by comparing their sequences. ClustIRR uses graphs to visualize the specificity structures of IRRs.

• compSPOT Clonal cell groups share common mutations within cancer, precancer, and even clinically normal appearing tissues. The frequency and location of these mutations may predict prognosis and cancer risk. It has also been well established that certain genomic regions have increased sensitivity to acquiring mutations. Mutation-sensitive genomic regions may therefore serve as markers for predicting cancer risk. This package contains multiple functions to establish significantly mutated hotspots, compare hotspot mutation burden between samples, and perform exploratory data analysis of the correlation between hotspot mutation burden and personal risk factors for cancer, such as age, gender, and history of carcinogen exposure. This package allows users to identify robust genomic markers to help establish cancer risk.

• CuratedAtlasQueryR Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a SingleCellExperiment object.

• CytoPipelineGUI This package is the companion of the CytoPipeline package. It provides GUI’s (shiny apps) for the visualization of flow cytometry data analysis pipelines that are run with CytoPipeline. Two shiny applications are provided, i.e. an interactive flow frame assessment and comparison tool and an interactive scale transformations visualization and adjustment tool.

• DCATS Methods to detect the differential composition abundances between conditions in singel-cell RNA-seq experiments, with or without replicates. It aims to correct bias introduced by missclaisification and enable controlling of confounding covariates. To avoid the influence of proportion change from big cell types, DCATS can use either total cell number or specific reference group as normalization term.

• decontX This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2023), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset.

• demuxSNP This package assists in demultiplexing scRNAseq data using both cell hashing and SNPs data. The SNP profile of each group os learned using high confidence assignments from the cell hashing data. Cells which cannot be assigned with high confidence from the cell hashing data are assigned to their most similar group based on their SNPs. We also provide some helper function to optimise SNP selection, create training data and merge SNP data into the SingleCellExperiment framework.

• dreamlet Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of these data, complex study designs, and low read count per cell mean that characterizing cell type specific molecular mechanisms requires a user-frieldly, purpose-build analytical framework. We have developed the dreamlet package that applies a pseudobulk approach and fits a regression model for each gene and cell cluster to test differential expression across individuals associated with a trait of interest. Use of precision-weighted linear mixed models enables accounting for repeated measures study designs, high dimensional batch effects, and varying sequencing depth or observed cells per biosample.

• easylift The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with Bioconductor’s GRanges objects and chain files from the UCSC Genome Browser, allowing for straightforward handling of genomic ranges across various genome versions. One noteworthy feature of easylift is its integration with the BiocFileCache package. This integration automates the management and caching of chain files necessary for liftover operations. Users no longer need to manually specify chain file paths in their function calls, reducing the complexity of the liftover process.

• enrichViewNet This package enables the visualization of functional enrichment results as network graphs. First the package enables the visualization of enrichment results, in a format corresponding to the one generated by gprofiler2, as a customizable Cytoscape network. In those networks, both gene datasets (GO terms/pathways/protein complexes) and genes associated to the datasets are represented as nodes. While the edges connect each gene to its dataset(s). The package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps enable the visualization of enriched terms into a network with edges connecting overlapping genes.

• fenr Perform fast functional enrichment on feature lists (like genes or proteins) using the hypergeometric distribution. Tailored for speed, this package is ideal for interactive platforms such as Shiny. It supports the retrieval of functional data from sources like GO, KEGG, Reactome, and WikiPathways. By downloading and preparing data first, it allows for rapid successive tests on various feature selections without the need for repetitive, time-consuming preparatory steps typical of other packages.

• gatom This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.

• gDNAx Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin.

• gDR Package is a part of the gDR suite. It reexports functions from other packages in the gDR suite that contain critical processing functions and utilities. The vignette walks through the full processing pipeline for drug response analyses that the gDR suite offers.

• gDRcore This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the pipeline function allowing analyzing the data in a straightforward way.

• gDRimport The package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose-response data provided in different file formats.

• gDRstyle Package fills a helper package role for whole gDR suite. It helps to support good development practices by keeping style requirements and style tests for other packages. It also contains build helpers to make all package requirements met.

• gDRutils This package contains utility functions used throughout the gDR platform to fit data, manipulate data, and convert and validate data structures. This package also has the necessary default constants for gDR platform. Many of the functions are utilized by the gDRcore package.

• GenomicPlot Visualization of next generation sequencing (NGS) data is essential for interpreting high-throughput genomics experiment results. ‘GenomicPlot’ facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig); both coverage and enrichment over input can be computed and displayed with respect to genomic features (such as UTR, CDS, enhancer), and user defined genomic loci or regions. Statistical tests on signal intensity within user defined regions of interest can be performed and represented as boxplots or bar graphs. Parallel processing is used to speed up computation on multicore platforms. In addition to genomic plots which is suitable for displaying of coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) plots can also be made for RNAseq or CLIPseq data as well.

• gg4way 4way plots enable a comparison of the logFC values from two contrasts of differential gene expression. The gg4way package creates 4way plots using the ggplot2 framework and supports popular Bioconductor objects. The package also provides information about the correlation between contrasts and significant genes of interest.

• ggkegg This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.

• ggsc Useful functions to visualize single cell and spatial data. It supports both ‘SingleCellExperiment’ and ‘Seurat’ objects. It also supports visualizing the data using grammar of graphics implemented in ‘ggplot2’.

• GloScope This package aims at representing and summarizing the entire single-cell profile of a sample. It allows researchers to perform important bioinformatic analyses at the sample-level such as visualization and quality control. The main functions Estimate sample distribution and calculate statistical divergence among samples, and visualize the distance matrix through MDS plots.

• GNOSIS GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.

• HarmonizR An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.

• HERON HERON is a software package for analyzing peptide binding array data. In addition to identifying significant binding probes, HERON also provides functions for finding epitopes (string of consecutive peptides within a protein). HERON also calculates significance on the probe, epitope, and protein level by employing meta p-value methods. HERON is designed for obtaining calls on the sample level and calculates fractions of hits for different conditions.

• hicVennDiagram A package to generate high-resolution Venn and Upset plots for genomic interaction data from HiC, ChIA-PET, HiChIP, PLAC-Seq, Hi-TrAC, HiCAR and etc. The package generates plots specifically crafted to eliminate the deceptive visual representation caused by the counts method.

• hoodscanR hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.

• iNETgrate The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes.

• iSEEde This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of differential expression results. This package does not perform differential expression. Instead, it provides methods to embed precomputed differential expression results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.

• iSEEindex This package provides an interface to any collection of data sets within a single iSEE web-application. The main functionality of this package is to define a custom landing page allowing app maintainers to list a custom collection of data sets that users can selected from and directly load objects into an iSEE web-application.

• iSEEpathways This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of pathway analysis results. This package does not perform pathway analysis. Instead, it provides methods to embed precomputed pathway analysis results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.

• IsoBayes IsoBayes is a Bayesian method to perform inference on single protein isoforms. Our approach infers the presence/absence of protein isoforms, and also estimates their abundance; additionally, it provides a measure of the uncertainty of these estimates, via: i) the posterior probability that a protein isoform is present in the sample; ii) a posterior credible interval of its abundance. IsoBayes inputs liquid cromatography mass spectrometry (MS) data, and can work with both PSM counts, and intensities. When available, trascript isoform abundances (i.e., TPMs) are also incorporated: TPMs are used to formulate an informative prior for the respective protein isoform relative abundance. We further identify isoforms where the relative abundance of proteins and transcripts significantly differ. We use a two-layer latent variable approach to model two sources of uncertainty typical of MS data: i) peptides may be erroneously detected (even when absent); ii) many peptides are compatible with multiple protein isoforms. In the first layer, we sample the presence/absence of each peptide based on its estimated probability of being mistakenly detected, also known as PEP (i.e., posterior error probability). In the second layer, for peptides that were estimated as being present, we allocate their abundance across the protein isoforms they map to. These two steps allow us to recover the presence and abundance of each protein isoform.

• lemur Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed.

• MICSQTL Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.

• Moonlight2R The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). We present an updated version of the R/bioconductor package called MoonlightR, namely Moonlight2R, which returns a list of candidate driver genes for specific cancer types on the basis of omics data integration. The Moonlight framework contains a primary layer where gene expression data and information about biological processes are integrated to predict genes called oncogenic mediators, divided into putative tumor suppressors and putative oncogenes. This is done through functional enrichment analyses, gene regulatory networks and upstream regulator analyses to score the importance of well-known biological processes with respect to the studied cancer type. By evaluating the effect of the oncogenic mediators on biological processes or through random forests, the primary layer predicts two putative roles for the oncogenic mediators: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As gene expression data alone is not enough to explain the deregulation of the genes, a second layer of evidence is needed. We have automated the integration of a secondary mutational layer through new functionalities in Moonlight2R. These functionalities analyze mutations in the cancer cohort and classifies these into driver and passenger mutations using the driver mutation prediction tool, CScape-somatic. Those oncogenic mediators with at least one driver mutation are retained as the driver genes. As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, Moonlight2R can be used to discover OCGs and TSGs in the same cancer type. This may for instance help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV). In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.

• MSstatsBig MSstats package provide tools for preprocessing, summarization and differential analysis of mass spectrometry (MS) proteomics data. Recently, some MS protocols enable acquisition of data sets that result in larger than memory quantitative data. MSstats functions are not able to process such data. MSstatsBig package provides additional converter functions that enable processing larger than memory data sets.

• MultiRNAflow Our R package MultiRNAflow provides an easy to use unified framework allowing to automatically make both unsupervised and supervised (DE) analysis for datasets with an arbitrary number of biological conditions and time points. In particular, our code makes a deep downstream analysis of DE information, e.g. identifying temporal patterns across biological conditions and DE genes which are specific to a biological condition for each time.

• multiWGCNA An R package for deeping mining gene co-expression networks in multi-trait expression data. Provides functions for analyzing, comparing, and visualizing WGCNA networks across conditions. multiWGCNA was designed to handle the common case where there are multiple biologically meaningful sample traits, such as disease vs wildtype across development or anatomical region.

• nipalsMCIA Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the Nonlinear Iterative Partial Least Squares method (NIPALS) proposed in (Hanafi et. al, 2010). Allows multiple options for row- and table-level preprocessing, and speeds up computation of variance explained. Vignettes detail application to bulk- and single cell- multi-omics studies.

• orthos orthos decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large database of contrasts (derived from ARCHS4, https://maayanlab.cloud/archs4/) to identify similar experiments. orthos furthermore provides plotting functions to visualize the results of such a search for similar contrasts.

• partCNV This package uses a statistical framework for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. Our method uses an EM algorithm with mixtures of Poisson distributions while incorporating cytogenetics information (e.g., regional deletion or amplification) to guide the classification (partCNV). When applicable, we further improve the accuracy by integrating a Hidden Markov Model for feature selection (partCNVH).

• phantasusLite PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.

• plasmut A Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.

• plyinteractions Operate on GInteractions objects as tabular data using dplyr-like verbs. The functions and methods in plyinteractions provide a grammatical approach to manipulate GInteractions, to facilitate their integration in genomic analysis workflows.

• QTLExperiment QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It is based on the ‘SummarizedExperiment’ class and contains functions for creating, merging, and subsetting objects. ‘QTLExperiment’ also stores experiment metadata and has checks in place to ensure that transformations apply correctly.

• raer Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.

• RAIDS This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.

• regionalpcs Functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic regions to summarize the variability in methylation levels across CpGs. The number of principal components is chosen using either the Marcenko-Pasteur or Gavish-Donoho method to identify relevant signal in the data.

• RegionalST This package analyze spatial transcriptomics data through cross-regional analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.

• RNAseqCovarImpute The RNAseqCovarImpute package implements multiple imputation of missing covariates and differential gene expression analysis by: 1) Randomly binning genes into smaller groups, 2) Creating M imputed datasets separately within each bin, where the imputation predictor matrix includes all covariates and the log counts per million (CPM) for the genes within each bin, 3) Estimating gene expression changes using voom followed by lmFit functions, separately on each M imputed dataset within each gene bin, 4) Un-binning the gene sets and stacking the M sets of model results before applying the squeezeVar function to apply a variance shrinking Bayesian procedure to each M set of model results, 5) Pooling the results with Rubins’ rules to produce combined coefficients, standard errors, and P-values, and 6) Adjusting P-values for multiplicity to account for false discovery rate (FDR).

• roastgsa This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.

• Rvisdiff Creates a muti-graph web page which allows the interactive exploration of differential expression results. The graphical web interface presents results as a table which is integrated with five interactive graphs: MA-plot, volcano plot, box plot, lines plot and cluster heatmap. Graphical aspect and information represented in the graphs can be customized by means of user controls. Final graphics can be exported as PNG format.

• SARC Imports a cov/coverage file (normalised read coverages from BAM files) and a cnv file (list of CNVs - similiar to a BED file) from WES/ WGS CNV (copy number variation) detection pipelines and utilises several metrics to weigh the likelihood of a sample containing a detected CNV being a true CNV or a false positive. Highly useful for diagnostic testing to filter out false positives to provide clinicians with fewer variants to interpret. SARC uniquely only used cov and csv (similiar to BED file) files which are the common CNV pipeline calling filetypes, and can be used as to supplement the Interactive Genome Browser (IGV) to generate many figures automatedly, which can be especially helpful in large cohorts with 100s-1000s of patients.

• scDesign3 We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools.

• scider scider is an user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.

• simona The package implements a rich set of methods for semantic similarity analysis on bio-ontologies. They include methods for information contents, similarities between two terms as well as similarities between two groups of terms. It also implements visualizations on DAGs.

• tadar This package provides functions to standardise the analysis of Differential Allelic Representation (DAR). DAR compromises the integrity of Differential Expression analysis results as it can bias expression, influencing the classification of genes (or transcripts) as being differentially expressed. DAR analysis results in an easy-to-interpret value between 0 and 1 for each genetic feature of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.

• TSAR This package automates analysis workflow for Thermal Shift Analysis (TSAS) data. Processing, analyzing, and visualizing data through both shiny applications and command lines. Package aims to simplify data analysis and offer front to end workflow, from raw data to multiple trial analysis.

New Data Experiment Packages

There are 10 new data experiment packages in this release of Bioconductor.

• cfToolsData The cfToolsData package supplies the data for the cfTools package. It contains two pre-trained deep neural network (DNN) models for the cfSort function. Additionally, it includes the shape parameters of beta distribution characterizing methylation markers associated with four tumor types for the CancerDetector function, as well as the parameters characterizing methylation markers specific to 29 primary human tissue types for the cfDeconvolve function.

• gDRtestData R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains RDS files with MAE data processed by gDR.

• HCATonsilData This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary.

• HiBED Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells) in bulk brain tissues.

• multiWGCNAdata Stores expression profiling data from experiments compatible with the multiWGCNA R package. This includes human postmortem microarray data from patients and controls (GSE28521), astrocyte Ribotag RNA-seq data from EAE and wildtype mice (GSE100329), and mouse RNA-seq data from tau pathology (rTg4510) and wildtype control mice (GSE125957). These data can be accessed using the ExperimentHub workflow (see multiWGCNA vignettes).

• orthosData orthosData is the companion ExperimentData package to the orthos R package for mechanistic studies using differential gene expression experiments. It provides functions for retrieval from ExperimentHub and local caching of the models and datasets used internally in orthos.

• raerdata raerdata is an ExperimentHub package that provides a collection of files useful for demostrating functionality in the raer package. Datasets include 10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome and RNA-seq data. Additionally databases of human and mouse RNA editing sites are provided.

• smokingMouse This is an ExperimentHub package that provides access to the data at the gene, exon, transcript and junction level used in the analyses of the smokingMouse project. See https://github.com/LieberInstitute/smokingMouse_Indirects. This datasets contain the expression counts of genes, transcripts, exons and exon-exon junctions across 208 mice samples from pup and adult brains and adult blood. They also contain relevant information of these samples and features, such as conditions, QC metrics and if they were used after filtering steps and also if the features were differently expressed in the different experiments.

• SpatialDatasets This is a collection of publically available spatial omics datasets. Where possible we have curated these datasets as either SpatialExperiments, MoleculeExperiments or CytoImageLists and included annotations of the sample characteristics.

• TumourMethData TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies.

New Annotation Packages

There are 8 new annotation packages.

• AlphaMissense.v2023.hg19 Store Google DeepMind AlphaMissense v2023 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.

• AlphaMissense.v2023.hg38 Store Google DeepMind AlphaMissense v2023 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.

• cadd.v1.6.hg19 Store University of Washington CADD v1.6 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.

• cadd.v1.6.hg38 Store University of Washington CADD v1.6 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.

• HPO.db Human Phenotype Ontology (HPO) was developed to create a consistent description of gene products with disease perspectives, and is essential for supporting functional genomics in disease context. Accurate disease descriptions can discover new relationships between genes and disease, and new functions for previous uncharacteried genes and alleles.We have developed the DOSE package for semantic similarity analysis and disease enrichment analysis, and DOSE import an Bioconductor package DO.db to get the relationship(such as parent and child) between MPO terms. But DO.db hasn’t been updated for years, and a lot of semantic information is missing. So we developed the new package HPO.db for Human Human Phenotype Ontology annotation.

• JASPAR2024 JASPAR (https://testjaspar.uio.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20 percent increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF-binding sites in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.

• MPO.db We have developed the human disease ontology R package HDO.db, which provides the semantic relationship between human diseases. Relying on the DOSE and GOSemSim packages we developed, we can carry out disease enrichment and semantic similarity analyses. Many biological studies are achieved through mouse models, and a large number of data indicate the association between genotypes and phenotypes or diseases. The study of model organisms can be transformed into useful knowledge about normal human biology and disease to facilitate treatment and early screening for diseases. Organism-specific genotype-phenotypic associations can be applied to cross-species phenotypic studies to clarify previously unknown phenotypic connections in other species. Using the same principle to diseases can identify genetic associations and even help to identify disease associations that are not obvious. Therefore, as a supplement to HDO.db and DOSE, we developed mouse phenotypic ontology R package MPO.db.

• SomaScan.db An R package providing extended biological annotations for the SomaScan Assay, a proteomics platform developed by SomaLogic Operating Co., Inc. The annotations in this package were assembled using data from public repositories. For more information about the SomaScan assay and its data, please reference the ‘SomaLogic/SomaLogic-Data’ GitHub repository.

New Workflow Packages

There are no new workflow packages in this release of Bioconductor.

New Online Books

There is one new online book.

• BiocBookDemo This package has been created using the BiocBook package. It serves as a demo of a BiocBook online book. Read BiocBook package documentation to know more about BiocBooks.

NEWS from existing Software Packages

adverSCarial

            Changes in version 0.99.54 (2023-10-22)                 

• Ready for production

             Changes in version 0.99.1 (2023-04-05)                 
  

• Modify package to remove warnings and notes from BiocCheck

             Changes in version 0.99.0 (2023-02-05)                 
  

• Submitted to Bioconductor

affxparser

             Changes in version 1.73.0 (2023-04-25)                 

Notes

• The version number was bumped for the Bioconductor develop version, which is now Bioconductor 3.18 for R (>= 4.4.0).

ALDEx2

                    Changes in version 1.33                         

NEW FEATURES (MPN, GBG

• aldex.clr: now takes a gamma parameter to incorporate scale modelling

• aldex.makeScaleMatrix: new method to make an explicit scale model

• all p-values calculated are now posterior p-values with consistent sign

AnVIL

                   Changes in version 1.14.0                        

NEW FEATURES

• (v 1.13.1) Add paged support for large tables in avtable_import() and avtable_import_set().

• (v 1.13.2) Only show avtable_paged() and avtable_import*() progress bar in interactive() sessions

• (v 1.13.4) Report messages when avtable_import_status() contains one. https://github.com/Bioconductor/AnVIL/issues/79

• (v 1.13.3) Use ‘op’ when .avworkflow_response() calls avstop_for_status(). https://github.com/Bioconductor/AnVIL/issues/80

• (v 1.13.7) Check requester pays for destination URIs when using gsutil_cp (@smgogarten, #82)

USER VISIBLE CHANGES

• (v 1.13.8) Update documentation on updating workflow configurations. (@amstilp, #84)

AnVILPublish

                   Changes in version 1.12.0                        

Bug Fixes

• (v. 1.11.3) Link Rmd (and / or ipynb) vignettes to dashboard

apeglm

                   Changes in version 1.23.1                        

• Sometimes prefit.beta was NaN, now properly handled in apeglm(). Resolves some “Error in optimHess” issue propagated to DESeq2.

aroma.light

             Changes in version 3.31.1 (2023-06-30)                 

Documentation

• Update redirecting and broken URLs.

• Fix R CMD check notes on “Escaped LaTeX specials: &”.

             Changes in version 3.31.0 (2023-04-25)                 
  

Notes

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.18 for R (>= 4.4.0).

ASpli

                   Changes in version 2.11.1                        

BUG FIXES

• Solve bug in readCounts. Undefined seqnames produced invalid junctions.orders

• Change package mantainer

                   Changes in version 2.10.1                        
  

BUG FIXES

• Solves jCounts() Error in av[at] <- a[at] : NAs are not allowed in subscripted assignments bug with large junction possitions.

ATACseqQC

                   Changes in version 1.25.2                        

• Add reNormalizeByDistalSig parameter to plotFootprints function.

                   Changes in version 1.25.1                        
  

• Fix the error ‘number of columns of matrices must match’ for TSSEscore.

BASiCS

             Changes in version 2.13.3 (2023-06-16)                 

• Reverts LazyData to false based on BiocCheck feedback

             Changes in version 2.13.2 (2023-06-16)                 
  

• Changes LazyData to true to avoid errors

             Changes in version 2.13.1 (2023-06-16)                 
  

• Fixes error in tests associated to the behaviour of matrixStats::colMedians

benchdamic

             Changes in version 1.7.5 (2023-10-13)                  

• Updated DA_Seurat() for the new version

• Waiting for bug-fix: DA_ANCOM() (random effects not working)

• Waiting for bug-fix: DA_mixMC() (multilevel analysis not working)

• Bug-fix: correct dataset name in unit tests

• Bug-fix: in DA_ALDEx2() replaced unlist() with as.vector()

• Minor documentation updates related to dependencies

             Changes in version 1.7.4 (2023-07-22)                  
  

• Reducing the number of comparisons in vignette to reduce build time

             Changes in version 1.7.3 (2023-07-11)                  
  

• Bug-fix: Minor changes in vignette

             Changes in version 1.7.2 (2023-07-09)                  
  

• Bug-fix for DA_Maaslin2() function

             Changes in version 1.7.1 (2023-07-07)                  
  

• New methods: linDA, Maaslin2, ZicoSeq

• New method: mixMC (temporarily unavailable)

• Add ‘alpha’ parameter in DA_ANCOM()

             Changes in version 1.7.0 (2023-04-25)                  
  

• Bump x.y.z version to odd y following creation of RELEASE_3_18 branch

             Changes in version 1.6.4 (2023-07-22)                  
  

• Porting the changes of devel version 1.7.4 to release

             Changes in version 1.6.3 (2023-07-11)                  
  

• Porting the changes of devel version 1.7.3 to release

             Changes in version 1.6.2 (2023-07-09)                  
  

• Porting the changes of devel version 1.7.2 to release

             Changes in version 1.6.1 (2023-07-08)                  
  

• Porting the changes of devel version 1.7.1 to release

BindingSiteFinder

                   Changes in version 1.7.12                        

• Updated the vignette to feature differential binding analysis

                   Changes in version 1.7.11                        
  

• assignToGenes() no requires binding sites to fully overlapp the gene range to be assigned to that gene

• added plotBsMA() and plotBsVolcano() to visualize differential binding output

                   Changes in version 1.7.10                        
  

• added calculateBsBackground() and calculateBsFoldChange() core function for differntial binding analysis

                    Changes in version 1.7.9                        
  

• fixed a bug in combineBSF() where meta data was not correctly merged

                    Changes in version 1.7.8                        
  

• added combineBSF() function to combine two or more object of type BSFDataSet

                    Changes in version 1.7.7                        
  

• Fixed a bug in exportToBED() which caused the export to fail if the last function exectuted was calculateSignalToFlankScore()

• Updated rangeCoveragePlot() to work with clipCoverage() function

• Added the clipCoverage() function as improoved function calculate coverage

                    Changes in version 1.7.6                        
  

• Update assignToGenes() to not require a gene annotation when options ‘remove’ or ‘keep’ is selected

                    Changes in version 1.7.5                        
  

• Update vignette to include all new options

• Exchanged default test object to fit new class definition

• Let estimateBsWidth() fail more gracefull when no maximum can be found

• Fix name space dependencies

                    Changes in version 1.7.4                        
  

• Added region length based normalization to transcriptRegionSpectrumPlot()

• Changed minWidth default from (3 -> 2) in makeBindingSites()

• Allow object subsetByChr() to handle multiple chromosomes

• Added calculateSignalToFlankScore() function

• Added binding site definedness plot

• Added a ‘local’ version to estimateBsWidth() if no maximum can be found on global level

• Added a ‘sensitivity’ mode to estimateBsWidth()

                    Changes in version 1.7.3                        
  

• Started major rework

• Restructuring of class definition

• Added BSFind() as core function

• Added workflow functions pureClipGlobalFilter(), estimateBsWidth(), pureClipGeneWiseFilter(), assignToGenes(), assignToTranscriptRegions()

• Reworked makeBindingSites(), reproducibilityFilter(), annotateWithScore()

• Added plotting functions processingStepsFlowChart(), pureClipGlobalFilterPlot(), estimateBsWidthPlot(), duplicatedSitesPlot(), mergeCrosslinkDiagnosticsPlot(), makeBsSummaryPlot(), reproducibilityFilterPlot(), reproducibilitySamplesPlot(), reproducibilityScatterPlot(), geneOverlapsPlot(), targetGeneSpectrumPlot(), transcriptRegionOverlapsPlot(), transcriptRegionSpectrumPlot(), bindingSiteDefinednessPlot()

                    Changes in version 1.7.2                        
  

• Added further input checks to reproducibilityFilter() function

                    Changes in version 1.7.1                        
  

• Fix Namesspace issues

                    Changes in version 1.6.1                        
  

• Fix bugs in colorPalette option

• Added custom coloring

bioCancer

                   Changes in version 1.29.05                       

• Comment pickGO during running examples: It works manually.

                   Changes in version 1.29.01                       
  

• Correct items format in NEWS file

• Import needed packages

• Add @method section in documentation of cgdsr methods

• Update links and reference in the vignette

BiocBaseUtils

                    Changes in version 1.4.0                        

New features

• Added isScalarLogical for completeness; identical to isTRUEorFALSE.

BiocCheck

                   Changes in version 1.38.0                        

BUG FIXES AND MINOR IMPROVEMENTS

• Exclude data docs with \\format tags in addition to ‘package’ docs when checking for \\value / @return in documentation.

• Resolve unknown macro warnings when using Rdpack (@LiNK-NY, #196)

• Improve the read.dcf operation that looks for any deprecated packages in both Bioconductor release and devel versions.

• Remove overwrite prompt when updating cached resources in deprecated packages check.

BiocFileCache

                     Changes in version 2.9                         

USER VISIBLE CHANGE

• (2.9.1) Add documentation for operating behind a proxy

BiocHubsShiny

                    Changes in version 1.2.0                        

Bug fixes and minor improvements

• Updated the NEWS.md file formatting

BioCor

                    Changes in version 1.26                         

• Added support for plots of similarities

BiocPkgTools

                   Changes in version 1.20.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• biocRevDepEmail accepts a vector of deprecated packages for whose reverse dependencies are to be notified.

• biocDownloadStats now filters out packages that are not part of the pkgType option and strictly returns stats for Bioconductor packages

• When package stats are not available for a particular year, biocDownloadStats will warn about the year there is no data for.

BUG FIXES

• Warn when a download stats URL is not available and filter out in pkgDownloadStats.

• pkgDownloadRank calculates the denominator for ranks using the VIEWS file; matches Bioc badges more closely.

BiocStyle

                   Changes in version 2.30.0                        

BUG FIXES

• Addressed issue where code chunks in HTML output did not have the correct background colour

• Fixed incompatibility with ragged2e LaTeX package distributed in TexLive 2023 (https://github.com/Bioconductor/BiocStyle/issues/105)

biocthis

                   Changes in version 1.11.3                        

BUG FIXES

• Fixed internal code on use_bioc_news_md(), use_bioc_readme_rmd(), and use_bioc_vignette() after usethis changed some of their un-exported functions that biocthis relies on.

                   Changes in version 1.11.2                        
  

BUG FIXES

• Ignore remotes::system_requirements(“ubuntu”, “20.04”) for now since that leads to a JSON error. See https://github.com/lcolladotor/biocthis/issues/41 but also https://github.com/LieberInstitute/spatialLIBD/commit/edc8b72505af097895dcbf35887df28da8122e3c.

                   Changes in version 1.11.1                        
  

BUG FIXES

• Resolved https://github.com/lcolladotor/biocthis/issues/40 reported by @lmweber with help from @bschilder and @LiNk-NY noted at https://github.com/neurogenomics/rworkflows/issues/58. Basically, there’s no longer a need to explicitly list the AnVIL repositories to benefit from those gains.

biodbHmdb

             Changes in version 1.7.1 (2023-09-20)                  

• Fix truncation of HMDB Metabolites XML file.

biomaRt

                   Changes in version 2.58.0                        

USER VISIBLE CHANGES

• getSequence() will now provide a more informative error message if requesting a flanking sequence and not provided with an upstream or downstream range.

• Remove references to the uswest mirror, which has now been retired (https://www.ensembl.info/2023/01/13/retirement-of-ensembl-us-west-aws-mirror/)

BioNAR

                     Changes in version 1.3                         

• Take into account edge weights in clustering algorithms and centrality measure calculations.
• Add calculation of the DYNAMO perturbation pattern from signed weight directed networks proposed in Santolini,M. and Barabasi,A.-L. (2018) PNAS 169, 201720589

• Decoupled from synaptome.db and synaptome.data packages. All code, related to graph building from the synaptome.db data is moved to synaptome.db package.

                    Changes in version 1.2.1                        
  

• Allow analysis of directed graphs and add four new centrality measures specific for the directed graphs.
• Modify annotation functions to allow annotate nodes not only by its name propety but by any other arbitrary property if its value uniquely identify the node.
• Added new framework for the visualisation and analysis of enrichment results.

biosigner

                   Changes in version 1.29.2                        

MINOR MODIFICATION

• minor update of the ‘show’ method

Biostrings

                   Changes in version 2.70.0                        

NEW FEATURES

• Character set of AAString/AAStringSet/AAStringSetList objects is now enforced (a long-due feature). Thanks to Aidan Lakshman ahl27@pitt.edu for implementing this.

BridgeDbR

                   Changes in version 2.11.2                        

BUG FIXES

• Fixed build/test process by including a long-running example into the dontrun{} environment

                   Changes in version 2.11.1                        
  

NEW FEATURES

• Migrated NEWS to NEWS.md
• Applied BioC code styling
• Added templates for issues and feature requests
• Added a method exists(mapper, xref) that checks if the xref is found in the mapping file

SIGNIFICANT USER-VISIBLE CHANGES

• loadDatabase() now reports an error if the given location does not exist

BUG FIXES

• Fixed backwards compatibility of map()
• Clarified in the vignette the output getMatchingSources()
• Fixed returning an empty data frame when no mappings are found for map()

BSgenomeForge

                    Changes in version 1.2.0                        

NEW FEATURES

• Two improvements to forgeBSgenomeDataPkgFromNCBI() when the NCBI assembly is registered in the GenomeInfoDb package:
  • The assembly name can be specified via the ‘assembly_accession’ argument instead of its GenBank or RefSeq accession.
  • The ‘organism’ argument no longer needs to be specified.

CaDrA

                   Changes in version 0.99.1                        

• Published in https://github.com/montilab/CaDrA
• CaDrA-Shiny repo for web interface: https://github.com/montilab/CaDrA-shiny
• Web Interface: https://cadra.bu.edu/

CAGEr

                    Changes in version 2.8.0                        

BUG FIXES

• Correct quantile positions, which were shifted by one base. This bug may have been introduced in version 1.22 or later.
• Ensure cluster objects are properly sorted. Fixes #79, introduced in version 2.6.0 and causing crashes or incorrect quantile calculations.
• Apply fix for #77 (aggregateTagClusters losing TCs), which slipped out of 2.6.0 because of Git branch mixup.
• Fix consensus cluster coordinates, where the maxDist padding was erroneously remaining in some parts of the computation.
• Corrected on-the-fly cumulative sum computation for consensus clusters when sample = NULL. The bug was causing incorrectly short quantile ranges.
• Force the cluster names to stay sorted, to avoid a bug desynchronising quantile information and genome coordinates.
• Fix accidental deletion of the record of the tag clustering method (#96).

NEW FEATURES

• Allow URLs to files in getCTSS() (Fixes #50).
• Accelerated the computation of quantile position by ~20 times.
• New resetCAGEexp() function.
• New flagByUpstreamSequences() function.
• The annotateCTSS and annotateConsensusClusters function gain a upstream and a downstream parameter to change the width of promoter regions.

Cardinal

             Changes in version 3.3.5 (2023-10-19)                  

BUG FIXES

• Allow ‘guess.max=Inf’ in ‘readImzML()’

             Changes in version 3.3.4 (2023-10-19)                  
  

SIGNIFICANT USER-VISIBLE CHANGES

• Bin peaks when importing centroid spectra with ‘readImzML()’

• Replaced all functions from deprecated ‘sp’ package

                    Changes in version 3.3.3                        
  

BUG FIXES

• Fixed I/O bugs introduced by matter v2.3.13 changes

                    Changes in version 3.3.2                        
  

BUG FIXES

• Fixed I/O bugs introduced by matter v2.3.11 changes

• Other I/O bugs fixed by matter v2.3.13 changes

                    Changes in version 3.3.1                        
  

BUG FIXES

• Merged 3.2.1 fixes to resolve R CMD check warnings

                    Changes in version 3.2.1                        
  

BUG FIXES

• Cleaned up escaped LaTeX specials in documentation

• Fixed ‘sprintf()’ => ‘snprintf()’ warning in C code

CardinalIO

                   Changes in version 0.99.2                        

NEW FEATURES

• Added support for additional binary data arrays

SIGNIFICANT USER-VISIBLE CHANGES

• Casefold checksums and UUIDs before comparison

                   Changes in version 0.99.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Added package-level ‘CardinalIO’ help page

                   Changes in version 0.99.0                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Update ‘Analyze75’ and ‘ImzML’ classes for Bioconductor

• Prepare for Bioconductor submission

cBioPortalData

                   Changes in version 2.14.0                        

Bug fixes and minor improvements

• Remove error when studyId build success is unknown (@vlaufer, #69)
• Parse tokens with different formats, e.g. genie token (@ZWael, #70)
• Clean up duplicate rows created in the sampleMap generated from the data
• Fixed warning trigger when empty molecularProfileId datasets are found

CCPlotR

             Changes in version 0.99.3 (2023-10-06)                 

• Made changes to address Bioconductor reviews

• added unit tests

• added validity checks and helpful error messages for function arguments

• set Lazydata to false

             Changes in version 0.99.2 (2023-09-19)                 
  

• Added extra optional paramaters to cc_circos and cc_network functions

             Changes in version 0.99.1 (2023-08-18)                 
  

• Submitted to Bioconductor

CellBarcode

                    Changes in version 1.7.0                        

New features

• bc_extract_sc_sam: function to extract single-cell barcodes from SAM file
• bc_extract_sc_fastq: function to extract single-cell barcodes from fastq file
• bc_plot_count: function to plot the count feature of the barcodes such as barcode reads versus total reads, reads per UMI distribution.

Incompatible changes

bc_extract now only accepts a vector or list, and returns BarcodeObj, instead of returning data.frame when the input is a single sample.

cellxgenedp

                     Changes in version 1.6                         

• (v 1.5.2) use CELLxGENE ‘Discover’ API, changing column names of some return values. See ‘API changes’ of the ‘Discover and download datasets…’ vignette.

cfdnakit

             Changes in version 0.99.4 (2023-05-28)                 

• fix required issues and suggesstion except code formatting including lien space and line length.

             Changes in version 0.99.0 (2022-11-09)                 
  

• Submitted to Bioconductor

cfTools

                    Changes in version 1.2.0                        

NEW FEATURES

• Add the cfSort() function, which is the first supervised tissue deconvolution approach with deep learning models.

• Publish the cfToolsData package to supply models and marker files for cfTools.

ChIPpeakAnno

                   Changes in version 3.35.3                        

• update documentation for the annotatePeakInBatch function

                   Changes in version 3.35.1                        
  

• fix the seqlevelsStyle check for custom species.

circRNAprofiler

                   Changes in version 1.15.2                        

• Possibility to use a maximum of 3 unsupported/‘other’ tools.

ClassifyR

                    Changes in version 3.6.0                        

• Balancing of non-censored event times across folds.

• Multiview methods with combinations of views have improved plots that switch to UpSet axis.

• Multiview methods have feature extractors to retain chosen features for analysis.

clusterProfiler

                    Changes in version 4.9.5                        

• fixed R check (2023-10-18, Wed)

                    Changes in version 4.9.4                        
  

• use check_installed() to check package dependency (2023-09-08, Fri, #621)

• use yread() in WikiPathway utilities (2023-09-07, Thu)

                    Changes in version 4.9.3                        
  

• enrichKEGG() and gseKEGG() now supports organism = ‘cpd’ to accept KEGG Compound ID (2023-08-31, Thu)
• gson_cpd() and gson_ko()
• use yulab.utils::yread() to parse file (2023-08-15, Tue)

• supports Pathways Common (2023-08-02, Wed, #613)

                    Changes in version 4.9.2                        
  

• append_kegg_category() function to add KEGG pathway category information to KEGG enrichment result and now it is the default behavior of enrichKEGG() and gseKEGG() (2023-07-12, Wed)
• parse KEGG Pathway Category information (2023-07-11, Tue)
• mv parse_gff() to GOSemSim::read.gaf() and re-export (2023-07-10, Mon)

• mv buildGOmap() to `GOSemSim::buildGOmap() and re-export

                    Changes in version 4.9.1                        
  

• getPPI() to query PPI network from ‘stringdb’ (2023-05-15, Mon)
• getTaxID() and getTaxInfo() functions to query taxonomy information (2023-05-14, Sun)

ClustIRR

                 Changes in version 0.99.28-29                      

• Accepted in Bioconductor

               Changes in version 0.99.20-0.99.26                   
  

• Functions added for: graph building, joining, plotting

• S4 object accessors added

                   Changes in version 0.99.16                       
  

• Changes after first round of review done

• Now we have two versions (old version=1 removed, unused)

• S4 object output of clust_irr

                   Changes in version 0.99.4                        
  

• Build errors/warnings fixed

                   Changes in version 0.99.0                        
  

• Submitted to Bioconductor

CNVfilteR

                   Changes in version 1.15.2                        

MINOR

• Fixed bug: CopyNumberPlots requires additional parameter

CNVMetrics

                    Changes in version 1.5.1                        

NEW FEATURES

• processSim() method generates simulated samples with copy number profiles derived from a specific sample.

SIGNIFICANT USER-VISIBLE CHANGES

• None

BUG FIXES

• None

compcodeR

                   Changes in version 1.37.3                        

• Removed support for baySeq since it has been deprecated

• Added runComparisonShiny function

compSPOT

                   Changes in version 0.99.10                       

• Edits made based on reviewer comments

                   Changes in version 0.99.0                        
  

• Submitted to Bioconductor

COTAN

                    Changes in version 2.1.8                        

Made passing clusterizations to COTAN functions more easy: now all functions that take a COTAN object and a clusterization as input parameters can also take a clusterization name

Added time-stamps to log entries when written on a log file

Fixed bug in the clustersMarkersHeatmapPlot function when given a clusterization not matching the latest added to the COTAN object

Fixed issue with the highest possible resolution in seuratClustering() function, needed when large datasets must be split in many clusters

                    Changes in version 2.1.7                        

Added new flag to the function cleanPlots() to suppress evaluation of the PCA on the normalized data. In particular, this allows to reduce significantly time spent within the function checkClusterUniformity()

Added initialResolution parameter to cellsUniformClustering(): it allows users to specify the initial resolution used in the calls to Seurat::FindClusters() method. It now uses the same default as Seurat

Added new method estimateNuLinearByCluster() that calculates nu ensuring that its average is 1.0 in each given cluster

                    Changes in version 2.1.6                        

Added function reorderClusterization(): it reorders the given clusterization so that near clusters have also near labels

The functions cellsUniformClustering() and mergeUniformCellsClusters() now return the result of this new function

Separated p-value calculations from DEAOnClusters() into the new function pValueFromDEA(). Those data.frames are no longer part of the list returned by the functions DEAOnClusters() and mergeUniformCellsClusters()

Added function getClusters() to retrieve the wanted clusterization from the cells’ meta-dataset

Added function calculateGenesCE(): it returns the cross-entropy between the expected absence of a gene reading against the observed state

Fixed minor issue with logThis() to file: it was always appending a new line even when appendLF was set to FALSE

Now checkClusterUniformity() returns more GDI stats like the percentage of genes above threshold or the last percentile of the GDI values

Revamped mergeUniformCellsClusters() to select in order all the the most likely candidates pairs of clusters to merge. Provided new user parameter to balance the merging of most possible candidates versus the time spent doing so

Improved dropGenesCells() method: it now retains all meta-data information that is not related to the results of the other methods

Added zoomed UDE plot to cleanPlots() return. It suggests a possible cut level for low UDE cells

                    Changes in version 2.1.5                        

Improved mergeUniformCellsClusters(): now it attempts to merge more clusters pairs

Now errors in the seuratClustering() function are interpreted as remaining cells not-clustered “-1”. This applies mostly to cases when Seurat finds only singlets

Added flag calcCoex to proceedToCoex() and automaticCOTANObjectCreation() functions to allow user not to spend time calculating the genes’ COEX when not needed

Solved potential issue in the clustersMarkersHeatmapPlot() regarding clusters’ labels

Added new internal function niceFactorLevels() that ensures all the factors’ levels will have labels with the same length, via padding the integers values with ‘0’ and string values with ‘_’

Relaxed tolerance on tests comparing against saved data

                    Changes in version 2.1.4                        

Speed-up by use of parallelDist::parDist() to calculate distances instead of stats::dist()

Fixed regression tests failing on non-Linux architectures

                    Changes in version 2.1.3                        

Completed function clustersMarkersHeatmapPlot()

Added new utility function normalizeNameAndLabels()

Added mergeClusters() and multiMergeClusters() functions

Added support to conditions in cells’ meta-data

Now clusterizations are stored as factors

Fixed COTAN::validity method in AllClasses.R

                    Changes in version 2.1.2                        

Fixed bug in proceedToCoex() in cases when saveObj == TRUE

                    Changes in version 2.1.1                        

Updated README.md and NEWS.md

Renamed methods dealing with housekeeping genes and fully-expressed cells to use the more proper names fully-expressed genes and fully-expressing cells

Added possibility to users to set the cutoff and thresholds used by the clean and related methods

                    Changes in version 2.1.0                        

First release in Bioconductor 3.18

CTdata

                     Changes in version 1.1                         

CTdata 1.1.5

• Assay from CT_methylation_in_tissues() converted from a tibble to a matrix.
• Suggest and load SingleCellExperiment in vignette.
• Update vignette figure.

CTdata 1.1.4

• New data: scRNAseq_HPA and testis_sce.
• Updated data: CT_methylation_in_tissues, CT_mean_methylation_in_tissues, TCGA_CT_methylation, CT_genes and CCLE_correlation_matrix.

CTdata 1.1.3

• Load SummarizedExperiment in vignette.

CTdata 1.1.2

• Suggest SummarizedExperiment.

CTdata 1.1.1

• Only display a small subset of CCLE_correlation_matrix() in the vignette.

CTdata 1.1.0

• New Bioconductor devel release.

cytomapper

             Changes in version 1.13.1 (2023-09-26)                 

• loadImages: fixed pattern argument to only test on the actual files and not the path.

CytoML

                    Changes in version 3.11                         

API Changes

• Rename argument sampNLoc -> sample_names_from in open_flowjo_xml
• All parsers (flowjo/cytobank/diva_to_gatingset) now return GatingSet based on cytoset rather than ncdfFlowSet
• Add trans argument to cytobank_to_gatingset to allow overriding of transformations from gatingML file (#76)
• gatingset_to_flowjo now uses a docker image with a compiled converter: hub.docker.com/r/wjiang2/gs-to-flowjo
• Some updates to how flowjo_to_gatingset searches for FCS files (#77)
• Add include_empty_tree option to flowjo_to_gatingset to include samples without gates
• Allow gatingset_to_flowjo to take a path to a GatingSet archive directory
• Add gating_graphGML to replace gating.graphGML method for openCyto::gating generic
• Filter samples by panel when parsing cytobank experiment and add ce_get_samples, ce_get_panels

Fixes/internal changes

• Automatic time scaling of samples from FlowJo workspaces now handled by flowjo_to_gatingset RGLab/cytolib#33
• Handle change to default stringsAsFactors=FALSE in R 4.0
• Eliminated extra intermediate files left in temp directory during workspace parsing
• Switch usage of GatingSetList to merge_gs_list
• Solve some Windows build issues
• Switch from experimental::filesystem to boost::filesystem in C++ FlowJo parser

• Add CytoML XSD to installation

                    Changes in version 3.10                         
  

API Changes

• Change handling of quad gates according to RGLab/cytolib#16

• Renaming of methods:

• openWorkspace -> open_diva_xml, open_flowjo_xml
• cytobankExperiment -> open_cytobank_experiment
• cytobank2GatingSet -> cytobank_to_gatingset
• parseWorkspace -> flowjo_to_gatingset, diva_to_gatingset
• getSampleGroups -> fj_ws_get_sample_groups, diva_get_sample_groups
• getSamples -> fj_ws_get_samples, diva_get_samples
• getKeywords -> fj_ws_get_keywords
• getCompensationMatrices -> ce_get_compensations
• getTransformation -> ce_get_transformations

• compare.counts -> gs_compare_cytobank_counts

• Renaming of classes:

• divaWorkspace -> diva_workspace

• flowJoWorkspace -> flowjo_workspace

• Add CytoML.par.set, CytoML.par.get for setting parameters in CytoML namespace

Fixes/internal changes

• Make gatingset_to_cytobank export cytobank ML with attribute namespaces
• Allow diva_to_gatingset to use compensation matrix from xml
• Pass … args from cytobank_to_gatingset appropriately down to FCS parser
• Fix some issues with scaling of gates parsed from Diva workspace (#64)
• Guard against unsupported transformations being added to GatingSet during Diva parsing
• Switch diva_to_gatingset to using flowjo_log_trans instead of logtGml2_trans
• Fix ported flowUtils::xmlTag to enable self-closing tags
• Make gating.graphGML lookup tailored gates by FCS name as well as file id
• Add some flexibility to getSpilloverMat used in gatingset_to_flowjo

CytoPipeline

                     Changes in version 1.1                         

CytoPipeline 1.1.5

• areSignalCols(), are FluoCols() can now accept a flowSet as input, on top of a flowFrame
• applyScaleTransforms() processing step has been improved (can take flowSet as input, checks channel concordance between transList and data object)

CytoPipeline 1.1.4

• updated fcs files, that are at the source of OMIP021Samples dataset

CytoPipeline 1.1.3

• in subSample(), renamed parameter ‘nSamples’ into ‘nEvents’, and added possibility for passing unused parameters, in order to support the use of the function as a processing step. Also amended the function as to keep the original order of the events (keep chronology). Finally, adds a ‘keepOriginalCellIDs’ parameter (default=TRUE).
• simplified the arguments of execute() related to the storage of the results after last pre-processing step.

CytoPipeline 1.1.2

• storage of phenoData into cache upon execution of CytoPipeline object (and back into CytoPipeline object when re-built from cache)
• changed the default behaviour of estimateScaleTransforms() so that the default method for scatter channels is now “none” instead of “linearQuantile”
• changed default behaviour of ggplotEvents() and ggplotFilterEvents(), when logicle scale is used but no logicle parameters provided, these are now estimated using flowCore::estimateLogicle(), instead of explicit default values

CytoPipeline 1.1.1

• tiny modifications to support upgrade to Bioc 3.18

CytoPipeline 0.99

CytoPipeline 0.99.6

• corrected the OMIP021Samples fcs data in order to keep the original file name
• bug correction: error message on execution with no sample file
• added phenoData slot in CytoPipeline object
• updated readSamples() to allow passing a pData parameters
• updated compensateFromMatrix() to allow passing a mapping based on a pData variable
• updated readSamples() to allow selecting a random number of samples and removed selectSamples()
• vignette with demo and links to videos

CytoPipeline 0.99.5

• reactivated unit tests for ggplot2 objects
• added man page for CytoPipeline package
• a few modifs in the vignette related to Bioc review process
• replaced withr::local_tempdir() by base::tempdir()
• removed extraneous whitespaces in CytoPipeline show() method
• removed LazyData: true in DESCRIPTION file
• replaced paste0(path, “/”, filename) by file.path(path, filename)
• updated License field in DESCRIPTION file

CytoPipeline 0.99.4

• improved CytoPipeline constructors (experimentName and sampleFiles are now parameters of all constructor version)
• centralized the production of standard outputs during pipeline execution, set all tuning parameters in execute() instead of slots in CytoPipeline object.

CytoPipeline 0.99.3

• some minor changes for BiocCheck()

CytoPipeline 0.99.2

• removed dependencies to a number of packages, moved corresponding implementations of CytoProcessingSteps (wrappers) into CytoPipelineUtils package

CytoPipeline 0.99.1

• Maintenance due to Bioc version change (3.17)
• removed use of openCyto::gate_tail() (disappeared w/o deprecation), replaced by flowDensity::deGate()
• implemented export of pre-processed file (writeFlowFrame as a CytoProcessingStep implementation)
• extended readSampleFiles : mapping between channels and markers
• selectRandomSamples (new CytoProcessing step implementation)

CytoPipeline 0.99.0

• Prior to Bioconductor submission

CytoPipelineGUI

                    Changes in version 0.99                         

CytoPipelineGUI 0.99.2

• added ShinyApps as additional BiocView

CytoPipelineGUI 0.99.1

• Modified man pages and vignettes to address comments raised during Bioconductor submission

CytoPipelineGUI 0.99.0

• First version

cytoviewer

             Changes in version 1.1.3 (2023-10-19)                  

• enlarged default display area and changed default color settings

             Changes in version 1.1.2 (2023-10-09)                  
  

• vignette updates

             Changes in version 1.0.1 (2023-07-27)                  
  

• added validation messages and fixes for metadata overlay

• added more tests and validation checks

DCATS

             Changes in version 0.99.7 (2023-05-25)                 

• Added CITATION.cff file

             Changes in version 0.99.6 (2023-05-25)                 
  

• Updated license information and changed the version of R requirement to R (>= 4.1.0)

             Changes in version 0.99.5 (2023-05-12)                 
  

• Updated version to trigger a new biuld in Bioconductor

             Changes in version 0.99.4 (2023-05-11)                 
  

• Made changes recommended in Bioconductor review process

             Changes in version 0.99.3 (2023-04-21)                 
  

• Added NEWS file

• Made changes recommended in Bioconductor review process

• Made changes recommended in Bioconductor review process

dearseq

             Changes in version 1.13.3 (2023-06-16)                 

• bug fix on Linux: default number of cores for parallel computations is now detect_cores(logical=FALSE) - 1

             Changes in version 1.12.1 (2023-05-28)                 
  

• weights_var2test_condi is enforced to FALSE for the permutation test

decontX

             Changes in version 0.99.5 (2023-10-19)                 

• First submission to Bioconductor after review.

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”)

DelayedArray

                   Changes in version 0.28.0                        

NEW FEATURES

• Add coercion from DelayedArray to SparseArray.

• Add efficient rowVars/colVars methods for DelayedMatrix objects. These methods, like all other row/col summarization methods implemented in the DelayedArray package, use block processing and can handle blocks of arbitrary geometry, that is, they can handle a grid of class ArbitraryArrayGrid (the most general type of grid).

• Add ‘useNames’ arg to row/colMins, row/colMaxs, row/colRanges, and row/colVars methods for DelayedMatrix objects.

• Add ‘current_viewport’ argument to set_grid_context().

SIGNIFICANT USER-VISIBLE CHANGES

• DelayedArray now depends on S4Arrays and SparseArray.

• Some improvements to the rowMeans/colMeans methods for DelayedMatrix objects.

DelayedMatrixStats

                    Changes in version 1.23                         

• colAnyMissings() and rowAnyMissings() are deprecated in favour of the long-recommended colAnyNAs() and rowAnyNAs(). These deprecated functions will be made defunct in the next release cycle.

demuxSNP

                    Changes in version 0.99                         

Submitted to Bioconductor

Features

Functions to create a supervised demultiplexing classification model using cell hashing and SNPs to aid in:

• SNP selection
• creating training data using demuxmix
• adding SNPs data to SingleCellExperiment objects
• cell assignment

DepecheR

             Changes in version 1.17.4 (2023-08-14)                 

• Adding collapse package to the description file.

• Correction of the generateSparseData function.

• Set.seed removed from two places and now non-present in the package.

             Changes in version 1.17.3 (2023-07-26)                 
  

• Correction to groupProbPlot, as the last version threw out the most significant cells.

             Changes in version 1.17.2 (2023-07-14)                 
  

• Correction to scale in groupProbPlot.

             Changes in version 1.17.1 (2023-07-13)                 
  

• A mode option is added to the neighSmooth function.

• The scale of the groupProbPlot output is corrected, to -100, over 50 to 100.

DESeq2

                   Changes in version 1.42.0                        

• collapseReplicates() now noisier (warning) about other assays.

• plotPCA() prints out the ngenes setting.

• Added pcsToUse for plotPCA (idea from Vince Carey)

• Added test that SE exist for lfcShrink (in case of glmGamPoi fitType).

                   Changes in version 1.41.13                       
  

• collapseReplicates() now noisier (warning) about other assays.

• plotPCA() prints out the ngenes setting.

                   Changes in version 1.41.8                        
  

• Use of MatrixGenerics

                   Changes in version 1.41.4                        
  

• Fixed dispersionFunction argument issue.

                   Changes in version 1.41.2                        
  

• Added pcsToUse for plotPCA (idea from Vince Carey)

                   Changes in version 1.41.1                        
  

• Added test that SE exist for lfcShrink (in case of glmGamPoi fitType).

DESpace

                    Changes in version 1.0.2                        

• sample-specific covariates allowed

                    Changes in version 1.0.1                        
  

• bug fixed in vignettes (giving error: “there is no package called ‘reticulate’”)

DifferentialRegulation

                   Changes in version 1.98.0                        

• bulk RNA-seq data allowed: the package now works with both bulk and single-cell RNA-seq data.

dittoSeq

                    Changes in version 1.14                         

• Feature Extensions:
  1. ‘dittoDotPlot()’ & ‘dittoPlotVarsAcrossGroups()’: Improved ‘group.by’ ordering control via retention of factor levels and addition of a new ‘groupings.drop.unused’ input to control retention of empty levels.
  2. ‘dittoHeatmap()’: Targeting Seurat clusters with the “ident” shortcut now works for the ‘annot.by’ input of ‘dittoHeatmap()’.
• Bug Fixes:
  1. ‘dittoHeatmap()’: Fixed a feature exclusion check in ‘dittoHeatmap()’ meant to remove features without any non-zero values. Previously, it removed all features with a mean of zero, which blocked plotting from pre-scaled data.
  2. ‘dittoDimPlot()’ & ‘getReductions()’: Eliminated cases where ‘getReductions()’ did not return NULL for ‘object’s containing zero dimensionality reductions. This fix also improves associated error messaging of ‘dittoDimPlot()’ where such cases were missed.

DMRcate

                   Changes in version 2.15.1                        

• DMR.plot() updated: ellipsis removed; biomaRt gene tracks now used; collapseTranscripts=”meta”; exonAnnotation=”symbol”; overlapping regions plotted as optional extra

• goregion() ontology changed to KEGG and for hypomethylated DMRs only

DNAcopy

                   Changes in version 1.75.5                        

• Fixed the bug in passing weights for weighted segmentation

                   Changes in version 1.75.4                        
  

• Updated the reference and source for Coriell data

                   Changes in version 1.75.3                        
  

• Added init.c to register native (Fortran) routines and to disable symbol search

• Gzipped cytoBand.tab and converted default.DNAcopy.bdry to rda file in data directory

                   Changes in version 1.75.2                        
  

• Added a NEWS.md file to track changes to the package.
• changed all dfloat in fortran to dble (Ripley email for CRAN/clinfun)

DOSE

                   Changes in version 3.27.3                        

• update TERM2NAME() to return term if corresponding name not found. (2023-10-09, Mon)

                   Changes in version 3.27.2                        
  

• use ‘MPO.db’ and ‘HPO.db’ to support phenotype ontology for mouse and human (2023-06-30, Fri)

                   Changes in version 3.27.1                        
  

• options(enrichment_force_universe = TRUE) will force enrichment analysis to intersect the universe with gene sets (2023-05-03, Wed)
• use inherits to judge the class of objects (2022-11-20, Sun)
• test whether slot in GSON object is NULL (e.g., GSON@keytype) when assigning it to enrichment result (2022-11-07, Mon)

dreamlet

                   Changes in version 0.99.28                       

• Sept 5, 2026

• Update error handling for processAssays() and fitVarPart()

                   Changes in version 0.99.26                       
  

• August 18, 2026

• Update error handling and documentation

                   Changes in version 0.99.23                       
  

• August 8, 2023

• run styler::style_pkg()

                   Changes in version 0.99.22                       
  

• August 8, 2023
• dreamletCompareClusters() now allows cell-level covariates in response to https://github.com/GabrielHoffman/dreamlet/issues/11

• Fix code for Bioconductor submission

                   Changes in version 0.99.21                       
  

• July 17, 2023

• Improve functionality and documentation of dreamlet::residuals()

                   Changes in version 0.99.20                       
  

• June 29, 2023
• in processAssays() use voomWithDreamWeights(…, span=”auto”) to estimate the lowess tuning parameter

• rare error in merge_metadata() when a cell type is not observed for all donors.

                   Changes in version 0.99.19                       
  

• June 28, 2023

• in dreamlet() fix issue when contrasts are specified and formula includes variable from metadata()

                   Changes in version 0.99.18                       
  

• June 27, 2023

• add assays argument to buildClusterTreeFromPB()

                   Changes in version 0.99.14                       
  

• June 16, 2023

• bug fix in processAssays() when assays is dropped

                   Changes in version 0.99.13                       
  

• May 31, 2023
• improved error reporting

• Compatibility with variancePartition v2.0.5 (renamed 1.31.1)

                   Changes in version 0.99.12                       
  

• May 24, 2023
• required zellkonverter (>= 1.10.1) to avoid issues with previous version

• issue solved by https://github.com/theislab/zellkonverter/blob/b56718d113327020c024e188d9ac67ea57eaf35d/R/AnnData2SCE.R#L351

                   Changes in version 0.99.11                       
  

• May 12, 2023

• Compatibility with variancePartition v2.0.1

                   Changes in version 0.99.10                       
  

• April 24, 2023
• Fix issue in raised in Bioconductor submission: https://github.com/Bioconductor/Contributions/issues/2955#issuecomment-1498070980

• Compatibility with variancePartition v2.0.0

                   Changes in version 0.99.6                        
  

• March 29, 2023

• fix topTable() for dreamletResult in the case where one or more cells didn’t estimate the coefficient of interest

                   Changes in version 0.99.3                        
  

• March 23, 2023
• reduce compiler time

• add computeNormCounts() and computeLogCPM()

                   Changes in version 0.99.1                        
  

• March 20, 2023

• fix Biocondcutor submission based on https://github.com/Bioconductor/Contributions/issues/2955#issuecomment-1476037237

                   Changes in version 0.99.0                        
  

• March 15, 2023
• Biocondcutor submission

dupRadar

                   Changes in version 1.30.3                        

• Fix warning associated with documentation

• Ignore installation of license file

                   Changes in version 1.30.2                        
  

• Correctly added roxygen2 imports to remove warnings on package checks

easylift

                    Changes in version 1.0.0                        

• Bioconductor release 3.18

                   Changes in version 0.99.9                        
  

• Bug fixes and further improvements to the code.

                   Changes in version 0.99.1                        
  

• Updated the code and documentation to reflect the changes suggested by the Bioconductor team.

                   Changes in version 0.99.0                        
  

• Submitted to Bioconductor

EBSeq

                    Changes in version 2.0.0                        

• A new implementation of the core functions EBTest and EBMultiTest, which scales up the computation for big number of conditions to compare.

edgeR

                    Changes in version 4.0.0                        

• New statistical methods implemented in glmQLFit() to ensure accurate estimation of the quasi-dispersion for data with small counts. The new method computes adjusted residual deviances with adjusted degrees of freedom to improve the chisquare approximation to the residual deviance. The new methodology includes the new argument ‘top.proportion’ for glmQLFit() to specify the proportion of highly expressed genes used to estimate the common NB dispersion used in the new method. The output DGEGLM object contains new components leverage, unit.deviance.adj, unit.df.adj, deviance.adj, df.residual.adj and working.dispersion. The new method can be turned on legacy=FALSE. By default, glmQLFit() will give the same results as in previous releases of edgeR.

• New argument ‘covariate.trend’ for glmQLFit() to allow a user-specified covariate for the trended prior used to estimate the quasi-dispersions.

• The gene set testing functions roast(), mroast(), fry(), camera() and romer() now have S3 methods for DGEGLM objects.

• The edgeR Introductory vignette is converted from Sweave and pdf to Rmd and html.

• Revised help pages for filterByExp() and catchSalmon().

enrichplot

                   Changes in version 1.21.3                        

• set_enrichplot_color(), a helper function to set colors (2023-09-13, Wed)
• change default color: from c(“red”, “blue”) to c(“#e06663”, “#327eba”)

• use check_installed() to check package dependency (2023-09-08, Fri, #254)

                   Changes in version 1.21.2                        
  

• introduce ‘facet’ parameter in dotplot() method for compareClusterResult. If facet = “intersect”, the dots will be separated by enriched pathway intersection among clusters. It can set to other variable that can be used for splitting the figure (e.g., “category” for KEGG results) (2023-08-21, Mon)

                   Changes in version 1.21.1                        
  

• fixed cnetplot.compareClusterResult() for only contains one cluster (2023-05-24, Wed, #243)

enrichViewNet

                   Changes in version 0.99.2                        

NEW FEATURES

• The man pages are respecting 80 character width.

                   Changes in version 0.99.1                        
  

NEW FEATURES

• The ‘Installation’ and ‘Introduction’ sections of the vignette have been updated.

                   Changes in version 0.99.0                        
  

NEW FEATURES

• The new ‘createEnrichMap()’ function enables the creation of an enrichment map from enrichment results.

ensembldb

                   Changes in version 2.25.1                        

• Skip reading gtf file from Ensembl ftp server in unit test.

epialleleR

             Changes in version 1.9.8 (2023-09-29)                  

• creates sample BAMs

• linearized MHL

             Changes in version 1.9.4 (2023-07-03)                  
  

• methylation calls for bwa-meth, etc

             Changes in version 1.9.2 (2023-06-21)                  
  

• both paired-end and single-end alignments

epigraHMM

                    Changes in version 1.9.1                        

• Fix normalization of log-probabilities in cpp code to avoid underflow

epistack

             Changes in version 1.7.1 (2022-07-21)                  

• New parameters in plotEpistack(): rel_widths and rel_heights, to adjust the relative widths and heights of the panels.
• In plotEpistack(), the boxMetric panel is now a bit higher.

• plotMetric() now have a ylab parameter, exposed in plotEpistack()

• left-most panel in plotEpistack() is a bit wider
• fixed a code typo in vignette

escheR

                    Changes in version 1.2.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Add generic functions to support SingleCellExperiment object by providing values to the argument dimred, and data.frame object
• Modify the generic function make_escheR.SpatialExperiment to support SpatialExperiment that is beyond Visium

• Update and add new vignette to show how to work with SingleCellExperiment to visualize dimred and color palette for bi-variate display.

                    Changes in version 1.1.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• The dependency on the package spatialLIBD are removed
• Revise the README file to add explanations for Gestalt Principles to help users grasp the big picture idea without going to read the manuscript.

esetVis

                   Changes in version 1.27.1                        

• rbokeh plot - fixes error:
  • when no aesthetic variable is specified
  • dataPlotWithAnnotationWthtNA not found
• add GO.db to the ‘Suggests’

EWCE

                    Changes in version 1.9.3                        

Bug fixes

• generate_bootstrap_plots
• Use stored gene_data object whenever possible.

• Only show filtered celltypes.

                    Changes in version 1.9.2                        
  

Bug fixes

• generate_bootstrap_plots

• Missing available parameters for check_ewce_genelist_inputs() call.

                    Changes in version 1.9.1                        
  

Bug fixes

• drop_uninformative_genes
• Hash out DGE options. Somehow these got re-exposed to users in Bioc>=3.16.

ExperimentHub

                    Changes in version 2.9.0                        

DOCUMENTATION

• (2.9.1) Document access behind a proxy

extraChIPs

                   Changes in version 1.5.14                        

• Added p_mu0 to output of fitAssayDiff()

• Added respectLevels and filtering to plotProfileHeatmap()

                   Changes in version 1.5.13                        
  

• Added handling of unquoted column names to most plotting functions
• Added passing of specific columns to dualFilter

• Added drop to addDiffStatus

                   Changes in version 1.5.12                        
  

• Added plotGrlCol()

                   Changes in version 1.5.11                        
  

• Added defineSeqinfo()

                   Changes in version 1.5.10                        
  

• Added bed format to importPeaks()

                    Changes in version 1.5.8                        
  

• Added control of side-axis label position for plotProfileHeatmap()

• Added option to return merged key-value ranges for mergeByHMP()

                    Changes in version 1.5.7                        
  

• Matched DiffBind and csaw settings for fitAssayDiff()
• Added min_win to all merging functions

• Added n_max to getProfileData()

                    Changes in version 1.5.6                        
  

• Added mapGrlCols()

                    Changes in version 1.5.5                        
  

• Added plotPairwise() and addDiffStatus()

                    Changes in version 1.4.2                        
  

• Added Fixed-width vignette & edited sliding window
• Added se and peaks as example data for man pages and vignettes
• Included defineRegions()
• Enabled plotHFCG() without Ideogram tracks
• Enabled use of offsets for normalisation in fitAssayDiff()

fastreeR

             Changes in version 1.5.2 (2023-08-24)                  

• Update java backend to BioInfoJavaUtils-1.4.0 (haploid GT in vcf).

             Changes in version 1.5.1 (2023-04-30)                  
  

• Update java backend to BioInfoJavaUtils-1.3.1 (fasta header name).

             Changes in version 1.5.0 (2023-04-27)                  
  

• Bump x.y.z version to odd y following creation of RELEASE_3_17 branch.

fenr

                   Changes in version 0.99.7                        

• Minor changes to prepare for Bioconductor release

• Reverting temporarily to readr version 1 to circumvent a vroom 1.6.4 bug

                   Changes in version 0.99.6                        
  

In response to reviewer’s comments

• The wording in the vignette was adjusted to more clearly convey the purpose of the package to users
• Rewritten the description in DESCRIPTION file to clearly convey the purpose of the package to users

BioPlanet seems defunct

• Removed BioPlanet for good, as their webpage is continuously down and the maintainer is not responding

Minor adjustments to speed up building and testing

• Removed KEGG from interactive example to speed up vignette building (GO and Reactome are sufficient for a simple example)
• Replaced yeast with simpler organisms in Wiki and KEGG tests to speed up testing

• Replaced yeast with simpler organisms in Wiki and KEGG examples to speed up checking

                   Changes in version 0.99.5                        
  

• Major overhaul following comments from Bioconductor’s reviewer.

                   Changes in version 0.99.4                        
  

• Taking BiocCheck new warnings into account: adding @return to data roxygens.

                   Changes in version 0.99.3                        
  

• Continuing issues with access to BioPlanet. fetch_bp example is now marked donotrun and testing fetch_bp is removed to ensure smooth build and check even when BioPlanet server is down.

             Changes in version 0.99.2 (2023-05-24)                 
  

• BioPlanet’s tripod.nih.gov SSL certificate seems to be fixed, so reversing to the original read_csv code.

             Changes in version 0.99.1 (2023-04-25)                 
  

• BioPlanet database vanished from internet and there is no sign of it coming back. Removing all BioPlanet-related code and replacing BioPlanet with GO in the vignette and examples (this, alas, makes it longer to check).
• OK, it is back, but I keep GO examples and vignettes.

• Minor improvements to documentation.

             Changes in version 0.99.0 (2023-04-20)                 
  

• Pre-release Bioconductor version.

fishpond

                    Changes in version 2.8.0                        

• Corrected a bug in the two-group interaction (without pairing) functionality, when the groups were imbalanced, as identified by Samuel Chen. Fixes GitHub issue #35.

                    Changes in version 2.7.1                        
  

• Corrected a bug in the two-group interaction (without pairing) functionality, when the groups were imbalanced, as identified by Samuel Chen. Fixes GitHub issue #35.

fmrs

                    Changes in version 2.0.1                        

IMPROVEMENTS SINCE LAST RELEASE

• Non-mixture of regression models are now added to the package.

BUG FIXES

• Several bugs are fixed.

                    Changes in version 2.0.0                        
  

IMPROVEMENTS SINCE LAST RELEASE

• The package is rewritten using .Call function.
• The codes for Weibull distribution are improved.

BUG FIXES

• Several bugs are fixed which caused the results to be different for the same analysis.

gcatest

             Changes in version 2.1.9 (2023-07-26)                  

• Commented out one more strict test (NA deviances) that fail too often on bioconductor.

             Changes in version 2.1.8 (2023-07-18)                  
  

• Commented out two more strict tests (for non-negative deviances) that fail too often on bioconductor.

             Changes in version 2.1.7 (2023-06-20)                  
  

• Commented out various excessive tests against glm, which differ more often than expected due to poor or lack of convergence.
• Removed unused LaTeX package dependencies from vignette to prevent errors restricted to specific testing platforms.

• Fixed ..density.. deprecation warning in vignette plot.

             Changes in version 2.1.6 (2023-05-25)                  
  

• Version bump for bioconductor devel.

             Changes in version 2.0.6 (2023-05-25)                  
  

• README.md upgraded links from http to https

• Minor doc reformatting automatically performed by roxygen2.

             Changes in version 2.0.5 (2021-06-18)                  
  

• Lots of minor changes for Bioconductor update.
• DESCRIPTION:
• Updated to Authors@R.
• Lengthened “Description” paragraph.
• Increased R dependency from 3.2 to 4.0.
• Reformatted this NEWS.md slightly to improve its automatic parsing.
• Added examples for function delta_deviance_lf.
• Updated vignette to reflect that lfa::read.bed has been deprecated in favor of genio::read_plink and BEDMatrix objects.
• Updated README.md, including corrections to examples.
• Updated citations:
• README.md: only had GCATest paper link, now has full citation and also full LFA citation.
• Vignette: used to point to LFA arXiv preprint, now points to published paper.
• inst/CITATION: didn’t exist! Now includes both LFA and GCATest papers.
• Added LICENSE.md.
• Internal changes:
• All unexported functions are now prefixed with a period.
• Replaced 1:x with seq_len(x) several functions.

• Reformatted all code with package reformatR and otherwise match Bioconductor guidelines.

           Changes in version 2.0.4.9000 (2021-05-13)               
  

• Function delta_deviance_lf debugged case where either LF0 or LF1 is a column matrix. Previously these 1-column matrices were getting dropped to a vector incorrectly, which resulted in the mysterious error message “Error: argument is of length zero”. This 1-column case is not typically observed in gcatest, but is common in the reverse-dependent jackstraw package.

           Changes in version 2.0.3.9000 (2021-05-11)               
  

• Added function delta_deviance_lf, which calculates the delta deviance from two logistic models and the genotype matrix data. This function is a more general version of gcat.stat (which uses the new function internally), to essentially consider models that differ by more than one degree of freedom. It was written in particular for an external application in mind, namely the jackstraw package.

• Internal function assoc_snp was renamed to delta_deviance_snp_lf and its last argument changed to match that of delta_deviance_lf (alternative logistic factors instead of trait).

           Changes in version 2.0.2.9000 (2021-03-01)               
  

• Added internal tests for deviance calculations against stats::glm.

• Deviance code (internal delta_deviance_snp) now returns NA instead of stopping when an “impossible” case is encountered (when the genotype x is non-zero but the fitted probabilities under either null or alternative model are zero, or the alternative allele dosage (x-2) has the same problem). These cases are clearly model fitting failures, and can arise for common ill-defined problems, particularly under binary adjustment variables passed to gcat together with rare variants; these individual cases are not handled any better by stats::glm, so it seemed most sensible to return NA at such loci and not stop.

           Changes in version 2.0.1.9000 (2021-02-16)               
  

• Documentation updates:

• Fixed links to functions, in many cases these were broken because of incompatible mixed Rd and markdown syntax (now markdown is used more fully).

           Changes in version 2.0.0.9000 (2020-11-13)               
  

Major overhaul from last version (1.3.2, last updated 2016-10-06). Visible differences are support for BEDMatrix and fewer cases in which association p-values are NA. Internally there was major code restructuring, and added unit tests for all functions.

• User-facing changes: Functions gcat/gcatest/gcat.stat

• added support for BEDMatrix objects for the genotype matrix X.
• This consumes lower memory when the number of loci m is very large, so it enables analysis of larger datasets.
• Fixed some cases where the test statistic (the delta deviance) and ultimately the p-values were NA or NaN and are no longer missing.
• One common case is when fitted probabilities were zero or one, which used to lead to NaN deviances when their correct contribution was instead zero (because the limit of p*log(p) as p goes to zero is zero, not 0 * (-Inf) = NaN).
• Other NA and NaN cases are avoided in the lfa function af_snp (fixed in lfa 2.0.0.9000, 2020-09-18) used to estimate the individual-specific allele frequencies used here to compute the delta deviance. However, in rare cases the logistic regression in af_snp fails to converge or there are other problems, resulting in NA values propagated to GCATest’s test statistic and p-values.

• Otherwise, the new delta deviance code (function delta_deviance_snp) is more numerically-stable than before.

• Internal changes

• Separated R functions into one source file each.
• Added more input checks to all functions.
• Added .gitignore files from another project.
• Added unit tests for all functions using testthat.
• Removed internal assoc C code
• Previously only used for genotype data without missingness (so practically not on real datasets)
• Was entirely redundant with lfa::af_snp, which is now called in all cases instead.
• Had bugs concerning handling of p == 0 or 1 cases that are better handled in assoc_snp R code
• Minor scattered changes solely to pass latest R CMD check requirements.

gDNAx

             Changes in version 0.99.6 (2023-05-26)                 

USER VISIBLE CHANGES

• Submission of the first version to the Bioconductor project.

gDR

             Changes in version 0.99.9 (2023-10-18)                 

• adjust NEWS to Bioc format

             Changes in version 0.99.8 (2023-08-17)                 
  

• update README

             Changes in version 0.99.7 (2023-08-17)                 
  

• clean-up
• update documentation

• simplify Docker-based installation

             Changes in version 0.99.6 (2023-05-22)                 
  

• format the vignette with BiocStyle

             Changes in version 0.99.5 (2023-05-11)                 
  

• fix related with data.table

             Changes in version 0.99.4 (2023-04-20)                 
  

• switch to OSI license

             Changes in version 0.99.3 (2023-04-13)                 
  

• update documentation (Bioc-compatibility)

             Changes in version 0.99.2 (2023-04-07)                 
  

• update maintainer

             Changes in version 0.99.1 (2023-04-04)                 
  

• update requirements (gDRcore)

             Changes in version 0.99.0 (2023-03-23)                 
  

• switch to Bioc compatible versioning

gDRcore

            Changes in version 0.99.43 (2023-10-17)                 

• adjust NEWS to Bioc format

            Changes in version 0.99.42 (2023-10-05)                 
  

• bump version of gDRtestData

• fix bug with merging controls in triple combo with additional perturbations

            Changes in version 0.99.41 (2023-09-25)                 
  

• add support for adding custom annotations inside input files

• improve the performance

            Changes in version 0.99.40 (2023-09-25)                 
  

• fix bug with subsetting wrong combo matrix value

            Changes in version 0.99.39 (2023-09-19)                 
  

• extend the logic for matching missing controls

            Changes in version 0.99.38 (2023-09-12)                 
  

• set Drug3 as an official tertiary drug in the experiment

            Changes in version 0.99.37 (2023-09-04)                 
  

• fill NA by average values when there is no match with plate

            Changes in version 0.99.36 (2023-09-01)                 
  

• fill NA during aggregation of ref and trt data with mean

            Changes in version 0.99.35 (2023-08-17)                 
  

• fix issue with missing subsetting Day0 data

            Changes in version 0.99.34 (2023-08-16)                 
  

• update logic for supporting manifest and template files sharing the same column

            Changes in version 0.99.33 (2023-08-10)                 
  

• update annotation column names for cell line annotation as per changes in the gDRutils

            Changes in version 0.99.32 (2023-07-25)                 
  

• extended logic for supporting cols with dash, e.g. additional perturbations with “-“

            Changes in version 0.99.31 (2023-07-19)                 
  

• update the logic for handling warnings in the pipeline

            Changes in version 0.99.30 (2023-07-13)                 
  

• fix issue with wrong merging of data.tables without nested confounders

            Changes in version 0.99.29 (2023-07-07)                 
  

• add information about source type for cases without metric data

• refactor the logic for splitting raw data from metadata (get rid of iterative approach)

            Changes in version 0.99.28 (2023-07-05)                 
  

• update logic for parallel computing

            Changes in version 0.99.27 (2023-06-29)                 
  

• optimize unit tests

            Changes in version 0.99.26 (2023-06-29)                 
  

• remove backward compatibility for old data model

            Changes in version 0.99.25 (2023-06-27)                 
  

• fix bug with missing rownames in normalized assay

            Changes in version 0.99.24 (2023-06-19)                 
  

• update logic for merging data.table objects

            Changes in version 0.99.23 (2023-06-13)                 
  

• replace order with data.table::setorder

            Changes in version 0.99.22 (2023-06-09)                 
  

• switch from merge to [[ for data.table objects

            Changes in version 0.99.21 (2023-06-06)                 
  

• switch from aggregate to data.table

            Changes in version 0.99.20 (2023-06-07)                 
  

• switch from zoo::rollmean to data.table::frollmean

            Changes in version 0.99.19 (2023-06-06)                 
  

• replaced reshape2 functions by functions from data.table

            Changes in version 0.99.18 (2023-05-31)                 
  

• fix managing of mixed types of raw data

            Changes in version 0.99.17 (2023-05-29)                 
  

• fix bug with subsetting data for calculating isobologram

            Changes in version 0.99.16 (2023-05-22)                 
  

• format the vignette with BiocStyle

            Changes in version 0.99.15 (2023-05-16)                 
  

• fix related with data.table

            Changes in version 0.99.14 (2023-05-15)                 
  

• rename excess to x to unify colnames in assay data

            Changes in version 0.99.13 (2023-05-10)                 
  

• refactor normalization_types in combo-specific assays

            Changes in version 0.99.12 (2023-05-09)                 
  

• utilize gDRutils::apply_bumpy_function in fit_SE

            Changes in version 0.99.11 (2023-05-05)                 
  

• fix bug with swapping untreated/vehicle values

            Changes in version 0.99.10 (2023-05-04)                 
  

• fix bug with data.table

             Changes in version 0.99.9 (2023-04-21)                 
  

• utilize gDRutils::apply_bumpy_function in average_SE

             Changes in version 0.99.8 (2023-04-20)                 
  

• switch to OSI license

             Changes in version 0.99.7 (2023-04-19)                 
  

• fix bug with replacing vehicle to untreated values

             Changes in version 0.99.6 (2023-04-19)                 
  

• moved wrapper fuctions from gDRtestData

             Changes in version 0.99.5 (2023-04-18)                 
  

• update dependencies

• add fix for bioc-devel (correct sorting in merge test)

             Changes in version 0.99.4 (2023-04-17)                 
  

• fix namespacing issue in examples
• add R 4.2 as dependency

• fix examples for normalize_SE

             Changes in version 0.99.3 (2023-04-12)                 
  

• add logic for retrieving raw data from assay data

             Changes in version 0.99.2 (2023-04-07)                 
  

• update maintainer

             Changes in version 0.99.1 (2023-04-04)                 
  

• bugfix for the logic in ‘cleanup_metadata’

             Changes in version 0.99.0 (2023-03-24)                 
  

• make the package Bioc-compatible

gDRimport

            Changes in version 0.99.25 (2023-10-17)                 

• adjust NEWS to Bioc format

            Changes in version 0.99.24 (2023-10-02)                 
  

• add functions & unit tests for converting gDR MAE to PSet

            Changes in version 0.99.23 (2023-09-22)                 
  

• correct plate size calculation

            Changes in version 0.99.22 (2023-09-20)                 
  

• set barcode as character in the manifest file

            Changes in version 0.99.21 (2023-09-14)                 
  

• disable support for ‘xls’ file format due to crashes

            Changes in version 0.99.20 (2023-08-25)                 
  

• refactor subsetting of data.table using colname

            Changes in version 0.99.19 (2023-07-19)                 
  

• update warning messages

            Changes in version 0.99.18 (2023-07-02)                 
  

• add BiocStyle

            Changes in version 0.99.17 (2023-06-27)                 
  

• add exception entry for invalid average dose-response data

            Changes in version 0.99.16 (2023-06-23)                 
  

• increase compression level (Tavor_2020.qs; < 5MB limit)

            Changes in version 0.99.15 (2023-06-22)                 
  

• replaced rds with qs

            Changes in version 0.99.14 (2023-06-13)                 
  

• switch from merge to [[

            Changes in version 0.99.13 (2023-06-05)                 
  

• replaced reshape2 functions by functions from data.table

            Changes in version 0.99.12 (2023-05-24)                 
  

• format the vignette with BiocStyle

            Changes in version 0.99.11 (2023-05-16)                 
  

• data.frame => data.table switch (next round of changes)

            Changes in version 0.99.10 (2023-05-04)                 
  

• switch from tibble to data.table in excel files

             Changes in version 0.99.9 (2023-04-25)                 
  

• refactor tibble, data.frame –> data.table

             Changes in version 0.99.8 (2023-04-20)                 
  

• switch to OSI license

             Changes in version 0.99.7 (2023-04-20)                 
  

• clean-up vignette

             Changes in version 0.99.6 (2023-04-19)                 
  

• add object S4 gdr_test_data

             Changes in version 0.99.5 (2023-04-19)                 
  

• mocked PSets tests

             Changes in version 0.99.4 (2023-04-17)                 
  

• add R 4.2 as dependency

• bugfix for Pset-related tests and examples (reset identifiers)

             Changes in version 0.99.3 (2023-04-13)                 
  

• add minor improvements (BiocCheck compatibility)

             Changes in version 0.99.2 (2023-04-11)                 
  

• add support for PharmacoGx

             Changes in version 0.99.1 (2023-04-07)                 
  

• update maintainer

             Changes in version 0.99.0 (2023-03-24)                 
  

• make the package Bioc-compatible

gDRstyle

            Changes in version 0.99.22 (2023-10-17)                 

• adjust NEWS to Bioc format

            Changes in version 0.99.21 (2023-10-02)                 
  

• add options to skip tests/lintering in checkPackage

            Changes in version 0.99.20 (2023-08-08)                 
  

• add deploy trigger to workflow template

            Changes in version 0.99.19 (2023-06-15)                 
  

• fix pattern for finding *.R files

• lintr R files from ‘inst/shiny’ (if present)

            Changes in version 0.99.18 (2023-06-09)                 
  

• add reshape2 to lintr config

            Changes in version 0.99.17 (2023-05-10)                 
  

• add check for data.frame-related functions

• update package versioning rules

            Changes in version 0.99.16 (2023-05-04)                 
  

• ignore note for exported functions without examples

• handle properly BiocCheck notes with mulitple lines (notes to be ignored)

            Changes in version 0.99.15 (2023-05-02)                 
  

• ignore note for 50 lines per function in biocCheck

            Changes in version 0.99.14 (2023-04-27)                 
  

• removed CRAN check from biocCheck

            Changes in version 0.99.13 (2023-04-21)                 
  

• add check for BiocCheck’s notes

            Changes in version 0.99.12 (2023-04-20)                 
  

• switch to OSI license

            Changes in version 0.99.11 (2023-04-17)                 
  

• avoid dependencies upgrade

• add examples check

            Changes in version 0.99.10 (2023-04-17)                 
  

• update style guide (package doc)

             Changes in version 0.99.9 (2023-04-17)                 
  

• add R 4.2 as a dependency

             Changes in version 0.99.8 (2023-04-13)                 
  

• fix format in NEWS.md

             Changes in version 0.99.7 (2023-04-07)                 
  

• update maintainer

             Changes in version 0.99.6 (2023-04-07)                 
  

• update the license

             Changes in version 0.99.5 (2023-04-06)                 
  

• update maintainer

             Changes in version 0.99.4 (2023-04-05)                 
  

• remove unstable test

             Changes in version 0.99.3 (2023-04-05)                 
  

• update examples

             Changes in version 0.99.2 (2023-04-04)                 
  

• update examples
• switch to lintr::linters_with_defaults

• add ‘test_mode’ parameter in installAllDeps

             Changes in version 0.99.1 (2023-04-04)                 
  

• change location of NEW.md file

             Changes in version 0.99.0 (2023-03-24)                 
  

• downgrade version to make it Bioconductor compatible
• fix unit tests

gDRutils

            Changes in version 0.99.34 (2023-10-18)                 

• adjust NEWS to Bioc format

            Changes in version 0.99.33 (2023-10-09)                 
  

• add support for flattening averaged assays

            Changes in version 0.99.32 (2023-09-22)                 
  

• fix bug in the case of conc=0 for evaluating efficacy

            Changes in version 0.99.31 (2023-09-19)                 
  

• add wide_structure param to convert_mae_assay_to_dt

            Changes in version 0.99.30 (2023-09-08)                 
  

• updated experimentalist description in schema

            Changes in version 0.99.29 (2023-09-05)                 
  

• add Replicate as a new identifier

            Changes in version 0.99.28 (2023-09-05)                 
  

• improve the logic of standardize_MAE to keep SE-specific metadata and be able to revert standardization

            Changes in version 0.99.27 (2023-08-01)                 
  

• keep unchanged names in DataFrame

            Changes in version 0.99.26 (2023-08-01)                 
  

• tidy code

            Changes in version 0.99.25 (2023-06-27)                 
  

• add assert for missing rownames

            Changes in version 0.99.24 (2023-06-22)                 
  

• replaced RDS with qs

            Changes in version 0.99.23 (2023-06-20)                 
  

• fix check in R 4.3

            Changes in version 0.99.22 (2023-06-12)                 
  

• switch from merge to [[

            Changes in version 0.99.21 (2023-06-12)                 
  

• replace order with data.table::setorder

• add support for custom identifiers in merge_SE

            Changes in version 0.99.20 (2023-06-07)                 
  

• switch from aggregate to data.table

            Changes in version 0.99.19 (2023-06-06)                 
  

• replaced reshape2 functions by functions from data.table

            Changes in version 0.99.18 (2023-05-22)                 
  

• format the vignette with BiocStyle

            Changes in version 0.99.17 (2023-05-22)                 
  

• fix related with data.table

• remove .get_treated_conditions and .get_untreated_conditions

            Changes in version 0.99.16 (2023-05-18)                 
  

• add support for merging combination-data assays

            Changes in version 0.99.15 (2023-05-12)                 
  

• update after unifying normalization types

            Changes in version 0.99.14 (2023-05-12)                 
  

• fix lintr

            Changes in version 0.99.13 (2023-05-09)                 
  

• removed cotreatment entry from EXPERIMENT_GROUPS

            Changes in version 0.99.12 (2023-05-09)                 
  

• fix bug in convert_mae_assay_to_dt

            Changes in version 0.99.11 (2023-05-08)                 
  

• refactor code with single ampersand in if statements

            Changes in version 0.99.10 (2023-04-28)                 
  

• change order of untreated tags

             Changes in version 0.99.9 (2023-04-24)                 
  

• changed data.frame to data.table

             Changes in version 0.99.8 (2023-04-20)                 
  

• switch to OSI license

             Changes in version 0.99.7 (2023-04-20)                 
  

• clean-up vignette

             Changes in version 0.99.6 (2023-04-18)                 
  

• extend the logic of apply_bumpy_function

             Changes in version 0.99.5 (2023-04-17)                 
  

• add R 4.2 as a dependency

             Changes in version 0.99.4 (2023-04-14)                 
  

• fix examples

             Changes in version 0.99.3 (2023-04-13)                 
  

• make linter happy

             Changes in version 0.99.2 (2023-04-12)                 
  

• add licence

             Changes in version 0.99.1 (2023-04-07)                 
  

• update maintainer

             Changes in version 0.99.0 (2023-03-28)                 
  

• downgrade version to make it Bioconductor compatible

gdsfmt

                   Changes in version 1.36.1                        

UTILITIES

• gdsfmt:::.reopen() allows forking

gemma.R

                    Changes in version 2.0.0                        

• Breaking change to get_dataset_differential_expression_analyses function in order to return annotations for contrasts with multiple characteristics.

GeneTonic

                    Changes in version 2.6.0                        

Bug fixes

• describe_gtl() correctly extracts the number of up and down regulated genes from the DE results
• Fortified the behavior of gs_scores() to handle cases where only one gene would be included in the signature to plot

GenomeInfoDb

                   Changes in version 1.38.0                        

NEW FEATURES

• Register the following NCBI assemblies:
  • bStrHab1.2.pri (Kakapo)
  • a few Salmo salar (Atlantic salmon) assemblies
  • a few African elephant (Loxodonta africana) assemblies

BUG FIXES

• Switch from HTTP to HTTPS for requests to *.ucsc.edu

• Remove library() calls from inst/registered/UCSC_genomes/*.R files

GenomicAlignments

                   Changes in version 1.38.0                        

• No changes in this version.

GenomicFeatures

                   Changes in version 1.54.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Fix flaw in heuristic for inferring exon ranks in makeTxDbFromGRanges(): makeTxDbFromGRanges() can guess the exon ranks of a given transcript either (a) based on their position on the chromosome (b) or by looking at the suffixes of the exon ids (e.g. .1, .2, etc…) if any Previously (i.e. in GenomicFeatures < 1.53.1) it was trying (b) first, and would fall back on (a) if (b) failed. Starting with GenomicFeatures 1.53.1, it does the opposite: it tries (a) first, and uses (b) only for exons for which (a) failed. This change addresses the problem that the suffixes of the exon ids cannot be trusted to infer the ranks of exons located on the minus strand. See https://github.com/Bioconductor/GenomicFeatures/issues/59 for an example.

• Try to more clearly distinguish between CDS and CDS parts in documentation.

BUG FIXES

• Switch from HTTP to HTTPS for requests to *.ucsc.edu

GenomicPlot

                   Changes in version 0.99.15                       

NEW FEATURES

None

SIGNIFICANT CHANGES

• Provide link to all external and internal data in manual
• Add examples to all plot functions

BUG FIXES

None

                   Changes in version 0.99.14                       

NEW FEATURES

None

SIGNIFICANT CHANGES

• Make txdb available in /inst/data to avoid repetitive generation of it in examples
• Store gf5_meta and gf5_genomic in /data so that they can be loaded by calling data()
• Create /R/data.R for data documentations

BUG FIXES

None

                   Changes in version 0.99.13                       

NEW FEATURES

None

SIGNIFICANT CHANGES

• Add ‘title’ to draw_combo_plot function arguments.

BUG FIXES

• Fixed a bug in plot_peak_annotation, such that txdb$user_genome is treated as a vector of strings rather than a single string

                   Changes in version 0.99.12                       
  

NEW FEATURES

• Add PCA plot in plot_bam_correlation.
• The function plot_5parts_metagene can generate profile plots for both 5 parts (Promoter, 5’UTR, CDS, 3’UTR, TTS) and 3 parts (Promoter, Gene, TTS) metagene.

SIGNIFICANT CHANGES

• The function plot_3parts_metagene is removed.
• Add setImportParams function to provide default import parameters.
• Add saveRds option to import parameters to control saving of imported data, the default is FALSE.
• Add data type and missing file checking for function arguments

BUG FIXES

None

GenomicRanges

                   Changes in version 1.54.0                        

NEW FEATURES

• Add ‘ignore.strand’ arg to gaps() method for GenomicRanges objects.

BUG FIXES

• Small tweaks to GRanges() constructor and to coercion from GPos to GRanges.

GenomicScores

                   Changes in version 2.14.0                        

USER VISIBLE CHANGES

• Added four new pathogenicity score sets and corresponding metadata for hg19 and hg38: AlphaMissense.v2023.hg19, AlphaMissense.v2023.hg38, cadd.v1.6.hg19 and cadd.v1.6.hg38.

• Updated vignette.

gg4way

                   Changes in version 0.99.2                        

• Documentation updates

                   Changes in version 0.99.1                        
  

• Revised based on: https://github.com/Bioconductor/Contributions/issues/3129

                   Changes in version 0.99.0                        
  

• Pre-release version of the package.

ggkegg

             Changes in version 0.99.3 (2023-08-25)                 

• Added new files

             Changes in version 0.99.2 (2023-08-25)                 
  

• Remove the unnecessary file to pass R CMD CHECK

             Changes in version 0.99.1 (2023-08-25)                 
  

• Revising the codes based on the Bioconductor review

             Changes in version 0.99.0 (2023-06-27)                 
  

• Submitted to Bioconductor

ggsc

                   Changes in version 0.99.11                       

• support density visualization for single and spatial transcriptomic data (2023-10-18, Wed)

                   Changes in version 0.99.10                       
  

• on Bioconductor (2023-10-16, Mon)
• add \value session in the reexports.Rd (2023-10-15, Sun)
• add package level man page and update vignette (2023-10-14, Sat)
• add examples in Rd to satisfy BiocCheck (2023-09-18, Mon, #7)
• sc_dim_count() function to generate a barplot from a dimension reduction plot (sc_dim() plot) to visualize the number of cells for each clusters (2023-09-13, Wed)

• add ‘biocViews’ in DESCRIPTION required by Bioconductor

                   Changes in version 0.99.0                        
  

• compatible with ‘SingleCellExperiment’ (2023-09-05, Tue, #5)
• using S4 OOP to reorganize the functions (2023-09-05, Tue, #4)
• rename the package to ‘ggsc’ as there is a package called ‘scplot’ in CRAN
• add H&E image to sc_spatial() (#3)

ggtree

                    Changes in version 3.9.1                        

• use rlang::check_installed() to check whether the suggested pkg is installed (2023-08-11, Fri, #580)
• allows using linewidth parameter (synonyms for size) in ggtree() (2023-07-15, Sat, #574)
• bug fixed in setting branch.length = “none” to plot ‘hclust’ object (2023-07-15, Sat, #574)

ggtreeDendro

                    Changes in version 1.3.2                        

• update according to the change of tidytree (2023-08-18, Fri)

                    Changes in version 1.3.1                        
  

• autoplot method for ‘dendro’ object (ggdendro::dendro_data() output) (2023-03-02, Thu)
• see also https://github.com/YuLab-SMU/treeio/pull/95

glmGamPoi

              Changes in version 1.13 (2023-07-03)                  

• Implement a likelihood ratio test based on the Chi-squared distribution, if test_de is called after setting overdispersion_shrinkage = FALSE. Note that this test is less reliable than than the quasi-likelihood F test that is run for overdispersion_shrinkage = TRUE.

GloScope

             Changes in version 0.99.5 (2023-10-23)                 

• Fix typos in README and CITATION files

             Changes in version 0.99.4 (2023-10-03)                 
  

• Improve example data and test cases

• Update documentation

• Fix Monte Carlo sampling edge case bug

             Changes in version 0.99.3 (2023-09-17)                 
  

• Address feedback from Bioconductor review

• Catch edge case where more GMM components specified by user than cells

             Changes in version 0.99.2 (2023-08-09)                 
  

• Fix issues in Bioconductor build report

             Changes in version 0.99.1 (2023-07-18)                 
  

• Update ROxygen examples and test cases to use SingleCellExperiment data

             Changes in version 0.99.0 (2023-06-01)                 
  

• This is the pre-submission version.

GNOSIS

             Changes in version 1.99.0 (2023-09-04)                 

• Made the following significant changes o added functionality to select and upload cBioPortal study o deprecated ability to save R script with executed code

• Submitted to Bioconductor

GOSemSim

                   Changes in version 2.27.3                        

• use check_installed() to check package dependency (2023-09-12, Tue, #43)

                   Changes in version 2.27.2                        
  

• read.blast2go() to parse ‘blast2go’ result (2023-07-10, Mon)

• move buildGOmap() and read.gaf() from ‘clusterProfiler’ (2023-07-10, Mon)

                   Changes in version 2.27.1                        
  

• semantic similarity measurement support for MPO (2023-04-06, Thu)
• TCSS semantic similarity measurement support for DO and MPO (2023-04-06, Thu)

goSorensen

                    Changes in version 1.3.0                        

We add the following functions

• allBuildEnrichTable: Given k lists of genes, it generates the k(k–1)/2 contingency tables of joint enrichment for all possible pairs of lists.
• allEquivTestSorensen: Accepts the objects created with allBuildEnrichTable as its first argument and quickly obtains the k(k–1)/2 equivalence tests.
• sorenThreshold: Implements an algorithm allowing the computation of the “equivalence threshold” dissimilarities matrix for all the k(k–1)/2 tests. According to what is indicated in the arguments, the results of this function are stored in a matrix for a specific ontology and level or a list with a matrix for more than one ontology and/or level.
• hclustThreshold: Generates an object of class “hclust”. For a specific ontology and level, plots a dendrogram where all the k(k–1)/2 comparisons are joined at the height of their respective “equivalence threshold” dissimilarity.
• allHclustThreshold: Performs the same calculations as hclustThreshold but for the specified GO ontologies and levels (all three ontologies PB, MF, and CC and levels from 2 to 10 by default)

In addition:

• We improve the vignette “An introduction to the goSorensen package” by implementing the new functions mentioned above and updating the results of the examples with the results of the latest version of Bioconductor.

GRaNIE

          Changes in version 1.5.2-1.5.3 (2023-08-20)               

New features

• say hello to a new function filterConnectionsForPlotting() that can be used to include or exclude particular connections from the stored eGRN for visualization purposes only (!). Note that this filter only applies to visualization and enables a flexible system to visually explore particular features of the stored eGRN. THis is particularly handy when the eGRN is large. For more details, see the help pages of the new function.
• similarly, the function visualizeGRN() now by default only visualizes connections that are marked as such (the result from filterConnectionsForPlotting()) - that is, it excludes connections that the user beforehand excluded from plotting. This allows to specifically plot only part of the eGRN network and explore specific T&F regulons, for example, a feature that before was not so easy to do.

• It is now possible to integrate SNP data into GRaNIE via the new function addSNPData(). For more information, see the Package vignette.

             Changes in version 1.5.1 (2023-06-19)                  
  

• version jump due to new Bioconductor development cycle

New features and stability improvements

• we replaced biomaRt for the full genome annotation retrieval in addData with a different approach that is more reliable, as we had more and more issues with biomaRt in the recent past. While using the old biomaRt approach is still an option, the default is now to use the AnnotationHub package from Bioconductor. This makes GRaNIE overall more stable and less reliant on biomaRt due to the strict timeouts and query size restrictions.

graphite

             Changes in version 1.47.1 (2023-10-11)                 

• Removed Clipper support.

• Updated all pathway data.

GreyListChIP

                   Changes in version 1.32.1                        

• Change maintainer email from Rory to Matt

GSVA

                    Changes in version 1.50                         

USER VISIBLE CHANGES

• The API has changed. The main function remains under the same name ‘gsva()’, but the way in which is called is different. From this release, it has three parameters only: the first is a parameter object whose class depends on the method to be used, the second is a flag to set verbosity and the third controls the parallelization of the calculations. The old way of using ‘gsva()’ has been deprecated, which means that during this release, the user may still use the old API, but will get a deprecation warning message. In the next release, the old way of using ‘gsva()’ will become defunct and prompt an error. Please check the help page of ‘gsva()’ for details.

BUG FIXES

• Bugfix for https://github.com/rcastelo/GSVA/issues/88 to correctly deal with a GeneSetCollection object as input gene sets, when the input expression data is a SingleCellExperiment object.

• Bugfix for https://github.com/rcastelo/GSVA/issues/90 to enable working with long vectors in the calls to C code by the GSVA algorithm.

HarmonizR

                   Changes in version 0.99.1                        

NEW FEATURES

• HarmonizR now accepts S4 summarized experiment input and will return the batch effect adjusted result as such

SIGNIFICANT OTHER CHANGES

• HarmonizR now imports SummarizedExperiment

HDF5Array

                   Changes in version 1.30.0                        

NEW FEATURES

• Add ‘dim’ and ‘sparse.layout’ args to H5SparseMatrixSeed().

SIGNIFICANT USER-VISIBLE CHANGES

• HDF5Array now imports S4Arrays.

HERON

                   Changes in version 0.99.0                        

• Submitted to Bioconductor

HIBAG

                   Changes in version 1.38.0                        

• fix a compiler warning of “unused-but-set-variable” on Apple ARM chips

                   Changes in version 1.36.3                        
  

• the output of hlaPredict(, type="response+prob") includes dosages

• new arguments ‘ret.dosage’, ‘ret.postprob’, ‘max.resolution’ and ‘rm.suffix’ in hlaPredMerge()

• new arguments ‘allele.list’ and ‘prob.cutoff’ in hlaAlleleToVCF() for more possible outputs

• hlaAlleleToVCF() accepts a list of ‘hlaAlleleClass’ as the first argument: output multiple ‘hlaAlleleClass’ objects to a single VCF file

HiCcompare

             Changes in version 1.23.1 (2023-06-03)                 

• Fix cooler2sparse function when a cool file has only a single chromosome. Thanks to @junjunlab, @agata-sm, https://github.com/dozmorovlab/HiCcompare/issues/28

• Update cool file handling in the vignette.

HiCDOC

             Changes in version 1.3.2 (2023-09-22)                  

• Move license to a LICENSE file, as asked by open access repo

             Changes in version 1.3.1 (2023-09-06)                  
  

• Add a cyclicLoessSpan parameter to speed technical bias normalization to speed the technical bias normalization if set (in normalizeTechnicalBiases())

• Remove 2 dependencies (ggpubr and ggExtra)

hoodscanR

                   Changes in version 0.99.5                        

Remove codes that are commented out.

                   Changes in version 0.99.4                        

user perspective/experience

• documentation update about output values
• output variable/names parameter added to many functions
• validity checks for spatialCoords are added to related functions

• for loops are gone.

                   Changes in version 0.99.3                        
  

code

• sapply change to vapply.
• validity checks on inputs are now added to all functions using either is(spe, “SpatialExperiment”) or is(m, “matrix”) etc.

vignette

• Explanation of plots and algorithm inside different functions are now added to the vignette briefly.
• BiocStyle are now used.
• BiocStyle to hyperlink packages are now used.
• Fixed typo

documentation

• data description of the test data has been added.
• cross-link key function have added to the package help page.
• the equation and theory of the calcMetrics are now added in the help page.

other

• Bioconductor installation instructions is now added to the readme file.
• code coverage is now almost 85%.

• The LICENSE placeholders is now edited.

                   Changes in version 0.99.0                        
  

First submission to Bioconductor.

HPAanalyze

                    Changes in version 1.19                         

• Changes in version 1.19.0
  • Starting devel for Bioconductor 3.18
• Changes in version 1.19.1
  • Bug fix: Correct url for rna_tissue_consensus

hypeR

                    Changes in version 2.0.1                        

• Dots plots are now explicitly sized with size_by=c(“genesets”, “significance”, “none”)

                    Changes in version 2.0.0                        
  

• Version bump for bioconductor

IgGeneUsage

                    Changes in version 1.15                         

• model for gene usage (GU) analysis

• model for multi-condition analysis, ANOVA like

illuminaio

             Changes in version 0.43.0 (2023-04-25)                 

Notes

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.18 for R (>= 4.4.0).

imcRtools

             Changes in version 1.7.8 (2023-10-19)                  

• spatialCoords are not initialised with rownames anymore

             Changes in version 1.7.7 (2023-10-02)                  
  

• Bug fix: in rare cases the testInteractions p-values were not correctly computed due to machine precision issues

             Changes in version 1.7.6 (2023-09-26)                  
  

• Updated example data in “inst” to newest version

             Changes in version 1.7.5 (2023-09-14)                  
  

• Added more internal validity checks for ‘read_steinbock’

• Changed the way messages in vroom are silenced

• Stop allowing Object numbers to be different between intensities and regionprops

• Stop allowing missing files in regionprops and neighbors

             Changes in version 1.7.4 (2023-08-09)                  
  

• Bug fix: correctly setting the “aspect.ratio” argument in plotSpatial to fix the physical units of the x- and y-axis

             Changes in version 1.7.3 (2023-06-20)                  
  

• More info on reproducibility using testInteractions

             Changes in version 1.7.1 (2023-06-07)                  
  

• More info on reproducibility using detectCommunity

immunoClust

                   Changes in version 1.33.6                        

• CHANGES
  • introducing method option for SON/ormalization

  • a bit clarification in E/M-calls interface

                   Changes in version 1.33.2                        
    

• CHANGES

  • SON/ormalization back to Version 1.31.9

                   Changes in version 1.33.1                        
    

• CHANGES
  • normalization variants for combine clustering

iNETgrate

            Changes in version 0.99.120 (2023-06-29)                

General

• After the iNETgrate package was added to Bioconductor, Habil removed it from the Bitbucket and Github repositories.

            Changes in version 0.99.102 (2023-06-12)                
  

Changes in existing functions

• In prepareSurvival and cleanAllData function, the default values changes as follows: riskLow=”Low” and riskHigh=”High”, respectively.

            Changes in version 0.99.100 (2023-06-09)                
  

Changes in existing functions

• The Labels argument is removed from analyzeSurvival. and the riskCol argument is added.

            Changes in version 0.99.96 (2023-06-08)                 
  

Changes in existing functions

• The abnormalityCol argument is removed from accelFailAnalysis.

• The otherLabel argument is removed from prepareSurvival and cleanAllData functions.

            Changes in version 0.99.94 (2023-06-08)                 
  

Changes in existing functions

• The computeEigengenes, computeEigenloci, and sample2atient functions were renamed to computEigengenes, computEigenloci, and sample2pat, respectively.

• The makeNetwork function now saves the result for each mu in a separate folder.

            Changes in version 0.99.74 (2023-05-24)                 
  

General

• Data were compressed using “xz” to save 20% space.

Changes in existing functions

• The downloaData function is not exported anymore because it is specific to the legacy TCGA data, which is no longer available.

            Changes in version 0.99.70 (2023-05-23)                 
  

Changes in existing functions

• Habil renamed downloadData to downloaData and updated the data.category argument of GDCquery.

• Habil removed the legacy option from the donwlowData function because it is no longer supported by TCGAbiolinks.

            Changes in version 0.99.64 (2023-05-11)                 
  

General

• Habil commented the installation command line in the vignette.

            Changes in version 0.99.50 (2023-04-14)                 
  

General

• Habil changed function names to camelCase i.e, from function.name to functionName.

            Changes in version 0.99.46 (2023-04-11)                 
  

General

• Habil changed getwd() to tempdr() in the docs.

• Habil changed most of occurrences of cat() to paste().

• Habil changed most of occurrences of print() to message() or Pigengene::message.if().

• Habil removed paste() inside all stop() to warning().

• Habil replaced dontrun with donttest.

            Changes in version 0.99.30 (2023-04-06)                 
  

General

• Tested on R 4.3.

• TCGAbiolinks (<= 2.24.3) because of issues with newer versions.

             Changes in version 0.5.42 (2021-10-31)                 
  

General

• Being prepared for submission to Bioconductor.

• Created.

IntEREst

                   Changes in version 1.26.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• IntSpan method is changed to count reads that span the whole intron precisely. Previous these were counted separayted for 5’ end and 3’ end of the introns.

• repeatsTableToFilter is ignored for IntSpana nd ExSkip as the skipped regions of the reads (denoted by N or sometimes D in the CIGAR of bam/sam file ) are taken into count for these benchmarks (not the mapped regions which are dentoed with Ms in the cigar).

IRanges

                   Changes in version 2.36.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Add link to revElements() in man page for reverse().

BUG FIXES

• Fix is.unsorted() methods for Compressed[Integer|Numeric]List objects (they were never working since their introduction years ago).

ISAnalytics

             Changes in version 1.11.2 (2023-07-26)                 

FIXES

• Fixed issues in html report for outlier filtering - reported incorrect numbers due to missing conversion in percentage
• Fixed warnings for bslib::nav deprecation

• Fixed minor issue in default_af_transform(), transformation failed if NAs were present in the columns

             Changes in version 1.11.1 (2023-05-09)                 
  

FIXES

• Fixed broken tests with new updates in underlying packages

iSEE

                   Changes in version 2.13.5                        

• Add generic .isBrushable to support panels that are not DotPlot extensions.

                   Changes in version 2.13.4                        
  

• Fix COLORMAP bug introduced in 2.13.3.

                   Changes in version 2.13.3                        
  

• Let app maintainer define colormap in the landing page.

                   Changes in version 2.13.2                        
  

• Fix bug introduced in 2.11.2 (DataBoxOpen would apply also to Visual parameters box)

                   Changes in version 2.13.1                        
  

• Define missing methods for generics for custom tables (issues #608 and #612)

iSEEde

                   Changes in version 0.99.0                        

NEW FEATURES

• Added a NEWS.md file to track changes to the package.

iSEEhub

                    Changes in version 1.3.2                        

BUG FIXES

• Cleaner version of bug fix introduced in version 1.3.1.

                    Changes in version 1.3.1                        
  

BUG FIXES

• Fix cleaning of missing rowData and colData.

iSEEindex

                   Changes in version 0.99.13                       

• Added possibility to inject custom header and footer in landing page.

                   Changes in version 0.99.12                       
  

• Added control over inclusion and location of default initial configuration amongst available choices.

                   Changes in version 0.99.11                       
  

• Added second example data set to replace copy of first one.

                   Changes in version 0.99.10                       
  

• Added support for custom tours through initial state configuration scripts.

                   Changes in version 0.99.9                        
  

• Disable GitHub CommonMark extensions and demonstrate target=”_blank” for issue #41.

                   Changes in version 0.99.8                        
  

• Fixed duplication of UI output displaying information about initial configuration.

                   Changes in version 0.99.7                        
  

• Fix package man page.

                   Changes in version 0.99.6                        
  

• Added man page for package.

                   Changes in version 0.99.5                        
  

• Changed options(width=120) in vignettes when displaying session info.

                   Changes in version 0.99.4                        
  

• Removed export of internal function in NAMESPACE.

                   Changes in version 0.99.3                        
  

• Deduplicated choice of initial configuration.

                   Changes in version 0.99.2                        
  

• Added \value section to fix BiocCheck::BiocCheck() WARNING.

                   Changes in version 0.99.1                        
  

• Trigger a new build on the Bioconductor Single Package Builder.

                   Changes in version 0.99.0                        
  

NEW FEATURES

• Added a NEWS.md file to track changes to the package.

iSEEpathways

                   Changes in version 0.99.2                        

MINOR UPDATES

• Added missing depedency to DESCRIPTION file (Bioconductor WARNING).
• Moved set.seed() out of functions (Bioconductor WARNING).

• Added \value section to man pages (Bioconductor WARNING).

                   Changes in version 0.99.1                        
  

MINOR UPDATES

• Added BiocViews (Bioconductor NOTE).

                   Changes in version 0.99.0                        
  

NEW FEATURES

• Added a NEWS.md file to track changes to the package.

IsoformSwitchAnalyzeR

                   Changes in version 2.01.14                       

• Update type: Minor.

• Update for Bioconductor

                   Changes in version 2.01.13                       
  

• Update type: Minor.

• Fixed a problem with analysis of 5_utr_seq_similarity in analyzeSwitchConsequences()

• importRdata() was updated to handle sva analysis better

• importRdata() was updated by removing the addIFmatrix argument as the IF matrix is now alwasy needed

• importRdata() had it’s detectAndCorrectUnwantedEffects argument updated to

• isoformSwitchTestDEXSeq was updated to not batch correct IF values as this is already done by importRdata

• Various documentation updates

                   Changes in version 2.01.12                       
  

• Update type: Minor.

• Update of switchPlot() to turn off topology plotting

• Update of importRdata() to better handle datasets with no replicates

                   Changes in version 2.01.11                       
  

• Update type: Minor.

• importRdata() was updated to fix problem with fasta import.

                   Changes in version 2.01.10                       
  

• Update type: Minor.

• Updated satuRn version requirement

• Updated importRdata() to allow skipping sva analysis incoperation.

• Updated importRdata() documentation accordingly.

• Updated importRdata() documentation to better describe the switchAnalyzeRlist created.

• Updated isoformSwitchTestSatuRn() to be more robust to various id types.

                   Changes in version 2.01.09                       
  

• Update type: Minor.

• Updated importRdata() to also handle when there are to few samples to run SVA.

                   Changes in version 2.01.08                       
  

• Update type: Minor.

• Updated importRdata() to use more stringent filtering (inspired by edgeR::filterByExpr()) before running SVA. Output in final switchAnalyzeRlist is not affected (aka that have not been filtered).

• Updated importRdata() to also handle when to many SVAs are found.

• Updated importRdata() to also handle when there are to few samples to run SVA.

                   Changes in version 2.01.07                       
  

• Update type: Minor.

• Fixed an edgecase bug in importRdata()

                   Changes in version 2.01.06                       
  

• Update type: Minor.

• Fixed an bug in isoformSwitchAnalysisPart2() that could result in problem when running without toplogy analysis.

• Introduced a better error message in analyzeORF().

                   Changes in version 2.01.05                       
  

• Update type: Minor.

• Updated switchPlotTranscript() to make a message instaed of an error when plotTopology=TRUE but isoform topology had not beed added.

• More detailed descriptions of analyzeDeepTMHMM() and analyzeDeepLoc2() added to the vignette.

                   Changes in version 2.01.04                       
  

• Update type: Minor.

• Fix to handle duplicated levels

                   Changes in version 2.01.03                       
  

• Update type: Minor.

• Fixes to accomodate dplyr updates

                   Changes in version 2.01.02                       
  

• Update type: Minor.

• Fixed a problem with batch correction in importRdata()

                    Changes in version 2.1.2                        
  

• Update type: Minor.

• Documentation update for Bioconductor

                   Changes in version 2.01.01                       
  

• Update type: Major.

• createSwitchAnalyzeRlist() was removed. All users should instead use importRdata().

• importRdata() now automatically detects un-annoated covariates in data via the sva package.

• importRdata() now automatically corrects abundance and isoform fractions for unwanted covariates (both used supplied and those found via sva).

• Accordingly all batch correction functionallity in the isoformSwitchTestDEXSeq() function was removed.

• isoformSwitchTestSatuRn() was introduced. This test uses satuRn for switch identification which works extremely well for larger sample sizes. Huge thanks to Jeroen Gilis making this functionality and the pull request!

• Accordingly the suboptimal isoformSwitchTestDRIMSeq function have been removed. All documentation was updated accordingly.

• IsoformSwitchAnalyzeR now depends on the R package pfamAnalyzeR for analyzing pfam domain isotypes.

• analyzeSignalP() was updated to support import of results predicted with SignalP6.

• analyzeDeepTMHMM() was introduced to add topological predictions to the switchAnalyzeRList.

• analyzeDeepLoc2() was introduced to add predictions of sub-cellular localization to the switchAnalyzeRList.

• analyzeIUPred2A() was tested against with result files from IUPred3 and seem to work.

• analyzeSwitchConsequences() was updated to predict a number of new consequences based on the new annoation described above.

• analyzeSwitchConsequences()’s AaFracCutoff default was updated from 0.5 to 0.8 resulting in more lenient differenceses being identified.

• extractSubCellShifts() was introduced to enable a deeper analysis of changes in sub-cellular localization due to isoform switches.

• Vignette was updated to recomend IsoQuant instead of TALON for long read data.

• analyzePFAM() was updated to import envelope (instead of alignment) coordinates as currently recomended. In practice this is a minor change for most domains.

• Example data was updated to reflect new annoation and consequences that can be predicted

• Various code corrections and improvements

• Various documentation improvements

                    Changes in version 2.1.1                        
  

• Update type: Minor.

• Update for Bioconductor

KEGGREST

                   Changes in version 1.42.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• keggCompounds lists compound IDs for a given pathway (@KristinaRiemer, #6).

BUG FIXES

• Update URL path in .get.kegg.url from tmp to kegg subfolder.

lefser

                   Changes in version 1.12.0                        

Significant user-visible changes

• The checkAbundances argument in lefser() checks that data are as relative abundances and warns if otherwise (@LiNk-NY @sdgamboa, #28)
• relativeAb helper function available to convert data (@LiNk-NY)
• Deprecate the expr argument and use relab (short for relative abundances)
• Add group labels to lefserPlot (@LiNk-NY #25, @asyakhl #31)
• ‘Interoperating with phyloseq’ section added to the vignette (#16)

lfa

             Changes in version 2.1.11 (2023-06-20)                 

• Commented out excessive test for internal function .lreg against glm, which differ more often than expected due to poor or lack of convergence.

• Removed unused LaTeX package dependencies from vignette to prevent errors restricted to specific testing platforms.

             Changes in version 2.1.10 (2023-05-25)                 
  

• Version bump for bioconductor devel.

limma

                   Changes in version 3.58.0                        

• New argument covariate for vooma(), which allows the variance trend to depend on extra covariates in addition to average log-expression.

• New argument ‘group’ to simplify the typical calling sequence for removeBatchEffect(). The group argument provides an alternative and possibly simpler way to specify the experimental conditions to be preserved.

• treat() now works when there are NA coefficients. Previously it gave an error if any estimated coefficient was NA.

• Fix behaviour of topTable() with adjust.method=NULL so that it gives “BH” adjustment as documented. Previously the argument was passed to p.adjust(), which gave “holm” adjustment.

• Convert Introduction vignette from Sweave/pdf from to Rmarkdown/html. The Introduction vignette is also somewhat expanded.

• cameraPR() has been addeed to the 10GeneSetTests.Rd help topic.

• The pdf limma User’s Guide is now formally listed as a vignette.

• Non-user-visible changes: limma now imports statmod rather than suggesting it. BiocStyle has been added to the Suggests field of DESCRIPTION.

maftools

                   Changes in version 2.18.0                        

NEW FUNCTIONS

• pathways and plotPathwaysfor summarizing & visualizing pathways Issue: 956
• coGisticChromPlot for plotting two GISTIC objects side-by-side. PR by biosunsci 954
• readGistic can take gistic output directory as an input. PR by biosunsci 954

BUG FIXES

• Bug fixes while processing custom pathways
• Bug fix in oncoplot for drawing borders. 958
• Bug fix in plotSignatures for hardcoded axis limits. 949
• Bug fix in mafSurvival legend when samples argument is give. 937
• Bug fix in subsetMaf while handling only CNV events. 908
• Error handling when no deep/shallow CNV events found. 899
• Bug fix in oncoplot for duplicated values in gene list. 889

ENHANCEMENTS

• Added argument collapsePathway to oncoplot. Issue: 956
• Improved annovarToMaf with better handling of indels and Variant_Type. Issue: 940
• Include absolute contribution of each signature in extractSignatures output. Issue: 939
• Added tsbToPIDs for custom names in oncoplot. Issue: Issue: 936
• Added DSEL protein to the database. Issue: 933
• Added MUC3A protein to the database. Issue: 932
• Added showOnlyPathway argument to oncoplot
• Added pathdb argument to PlotOncogenicPathways. Issue: 923
• Emit warnings when fishers test can not be performed during somaticInteractions. Issue: 921
• Added leftMar and topMar arguments to somaticInteractions. Issue: 913
• Added toptBarLims argument to oncoplot. Issue: 910
• Added data argument to lollipopPlot function. Issue: 894
• Added sortByM1 and sortByM2 argument to coOncoplot. Issue: 888
• Added arguments leftBarVline, leftBarVlineCol, rightBarVline, rightBarVlineCol topBarHline topBarHlineCol to oncoplot. Issue: 874
• Added revPal argument to somaticInteractions. Issue: 859
• Fix legend and color codes for numeric annotations in oncoplot. Issue: 363

magpie

                    Changes in version 1.1.3                        

• Added a NEWS.md file to track changes to the package.

MatrixGenerics

                   Changes in version 1.13.1                        

• Apply matrixStats 1.0.0 breaking change for useNames’s default: All generic functions and methods defined in MatrixGenerics now set the useNames argument to TRUE instead of NA by default. See https://github.com/Bioconductor/MatrixGenerics/issues/31 for a discussion of this change.

MatrixQCvis

             Changes in version 1.9.1 (2023-07-19)                  

• fix bug in scree plot (subset the dimensionReduction object)

matter

                   Changes in version 2.3.18                        

BUG FIXES

• Fixed bug in ‘kdtree()’ stack size allocation

• Cleaned up a few C++ compiler warnings

                   Changes in version 2.3.17                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Parameter ‘filename’ in ‘struct()’ is now ‘path’

                   Changes in version 2.3.16                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Added ‘checksum’ method for character vectors (i.e., files)

                   Changes in version 2.3.15                        
  

BUG FIXES

• Fixed erroneous warning in ‘matter_list’ or ‘matter_arr’ constructors with existing files but no ‘data’ argument

                   Changes in version 2.3.14                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Added ‘append’ argument to matter constructors

• Simplified ‘sparse_arr’ implementation by removing shared index representation (which was not really used)

• When writing to an output file, ‘chunkApply()’ and friends now write entire chunks instead of each element

• Added coercions from ‘matter_list’ to ‘matter_arr’, etc.

BUG FIXES

• No longer truncate existing files when creating a matter object if nonexistent files are also included in the path

                   Changes in version 2.3.13                        
  

BUG FIXES

• Fixed translation from aliased C types to R types

                   Changes in version 2.3.12                        
  

NEW FEATURES

• Added ‘image’ method for formulas

                   Changes in version 2.3.11                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Changed specification of ‘atoms’ data types

• Use ‘int16’, int32’, ‘uint32’, etc. for integer types

• Use ‘float32’ and ‘float64’ for floating point typess

• Added aliases so ‘short’, ‘int’, ‘double’, etc., still work

                   Changes in version 2.3.10                        
  

NEW FEATURES

• Added ‘rowMaj’ S4 generic and methods

SIGNIFICANT USER-VISIBLE CHANGES

• Remove defunct S4 generics

BUG FIXES

• Fixed bug in ‘approx1’ for “max” and “min” interpolation

                    Changes in version 2.3.9                        
  

NEW FEATURES

• Added ‘vizi_pixels’ for image plotting

• Added ‘vizi_voxels’ for 3D image plotting

SIGNIFICANT USER-VISIBLE CHANGES

• In estnoise_xxx() functions, renamed argument ‘width’ to ‘n’

                    Changes in version 2.3.8                        
  

NEW FEATURES

• Added PLS (partial least squares)

• Added ‘pls_nipals’ (NIPALS)

• Added ‘pls_simpls’ (SIMPLS)

• Added ‘pls_kernel’ (kernel algorithms #1 and #2)

• Added OPLS (orthogonal PLS)

• Added ‘opls_nipals’ (NIPALS)

• Added FastMap projection with ‘fastmap()’

• Added ‘rowDists()’ and ‘colDists()’

• Added ‘convolve_at()’

SIGNIFICANT USER-VISIBLE CHANGES

• Added regularization to NMF functions for stability

                    Changes in version 2.3.7                        
  

NEW FEATURES

• Added NMF (nonnegative matrix factorization)

• Added ‘nnmf_mult()’ (multiplicative updates)

• Added ‘nnmf_als()’ (alternating least squares)

• Exported ‘prcomp_lanczos()’

SIGNIFICANT USER-VISIBLE CHANGES

• Accessing matter objects now checks for user interrupts

                    Changes in version 2.3.6                        
  

NEW FEATURES

• Added ‘rowdist()’ and ‘coldist()’

• Added ‘rowdist_at()’ and ‘coldist_at()’

• Added parallelization support for matrix multiplication

                    Changes in version 2.3.5                        
  

NEW FEATURES

• Added ‘enhance_hist()’ for histogram equalization

• Added ‘enhance_adapt()’ for CLAHE

BUG FIXES

• Fixed handling of missing values in smoothing filters

                    Changes in version 2.3.4                        
  

NEW FEATURES

• Added CWT based peak detection with ‘findpeaks_cwt()’, ‘findridges()’ and ‘cwt()’

• Added ‘estnoise_quant()’

• Added ‘filt1_conv()’

• Added ‘filt2_conv()’

                    Changes in version 2.3.3                        
  

NEW FEATURES

• Added ‘trans2d()’ for affine transformations

• Added ‘warp2_trans()’ for transformation-based image registration using ‘optim()’

                    Changes in version 2.3.2                        
  

NEW FEATURES

• More new signal processing features!

• Added ‘approx2()’ for 2D signal resampling and interpolation of scattered data

• Added 2D filtering including: ‘filt2_ma()’, ‘filt2_gauss()’, ‘filt2_bi()’, ‘filt2_adapt()’, ‘filt2_guide’

• Added nonlinear diffusion ‘filt1_diff()’ and ‘filt2_diff()’

• Added the traditional Savitzky-Golay filter ‘filt1_sg()’

• Added ‘kdsearch()’ and ‘kdtree()’ for K-dimensional searches

SIGNIFICANT USER-VISIBLE CHANGES

• Updated package DESCRIPTION

                    Changes in version 2.3.1                        
  

NEW FEATURES

• Lots of new signal processing features!

• Added ‘approx1()’ for signal resampling and interpolation

• Added 1D filtering including: ‘filt1_ma()’, ‘filt1_gauss()’, ‘filt1_bi()’, ‘filt1_adapt()’, ‘filt1_guide()’, ‘filt1_pag()’

• Added 1D warping and alignment including: ‘warp1_loc()’, ‘warp1_dtc()’, ‘warp1_cow()’

• Added continuum estimation including: ‘estbase_loc()’, ‘estbase_hull()’, ‘estbase_snip()’, ‘estbase_med()’

• Added local noise estimation including: ‘estnoise_sd()’, ‘estnoise_mad()’, ‘estnoise_diff()’, ‘estnoise_filt()’

• Added peak processing including: ‘findpeaks()’, ‘peakwidths()’, ‘peakareas()’, ‘binpeaks()’, ‘mergepeaks()’

• Added ‘downsample()’ for signal and time series visualization

• Added ‘vizi_plot’ visualization methods

BUG FIXES

• Fix missing <cstdint> include for gcc 13.1.1 compatibility

mbQTL

             Changes in version 1.1.4 (2023-08-16)                  

• changes made on vignette

             Changes in version 1.1.3 (2023-08-16)                  
  

• changes made on vignette

             Changes in version 1.1.2 (2023-08-15)                  
  

• changes made on vignette

             Changes in version 1.1.1 (2023-08-15)                  
  

• changes made on vignette and fixed bug

metabCombiner

                   Changes in version 1.11.1                        

• m/z group size limit eliminated (previous: 10000 maximum)

MetaboAnnotation

                     Changes in version 1.5                         

Changes in 1.5.9

• Addition of global function createStandardMixes

Changes in 1.5.8

• Fix .randomize_grouping to prevent collapsing of matrix when input in a single column

Changes in 1.5.7

• Add function .group_standards_iteration and .randomize_grouping to allow iteration through matrix of standards and group them if they are dissimilar enough.

Changes in 1.5.6

• Fix issue in the vignette. Thanks @RemyDeB for the fix.

Changes in 1.5.5

• Update objects to the new definitions in Spectra version 1.11.10.

Changes in 1.5.4

• Add functions targetIndex and queryIndex to extract the indices of the matched pairs query-target.
• Add examples and a section to the vignette explaining their use.

Changes in 1.5.3

• Add support to matchValues for matching between data.frame and Spectra objects.

Changes in 1.5.2

• Fix vignette, examples and unit tests using QFeatures.
• Import query from AnnotationHub.

Changes in 1.5.1

• Add possibility to select the spectra variable for retention time matching in matchSpectra (issue #98).

MetaboCoreUtils

                     Changes in version 1.9                         

MetaboCoreUtils 1.9.4

• Add function mclosest (issue #20).

MetaboCoreUtils 1.9.3

• isotopologues checks if provided m/z values are increasingly ordered.

MetaboCoreUtils 1.9.2

• countElements returns NA for invalid elements instead of silently dropping them ( PR #65).

MetaboCoreUtils 1.9.1

• countElements, subtractElements and addElements returns NA if an input arguments is NA (issue #61, PR #62).

metabolomicsWorkbenchR

                   Changes in version 1.11.1                        

• further vignette cache improvements

• use httptest to cache responses when building vignette

metaseqR2

             Changes in version 1.13.2 (2023-10-04)                 

NEW FEATURES

• None.

BUG FIXES

• Removed the deprecated baySeq from PANDORA

methylKit

Version: 1.27.1 Category: IMPROVEMENTS AND BUG FIXES Text: fix R cmd check warnings: - fix “Undocumented arguments in documentation object” by documenting ‘…’, ‘treatment’ arguments for methylRawList and methylRawListDB constructors - methCall: replace variable length char with vector of chars to fix the warning: “variable length arrays are a C99 feature [-Wvla-extension]” - methCall: simplify the parsing of cigar string and replace calls to deprecated std::sprintf with std::snprintf

Version: 1.27.1 Category: IMPROVEMENTS AND BUG FIXES Text: add test for processBismarkAln to check that reading sam and bam

Version: 1.27.1 Category: returns the same object for the same content Text:

mia

                     Changes in version 1.9                         

• loadFromMetaphlan: Bugfix, not all files include ID column.

• cluster: added wrapper for bluster’s clusterRows function

• Added loadFromHumann

• calculateDMM: deprecated/updated outdated functions

• Added Tengeler2020 dataset

• *RDA & *CCA: calculate also statistical significance

• altExp support for meltAssay

• Deprecate mergeRows, mergeCols, agglomerateByRank, agglomerateByPrevalence

• Removed getAbundanceSample and getAbundanceFeature

• Updated test to avoid warning from deprecated functions

• Export mergeFeaturesByRank

• *RDA & *CCA: scores parameter for specifying output

• Improve mergeSEs and loadFromBiom

• Faith index: bugfix

miaViz

                     Changes in version 1.9                         

• Updated plotDMN to work with newest mia version

• Added plotCCA and plotRDA functions

MicrobiomeProfiler

                    Changes in version 1.7.1                        

• Change maintainer from Meijun to Guangchuang

MicrobiotaProcess

                   Changes in version 1.13.3                        

• fix the issue when assays is dgCMatrix other sparse matrix class. (2023-09-12, Tue)
• using internal functions to convert dist object to tbl_df or tbl_df to dist in mp_cal_dist and fix a bug of mp_extract_abundance when rowData contains list metadata information. (2023-08-21, Mon)
• update the doc of rmun argument in mp_plot_abundance to avoid misunderstanding. (2023-08-18, Fri) https://github.com/YuLab-SMU/MicrobiotaProcess/issues/99
• update mp_import_humann_regroup() to keep the abundance of contributed taxa in each sample with keep.contribute.abundance=TRUE. (2023-08-15, Tue)
• use rlang::check_installed() to check if a suggested package is installed, which will offer to install the package before continuing. (2023-08-02, Wed)
• introduce order.by.feature argument in mp_plot_abundance to adjust the sample order. (2023-07-24, Mon)

• update the format of citation and suppress the message introduced by tidytree. (2023-07-14, Fri)

                   Changes in version 1.13.2                        
  

• update mp_plot_ord to display the result of mp_adonis with show.adonis = TRUE. (2023-06-21, Wed)
• using theme_blinds of ggfun. (2023-06-20, Tue)
• add mp_import_humann_regroup function to parsing the output of humann_regroup_table. (2023-05-15, Mon)
• add fortify method for MPSE object. (2023-05-18, Thu)

• fix a bug of mp_plot_diff_res when ggnewscale updated to 0.4.9. (2023-05-30, Tue)

                   Changes in version 1.13.1                        
  

• fix a bug for the abundance calculation with force = TRUE and relative = FALSE. (2023-04-28, Fri)

MICSQTL

                   Changes in version 0.99.17                       

• Fix file name in vignette.

MICSQTL 0.99.16

• Enhance PGD to handle a wider range of omics data inputs.

                   Changes in version 0.99.15                       
  

• Update deconv and ajive by integrating a novel feature selection approach and improved deconvolution method.

                   Changes in version 0.99.14                       
  

• Update deconv by allowing proteins selected by loadings.

                   Changes in version 0.99.13                       
  

• Update ajive_decomp by adding option to output loadings.

                   Changes in version 0.99.12                       
  

• Update package loading in vignette.

                   Changes in version 0.99.11                       
  

• Add @return to data documentation.

                   Changes in version 0.99.10                       
  

• Merge cns_plot to ajive.
• Remove extra space.

• Downsize data in example code.

                   Changes in version 0.99.9                        
  

• Update email address.

                   Changes in version 0.99.8                        
  

• Remove unused lines and update importFrom.
• Add unit tests.

• Update abstract and intro.

                   Changes in version 0.99.7                        
  

• Add iteration option in deconv function.

                   Changes in version 0.99.6                        
  

• Remove unwanted lines.

• Update documentation.

                   Changes in version 0.99.5                        
  

• Update pkg loading.

                   Changes in version 0.99.4                        
  

• Reformat function and documentation.

                   Changes in version 0.99.3                        
  

• Resolve errors in different OS systems.

• Fix unrecognized unicode.

                   Changes in version 0.99.2                        
  

• Add a NEWS file to track changes to the package.

mistyR

                     Changes in version 1.9                         

                    Changes in version 1.8.1                        

• Requires dplyr >=1.1.0 due to change of sorting order in arrange()

MoleculeExperiment

             Changes in version 1.1.4 (2023-10-06)                  

• show method has been improved, and package is less verbose.

             Changes in version 1.1.3 (2023-08-22)                  
  

• feature_name is not called feature_id for consistency with segment_id.

             Changes in version 1.1.2 (2023-07-26)                  
  

• IMPORTANT: readCosmx and readMerscope can now also handle reading in and standardising boundary information!!

monaLisa

                    Changes in version 1.7.1                        

• allow modification of heatmap graphical parameters by forwarding … argument in plotMotifHeatmaps to all calls to ComplexHeatmap::Heatmap

Moonlight2R

                   Changes in version 0.99.14                       

Summary

• made test for GRN and arm64 less stringent to account for architectural differences

                   Changes in version 0.99.13                       
  

Summary

• refactored examples to make them faster

                   Changes in version 0.99.12                       
  

Summary

• added data loadings in functions

                   Changes in version 0.99.11                       
  

Summary

• added missing data loadings in vignette

• changed handling of null cases in PRAToTibble

                   Changes in version 0.99.10                       
  

Summary

• updated code style in all functions

                   Changes in version 0.99.9                        
  

Summary

• fixed hardcoded plot title in plotFEA
• updated reference in docs to published paper
• fixed excessively long example line in GLS function
• moved globalVariables calls after function definitions

• turned LazyData to false and issued connected fixes

                   Changes in version 0.99.8                        
  

Summary

• replaced number sequences generation (e.g. using seq(n) instead of 1:n) in all functions

                   Changes in version 0.99.7                        
  

Summary

• added bindings for global variables in majority of functions

                   Changes in version 0.99.6                        
  

Summary

• switched \dontrun to \donttest in some examples

• fixed vignette to have fewer eval=FALSE chunks

                   Changes in version 0.99.5                        
  

Summary

• added several checks for correctness of main function arguments

                   Changes in version 0.99.4                        
  

Summary

• changed instances of sapply to vapply

                   Changes in version 0.99.3                        
  

Summary

• added tests with testthat

• updated following example data: dataFEA, dataGRN, dataURA, dataPRA and cscape_somatic_output

• added following example data: dataURA_plot, dataGRN_no_noise

                   Changes in version 0.99.2                        
  

Summary

• added GLS (Gene Literature Search) function

• fixed library problems with vignettes

                   Changes in version 0.99.1                        
  

Summary

• removed package documentation from Rdata.R

                   Changes in version 0.99.0                        
  

Summary

• first release of Moonlight2R.

New features (added or significantly changed respect to MoonlightR)

• DMA Driver mutation analysis

• plotDMA Creates one or more heatmap of the output from DMA

• plotMoonlight Creates heatmap of Moonlight Gene Z-scores for selected genes

• EncodePromoters Experimentially verified promoter sites

• LOC_protein Level of consequence protein

• LOC_translation Level of consequence translation

• LOC_transcription Level of consequence transcription

• NCG Network of Cancer Genes 7.0

• dataPRA output from PRA function

• dataMAF Mutation data from TCGA-LUAD

• dataDMA Output from DMA function

• cscape_somatic_output Cscape-somatic annotations of TCGA-LUAD

• DEG_Mutations_Annotations Differentially expressed genes’s Mutations

• Oncogenic_mediators_mutation_summary Oncogenic Mediators Mutation Summary

• moonlight Function to run moonlight pipeline

MoonlightR

                   Changes in version 1.26.1                        

BUG FIX

• changed arguments for downloading datasets following updates to TCGAbiolinks

• added suggested package to fix install crash FIRST VERSION - FEATURES

  • dataFilt Gene Expression (Rnaseqv2) data from TCGA LUAD
  • dataGRN GRN gene regulatory network output
  • dataURA Output example from function Upstram Regulator Analysis
  • DEGsmatrix DEG Differentially expressed genes
  • DiseaseList Information on 101 biological processes
  • DPA DPA
  • EAGenes Information about genes
  • FEA FEA
  • GDCprojects Information on GDC projects
  • geneInfo Information about genes for normalization
  • GEO_TCGAtab Information on GEO data (and overlap with TCGA)
  • getDataGEO getDataGEO
  • getDataTCGA getDataTCGA
  • GRN Generate network
  • GSEA GSEA
  • knownDriverGenes Information on known cancer driver gene from COSMIC
  • listMoonlight Output list from Moonlight
  • LPA LPA
  • moonlight moonlight pipeline
  • MoonlightR MoonlightR
  • PEA PEA
  • plotCircos plotCircos
  • plotFEA plotFEA
  • plotNetworkHive plotNetworkHive: Hive network plot
  • plotURA plotURA: Upstream regulatory analysis heatmap plot
  • PRA Pattern Recognition Analysis (PRA)
  • tabGrowBlock Information growing/blocking characteristics for 101 selected biological processes
  • URA URA Upstream Regulator Analysis

motifStack

                   Changes in version 1.45.1                        

• Fix the issue of ‘This picture was not generated by Cairo graphics’ for importSVG.

msa

                   Changes in version 1.33.2                        

• update of Makevars: added -lpthread to PKG_LIBS in order to make sure that package also builds correctly on Bioconda

                   Changes in version 1.33.1                        
  

• update of msaConsensusSequence() and msaConsensusSequence() methods to account for recent change in function Biostrings::consensusMatrix()

                   Changes in version 1.33.0                        
  

• new branch for Bioconductor 3.18 devel

MSA2dist

             Changes in version 1.5.2 (2023-05-24)                  

Major changes

Minor improvements and bug fixes

• added aa2selfscore

             Changes in version 1.5.1 (2023-05-22)                  
  

Major changes

Minor improvements and bug fixes

• additional option to use asymmetric score matrix (symmetric=FALSE)
• changed rcpp_distSTRING.cpp
• changed rcpp_pairwiseDeletionAA.cpp
• changed rcpp_pairwiseDeletionDNA.cpp
• changed aastring2dist.R
• changed dnastring2dist.R

MsBackendSql

                     Changes in version 1.1                         

Changes in 1.1.5

• Add dbconn methods for MsBackendSql and MsBackendOfflineSql.

Changes in 1.1.4

• Improve performance of createMsBackendSqlDatabase by using also parallel processing for the peaksData call.

Changes in 1.1.3

• Add support for setBackend to MsBackendOfflineSql.

Changes in 1.1.2

• Mention in documentation that MsBackendSql can not be saved to disk.
• Expand vignette adding related documentation.

Changes in 1.1.1

• Fix for filterRt avoiding to filter if range is infinite.

MsCoreUtils

                    Changes in version 1.13                         

MsCoreUtils 1.13.1

• Add functions entropy and nentropy.

MSnbase

                    Changes in version 2.27                         

MSnbase 2.27.1

• Fix declarations of centroided/smoothed setters for OnDiskMSnExp objects (from Hervé Pagès via Github).

MSnbase 2.27.0

• New devel

msPurity

                   Changes in version 1.27.1                        

• createMSP fix - now uses the median precursor MZ and precursor RT in the MSP file

MsQuality

                     Changes in version 1.1                         

Changes in version 1.1.3

• update tests after update of OBO file / rmzqc

Changes in version 1.1.2

• Fix implementation of mzAquisitionRange
• add numberEmptyScans in qualityMetrics function
• add unit tests for export in rmzqc format
• add interpretation aid of metrics in vignette

Changes in version 1.1.1

• move msdata from Suggests to Imports
• rename function rtDuration to chromatographyDuration
• rename function rtOverTicQuantiles to ticQuartersRtFraction
• create function numberEmptyScans
• add attributes (MS QC terms) to the output of the Spectra metrics functions if the output matches the described term
• add rmzqc to IMPORTS
• add functionality to export quality metrics as in rmzqc format
• adjust documentation to newest version of PSI MS CV obo file
• add to the vignette information on how the metrics are calculated
• add argument filterEmptySpectra to remove entries of length 0 or that have intensity 0, implement the argument in the functions calculateMetricsFromOneSampleSpectra, calculateMetricsFromSpectra, calculateMetricsFromMsExperiment, and calculateMetrics

MultiAssayExperiment

                   Changes in version 1.28.0                        

New features

• Dropped experiments are no longer kept in the metadata slot. They can be seen with drops() (@LTLA, #323).

Bug fixes and minor improvements

• Checking colnames in sampleMap vs ExperimentList is more robust by only comparing unique and sorted values in each.

MultiRNAflow

                   Changes in version 0.99.9                        

Suggestions and remarks from a bioconductor team member

• modification of outputs in order to replace list ouputs by SE class object
• Vignette (Running_analysis_with_MultiRNAflow.Rmd)
• modification because ouputs modification

• More unit tests (now 197 unit tests in 31 files), coverage = 60/100

                   Changes in version 0.99.8                        
  

Suggestions and remarks from a bioconductor team member

• Correction of DESCRIPTION file
• add a new function to improve inputs in others function
• modification of R functions depending on previous inputs
• Vignette (Running_analysis_with_MultiRNAflow.Rmd)
• code-style to highlight (function, variable, package names)
• keeping includegraphics only for the introduction part
• More unit tests (now 45 unit tests in 25 files)

• add the R file MultiRNAflow-package.R for man folder

                   Changes in version 0.99.7                        
  

Suggestions and remarks from a bioconductor team member

• Correction of DESCRIPTION file
• Vignette (Running_analysis_with_MultiRNAflow.Rmd)
• code-style to highlight (function, variable, package names)
• More details about the vignette
• eval=FALSE replaced by eval=TRUE

• More unit tests

                   Changes in version 0.99.6                        
  

Bug fixes

• Necessary correction by the automated single package builder of bioconductor.org.

                   Changes in version 0.99.0                        
  

• Added a NEWS.md file to track changes to the package.

multiWGCNA

                   Changes in version 0.99.4                        

• Added BiocStyle to suggests

                   Changes in version 0.99.3                        
  

• Added suggested importFroms in R check

• Added Coexpression Line graph function documentation and to vignette

                   Changes in version 0.99.2                        
  

• All ERRORS and WARNINGS from R CMD CHECK and BiocCheck have been addressed

                   Changes in version 0.99.1                        
  

• Added a NEWS.md file to track changes to the package.

MungeSumstats

                   Changes in version 1.9.19                        

New features

• infer_eff_direction parameter added so user can decide whether to run the check

Bug fix

• Typo in unit test for infer effect direction.

• IEU GWAS unit tests updated to account for server outages.

                   Changes in version 1.9.18                        
  

Bug fix

• Fixed column header mappings
• Made all uncorrected header names uppercase and removed duplicates
• “TOTALSAMPLESIZE” now maps to “N” instead of “NSTUDY”
• “MAJORALLELE”, “MAJOR_ALLELE”, “MAJOR-ALLELE”, and “MAJOR ALLELE” now map to “A1” instead of “A2”
• Removed the mappings for “OR-A1”, “OR.A1”, “OR_A1”, and “BETA1” because MSS assumes that A2 is the effect allele
• Removed mappings for “A1FREQ”, “A1FRQ”, “AF1”, “FREQ.A1.1000G.EUR”, “FREQ.A1.ESP.EUR”, “FREQ.ALLELE1.HAPMAPCEU”, “FREQ1”, “FREQ1.HAPMAP”, and “FRQ_A1” because MSS defines “FRQ” to be the allele frequency of A2
• Removed mappings for “CHR36”, “BASE_GRCH36”, “POSITION36”, “POSGRCH36”, “BASEGRCH36”, “POS36”, “POS GRCH36”, “POS.GRCH36”, “POS-GRCH36”, and “POS_GRCH36” because MSS does not support the GRCh36 genome build
• Removed the ambiguous mapping “NMISS” -> “N” because “NMISS” can refer to the number of samples with missing data
• Removed the ambiguous mapping “WEIGHT” -> “N” because “WEIGHT” can refer to coefficient weights
• Fixed inference of allele where ambiguous (A1, A2) naming used (see infer_effect_column.R for code) but in short:
• Three checks now made to infer which allele the effect/frequency information relates to. See infer_effect_column.R for further details.
• See get_eff_frq_allele_combns.R for how effect/frequency columns that infer the allele are captured in the mapping file

New features

• New column header mappings:
• “VARIANT_ID” and “RSIDS” –> “SNP”
• “P_BOLT_LMM” –> “P”
• “NCASES” –> “N_CAS”
• “N_EFFECTIVE”, “N_INFORMATIVE”, and “TOTAL_N” –> “N”
• “HET_P” –> “HETPVAL”
• “HET_ISQ” –> “HETISQT”
• “ALL_AF” –> “FRQ”
• “DIRECT” –> “DIRECTION”
• “ALT_EFFSIZE” –> “BETA”

• “INFORMATIVE_ALT_AC” –> “AC”

                   Changes in version 1.9.17                        
  

Bug fix

• Cases checking ref genome where there are no indels would sometimes cause an error when joining. This resolved this issue.

                   Changes in version 1.9.16                        
  

New features

• flip_frq_as_biallelic parameter added enabling frequencies of non-bi-allelic SNPs to be flipped as if they were bi-allelic (1 - frequency) i.e. ignoring the frequencies of other alternative alleles (assuming these will be negligible). Note this will not be done as default as it is not fully correct but may be useful for some users.

                   Changes in version 1.9.15                        
  

Bug fix

• Fix for imputation column when imputing RS ID from CHR:BP. Avoids crash and ensures correct identification of imputed SNPs.

• Avoid running compute_nsize function when no imputation is wanted by user - also avoids message output in this situation.

                   Changes in version 1.9.14                        
  

Bug fix

• Fix reporting of genome-wide sign variants before formatting.

                   Changes in version 1.9.13                        
  

Bug fix

• In check_bp_range ensure that the BP column is numeric.

                   Changes in version 1.9.12                        
  

Bug fix

• In check_no_rs_snp the order of operations had to be reversed to ensure all values were present before sorting column headers when imputation_ind=TRUE and imputing rsIDs.

                   Changes in version 1.9.11                        
  

New features

• The rmv_chrPrefix parameter in format_sumstats() has been replaced with the new chr_style parameter, which allows users to specify their desired chromosome name style. The supported chromosome styles are “NCBI”, “UCSC”, “dbSNP”, and “Ensembl” with “Ensembl” being the default.

• check_chr() now automatically removes all SNPs with nonstandard CHR entries (anything other than 1-22, X, Y, and MT in the Ensembl naming style).

                   Changes in version 1.9.10                        
  

Bug fix

• Better method to detect vcf files - looks for vcf in extension not in name.

                    Changes in version 1.9.9                        
  

Bug fix

• Check ref genome change - if not match found for either genome build, an error will now be thrown.

• Checks has been added so that if chrom col has chr as a prefix, this will be removed before testing genome build.

                    Changes in version 1.9.8                        
  

Bug fix

• Bug fix when using imputation_ind with NA in chr column.

                    Changes in version 1.9.7                        
  

New features

• ignore_multi_trait parameter added which will ignore any multi-trait p-values if set to TRUE. By default it is false to maintain the current default running conditions for MSS.

muscat

                   Changes in version 1.15.1                        

• bug fix in ‘pbDS’: too stringent filtering causing no genes in any clusters to be tested previously resulted in a ‘subscript out of bounds’ error; execution is stopped and an informative error thrown instead.

• bug fix in ‘mmDS’: ‘dream’ (new version?) wouldn’t recognize model variables provided as data; fixed via adding ‘as.formula()’.

• “analysis” vignette: replaced suspended ‘dplyr’ function ‘top_n’ with ‘slice_min’ when filtering for top DS hits; fixed some typos; updated preprint to journal reference.

                   Changes in version 1.15.0                        
  

• Bioconductor release v3.17

mzR

                   Changes in version 2.35.1                        

• fix compilation on Fedora 38 / R-4.3.0. Thanks to Christian Iseli! Closes #282

NanoTube

                    Changes in version 1.7.2                        

• runLimmaAnalysis now allows optional arguments, which are passed to limma::lmFit.

                    Changes in version 1.7.1                        
  

• The codeclass.retain option now allows runLimmaAnalysis() to be run using a CodeClass/CodeClasses specified by the user, instead of automatically removing non-endogenous genes. See help(runLimmaAnalysis) for details.
• processNanostringData() can now handle a vector of .rcc files, in addition to the previous options for loading NanoString data.

ngsReports

                    Changes in version 2.3.5                        

• added support for rnaseqc metrics files

nipalsMCIA

             Changes in version 0.99.7 (2023-10-07)                 

Minor Changes

• Updated readme to reflect MAE changes.
• Updated citation.

• Fixed bug in documentation for nipals_multiblock.

             Changes in version 0.99.6 (2023-09-09)                 
  

Major changes

• Switched primary input to nipals_multiblock() to a MultiAssayExperiment object.
• nipals_multiblock() now outputs an object of the NipalsResult class.
• Converted all downstream analysis functions to work with the NipalsResult class.

Minor improvements and bug fixes

• Added simple_mae() function to convert a list of dataframes to a MultiAssayExperiment object.

• Fixed missing \value fields in man page for NipalsResult class.

             Changes in version 0.99.5 (2023-06-22)                 
  

Major changes

• Bumping version number to trigger re-build following bug in BiocCheck.

             Changes in version 0.99.4 (2023-06-01)                 
  

Major changes

• Fixed data corruption issues from v0.99.3

             Changes in version 0.99.3 (2023-06-01)                 
  

Major changes

• Changed the eigenvalue calculation in nipals_iter() to compute the variance of the global score at each deflation step. Prior versions used an SVD method to compute the singular values of the deflated data matrix directly.
• Fixed bug in projection_plot() where there was a mismatch between color labels and plotting order.
• Added parameter to nipals_multiblock that specifies whether the samples are in the rows or the columns

Minor improvements and bug fixes

• Changed vignette styling from rmdformats to BiocStyle and added installation sections to all of the vignettes.
• Removed empty helper.R
• Added significantly more unit testing.
• Fixed bug in projection_plot() when metadata was provided but no color_col was selected.
• Renamed the associated output of col_preproc_method in nipals_multiblock. The metadata field is also now available in the output independent of whether metadata is provided in the input.

• Added checks for consistency in sample names across data blocks and metadata.

             Changes in version 0.99.2 (2023-03-25)                 
  

Major changes

• Shrank the vignettes sizes (especially Vignette 2).

Minor improvements and bug fixes

• Restructured Vignette 2 to be more streamlined and have more explanations.

• Add an additional single cell data file to the repository using piggyback.

             Changes in version 0.99.1 (2023-02-26)                 
  

Major changes

• Included support for MultiAssayExperiment in nipals_multiblock.
• Improved access to existing data objects.

Minor improvements and bug fixes

• Made get_colors() more flexible for different color palette options.

             Changes in version 0.99.0 (2022-10-21)                 
  

• Added single cell data to the repository using piggyback.

nnSVG

             Changes in version 1.5.3 (2023-05-30)                  

• use model formula without intercept for non-spatial model - to enable weighted model

NormalyzerDE

                   Changes in version 1.19.7                        

• Remove RCmdrMisc as dependency, resolving a fatal crash caused by updated signature of RCmdrMisc CV calculation function

• Updating code to remove deprecation warnings for ggplot2 code

oncoscanR

                    Changes in version 1.4.0                        

Versions on bioconductor and Github have been merged and, from now on, will have consistent version numbers.

OncoSimulR

             Changes in version 4.3.3 (2023-07-17)                  

• One test failing on Linux aarch64: fixed (by commenting out, which is the right thing to do).

             Changes in version 4.3.2 (2023-06-03)                  
  

• Allow passing a seed to MAGELLAN’s random fitness landscapes in rfitness function.

• Fixed bug in rfitness when using a 3-element vector for scaling, and one or more fitness values had the same value as WT.

Organism.dplyr

                   Changes in version 1.30.0                        

BUG FIXES

• src_ucsc() failed to correctly handle new ‘hs1’ resources (T2T genomes) for ‘human’

orthogene

                    Changes in version 1.7.2                        

Bug fixes

-

                    Changes in version 1.7.1                        

New features

• remove_all_nas
• Can handle multiple cols.
• plot_orthotree
• New arg clades_rotate
• New func: rotate_clades

Bug fixes

• add_columns
• Handle both vectors and columns.
• sort_rows_func
• Handle both vectors and columns.
• filter_gene_df
• Avoid coercing single-col dataframe into vector.
• Flagged in #34
• Fix test-report_orthologs
• Recognize either Gene.symbol or input_gene cols depending on when ortholog conversion was done.
• Fix test-convert_orthologs
• Line 99 test had wrong number of cols.
• map_genes_planosphere

• Add backup download strategy.

                    Changes in version 1.7.0                        
  

New features

• Bump version.

orthos

                   Changes in version 0.99.4                        

• Temporary inactivate failing Windows tests

                   Changes in version 0.99.3                        
  

• Pinning more packages

                   Changes in version 0.99.2                        
  

• Pinning more packages

• updated stick with Bioconductor url

                   Changes in version 0.99.1                        
  

• make all function examples runnable
• added scheduled cron runs on R-CMD-check.yaml

• added inst/scripts to describe extdata generation

                   Changes in version 0.99.0                        
  

• prepare package for submission to Bioconductor.

                    Changes in version 0.1.0                        
  

• Added a NEWS.md file to track changes to the package.

OutSplice

             Changes in version 1.0.1 (2023-06-21)                  

• Fixed issue where nonsignificant events would be listed in ASE.types when no under-expressed outliers were found

pairedGSEA

                    Changes in version 1.1.2                        

• Fix bug where DEXSeq fails if there are NAs in the metadata

                    Changes in version 1.1.1                        
  

• Improved how surrogate variables are transferred in the design formulas

                    Changes in version 1.1.0                        
  

• paired_ora now adjusts gene background for analysis to reduce bias
• paired_ora now also does an ora combining the genes from the two analyses
• Added plotting mode paired = TRUE to plot_ora for the new paired_ora analysis type
• Added baseMean to gene-level aggregation output

partCNV

                   Changes in version 0.99.2                        

Changes

• Added unit tests.

peakPantheR

             Changes in version 1.15.3 (2023-10-03)                 

• correct plotAnnotationDiagnosticMultiplot axes limit after change in ggplot2 behaviour following a rotation

             Changes in version 1.15.2 (2023-10-02)                 
  

• ROI, uROI and FIR input checks for NA in rtMin, rtMax, mzMin and mzMax

             Changes in version 1.15.1 (2023-08-06)                 
  

• corrections in vignettes

phantasus

                   Changes in version 1.21.3                        

• Advanced normalizations: TMM & voom

• Complex differential expression design for limma & DESeq2

• Rework of count meta files (breaks backward compatibility)

phenomis

                    Changes in version 1.3.8                        

• writing (SummarizedExperiment & MAE): metadata.l argument now included

                    Changes in version 1.3.6                        
  

• writing (SummarizedExperiment): now saves the metadata as an additional _metadata.rds file

                    Changes in version 1.3.4                        
  

• hypotesting: minor documentation update

                    Changes in version 1.3.2                        
  

• UTF-8 file encoding for writing (utils::write.table)

PhyloProfile

                   Changes in version 1.16.0                        

• extended options in config file

• option to specify IP and port

• able to generate domain plot from main/customized profile tab

• highlight multiple genes/taxa; division lines for taxon group (#110)

• simplify gene IDs in detailed plot; show taxonomy hierarchy (#110)

• option to filter features in architecture plot (#110)

• option to show all input taxa (#110)

• added more info to domain plot (e-value, bit-score, pHMM)

• option to specify host and port for runPhyloProfile() fn

• fixed bug when lowest rank is subspecies

                   Changes in version 1.14.5                        
  

• improved highlighted duplicated ortho IDs

                   Changes in version 1.14.4                        
  

• fixed bug ordering genes

• auto identify lowest rank

                   Changes in version 1.14.2                        
  

• option to use user defined taxonomy DB (#124)

                   Changes in version 1.14.1                        
  

• option for highlight duplicated ortholog IDs

• option for cluster profiles based on ortholog IDs

• speedup by pre-calculating taxonomy tree (#123)

• disable rank selection after plotting

• turn on profile clustering by default

• changed “ftp://” to “https://” for taxdmp.zip

• fixed #126

Pigengene

            Changes in version 1.27.16 (2023-06-16)                 

Changes in existing functions

• Scaling is done in the compute.pigengene() function to avoid the following error that Sogand detailes on her lano: Error in La.svd(x, nu, nv) : error code 1 from Lapack routine ‘dgesdd’

             Changes in version 1.27.2 (2023-05-12)                 
  

Changes in existing functions

• The compute.pigengene() function does not warn about almost constant genes.

planet

                    Changes in version 1.9.2                        

                    Changes in version 1.9.1                        

plasmut

                   Changes in version 0.99.7                        

SIGNIFICANT USER-VISIBLE CHANGES

• Initial plasmut package release:

• Adds importance sampling method for Bayesian inference through importance_sampler()

plotgardener

                    Changes in version 1.7.7                        

BUG FIXES

• params parsing removes non-standard chromosomes when identifying gene transcripts

                    Changes in version 1.7.6                        
  

BUG FIXES

• colorby logic parsing is patched.

                    Changes in version 1.7.5                        
  

NEW FEATURES

• plotPairs, plotPairsArches, and plotRanges allow NA fill.

                    Changes in version 1.7.4                        
  

BUG FIXES

• Removed extra page creation with annoYaxis axisLine = FALSE.

                    Changes in version 1.7.3                        
  

BUG FIXES

• Removed blank page creation with pdf() calls for all major plotting functions.

                    Changes in version 1.7.2                        
  

BUG FIXES

• Fixed plotMultiSignal width and height parsing bug.

                    Changes in version 1.7.1                        
  

NEW FEATURES

• plotManhattan y-scales can be reversed for Miami plot-style layouts.

                    Changes in version 1.7.0                        
  

Version bump for Bioconductor 3.17 release.

plyinteractions

                   Changes in version 0.99.6                        

• Added validity functions for new classes
• Added tests (~90% coverage at this point)
• Improved doc:
• Fixed lines with > 80 characters

• Moved generics and classes to separate R files

                   Changes in version 0.99.5                        
  

• Initiated NEWS.md
• Internal refactoring:
• Removed paste calls in condition signals
• Moved classes and generic definitions in AllClasses.R and AllGenerics.R
• Fixed R minimum working version (4.3.)
• LazyData set to FALSE following Bioc recommendations
• Added package-level documentation
• Improved vignettes

PoDCall

             Changes in version 1.9.3 (2023-05-15)                  

• Added PoDCall publication citation

             Changes in version 1.9.2 (2023-05-10)                  
  

• Bugfixes

             Changes in version 1.9.1 (2023-05-03)                  
  

• Made PoDCall compatible with new BioRad software QX Manager

polyester

                   Changes in version 1.99.3                        

• NB function now exported

• note that version 1.99.3 on GitHub was version 1.1.0 on Bioconductor.

                   Changes in version 1.99.2                        
  

• bug fix in fragment generation (last 2 bases of transcript were never sequenced)

pRolocGUI

                    Changes in version 2.11                         

CHANGES IN VERSION 2.11.0

• New version for Bioc devel

CHANGES IN VERSION 2.11.1

• Fix bug in DT table when fData column is a matrix see issue #117

ProtGenerics

                   Changes in version 1.33.1                        

• rename uniqueMsLevel() to uniqueMsLevels()

PureCN

                    Changes in version 2.8.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Make processMultipleSamples temporarily defunct because the copynumber package was removed from Bioconductor

• Make it possible to specify saveRDS version to make output files readable by old R versions prior to 3.6.0 (#255)

BUGFIXES

• Fixed an issue with callLOH and –model-homozygous (#254)

• Fixed crash when VCF contained NAs in base quality scores (#249)

• Fixed wrong check for outdir write permissions in Coverage.R and NormalDB.R (#258)

• Fixed inverted return codes in couple of scripts (#284)

• Fixed an issue in callAlterations where the id argument was largely ignored (#292)

• Fixed broken support for GenomicsDB-R from their developer branch (#296)

• Fixed crash in plotAbs (#260)

• Fixed an issue with gene-level calls when annotation contained non-official symbols found on multiple chromosomes (#298)

• Fixed a wrongly formatted error message when no germline database information was found (#302)

• Fixed a crash when DB field in VCF only contains NAs(#301)

• Added –min-base-quality argument for PureCN.R (#320)

QFeatures

                    Changes in version 1.11                         

QFeatures 1.11.2

• Update message to fix test upon recent changes in MAE.

QFeatures 1.11.1

• Update nNA() and filterNA() and man pages to clarify percentages and proportions (see #189).

QFeatures 1.11.0

• New Bioconductor 3.18 (stable) release

qsvaR

                    Changes in version 1.5.3                        

BUG FIXES

• Fixed the error messages displayed by k_qsvs() to handle different types of situations. We implemented this update with @HediaTnani, @reneegf, and @lahuuki.

                    Changes in version 1.5.2                        
  

BUG FIXES

• Fixed a bug in qSVA() which was not passing sig_transcripts to getDegTx(). Related to https://github.com/LieberInstitute/qsvaR/issues/29.

• Fixed the documentation to highlight when users should use set.seed() to ensure the reproducibility of their results. Related to https://github.com/LieberInstitute/qsvaR/issues/28.

                    Changes in version 1.5.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Hedia Tnani is now the maintainer of qsvaR.

raer

                   Changes in version 0.99.12                       

• Changes made to prepare for bioc submission

                   Changes in version 0.99.11                       
  

• Replaced base R fisher test with c-wrapper to call htslib fisher test, which speeds up execution many fold.

                   Changes in version 0.99.10                       
  

• The options to write to tabix indexed output files have been removed from pileup_sites() as they have limited utility and introduce unwanted code complexity.

                   Changes in version 0.99.9                        
  

• The genomic-unstranded option for the library-type argument in FilterParam() has been renamed to unstranded, and the unstranded option has been removed.

                   Changes in version 0.99.8                        
  

• Function arguments involving a fasta file have been renamed to all be fasta

                   Changes in version 0.99.7                        
  

• added a single cell specific AEI calculation (calc_scAEI())

                   Changes in version 0.99.6                        
  

• added method to count base consensus base when counting UMIs with pileup_cells() using the sum of base qualities to select consensus.

                   Changes in version 0.99.5                        
  

• pileup_cells() now allows for multiple alleles to be queried at a site.

• Fixed an indexing bug in pileup_cells() that misassigned sites to counts.

                   Changes in version 0.99.4                        
  

• annot_snps will now compare the site allele to the SNP allele and return a column snp_matches_site indicating if the site matches the snp.

• added new function, find_scde_sites() to identify differentially editing sites in single cell data using fishers exact tests.

• pileup_cells now respects the min_depth and min_variant_reads FilterParameters.

                   Changes in version 0.99.3                        
  

• support BamFile and BamFileList inputs to pileup_sites() and pileup_cells(), which provides an option to provide custom BAI index file names.

                   Changes in version 0.99.2                        
  

• rename prep_for_de() and perform_de() to make_de_object() and find_de_sites().

                   Changes in version 0.99.1                        
  

• default values for edit_from and edit_to for calc_edit_frequency() have been changed to A and G respectively.

• renamed type argument in perform_de to test and removed type argument in prep_for_de

                   Changes in version 0.99.0                        
  

• added support for processing multiple BAM files with calc_AEI().

• Dropped minimally used bad_reads and reads parameters from pileup_sites()

• Added utility to screen scRNA-seq bam files for regions with oligo-dT mispriming (find_mispriming_sites()).

• add option to query ref and alt SNP alleles

• added tests for SummarizedExperiment filtering approaches

• added a strand bias stat sor using approach from GATK (StrandOddsRatio), and a confidence score calc_confidence() from SAILOR pipeline.

• ‘N’ bases in read or reference are ignored

• Removed outdated or unused functionality:

• bed indexing (indexBed and related C code)
• bam tag indexing (build_tag_index, show_tag_index, get_tag_bam, )
• bam tag index based single cell approach (sc_editing)
• bam tag indexing C code from bri (src/bri/*)
• sparse matrix merging for merge_pileups().
• unneeded utilities (filter_by_coverage)
• Remaining (and mostly unused) Rcpp code
• Removed fastmap, Rcpp, zlibbioc, RColorBrewer, and BiocGenerics dependencies

• Removed system requirements for C libraries used by bri

• The bed indexing used in pileup_sites() has been replaced with the region indexing approach from pileup_cells().

• pileup_sites() now requires a GRanges object rather than a bed file. The bedfile parameter has been removed and replaced with a sites parameter.

• Renamed Ref and Var output columns to REF and ALT and nVar was renamed to nAlt. This provides consistency with VCF format and consistency across pileup_cells() and pileup_sites() function calls

• pileup_cells() gained functionality to process multiple smart-seq2 style bam files.

• Changed filterParam argument in pileup_sites and pileup_cells to param for simplicity.

• Added FilterParam to exclude multi-allelic sites report_multiallelic, or exclude reporting a variant in the Var assay based on allelic frequency (min_allelic_freq).

• The bam_flags parameter used in pileup_sites and pileup_cells has been moved into the FilterParam class.

• The bedindex parameter for pileup_sites has been removed. This option is not needed at the user level and is planned to be replaced by the regional indexing used in pileup_cells().

• Added FilterParam option to trim reads based on fractional distance from 5’ (ftrim_5p) or 3’ end (ftrim_3p).

• Incorporated RBPZ and VDB statistics from bcftools, now returned as rowData columns when calling pileup_sites.

• A RangedSummarizedExperiment object is now directly returned from pileup_sites. Using merge_pileups is no longer necessary and is not an exported function.

• Renamed get_pileup to pileup_sites and create_se to merge_pileups

• Rename remove_clustered_variants, remove_multiallelic, and remove_splice_variants to filter_* for consistency.

• Rewrote and renamed the single cell editing function sc_editing to pileup_cells(). pileup_cells() does not require sorting and index by cell barcode, uses a new format to specify sites to query and requires providing the reference and alternate alleles of interest, writes to disk in a sparse matrix compatible format to reduce memory usage, and should have more performance as there is no need to query a fasta index.

• Implemented method to collapse reads with duplicate UMIs.

• Added option to filter sites in pileup based on number of reads containing a variant (#54)

• Added a NEWS.md file to track changes to the package.

RaggedExperiment

                   Changes in version 1.26.0                        

New features

• Added a contributed vignette for ASCAT workflows (@Lydia-King, #28).

RAIDS

                   Changes in version 0.99.15                       

SIGNIFICANT USER-VISIBLE CHANGES

• Updating installation section in vignette.

                   Changes in version 0.99.14                       
  

SIGNIFICANT USER-VISIBLE CHANGES

• Adding missing author David Tuveson.

• Updating BiocViews terms.

                   Changes in version 0.99.13                       
  

SIGNIFICANT USER-VISIBLE CHANGES

• Update in Reference GDS vignette.

                   Changes in version 0.99.12                       
  

SIGNIFICANT USER-VISIBLE CHANGES

• Seven new loadable objects are available in the package.

• The new readSNVVCF() function enable the use of VCF SNP files as input for the runExomeAncestry() and runRNAAncestry() functions.

                   Changes in version 0.99.11                       
  

SIGNIFICANT USER-VISIBLE CHANGES

• Update main vignette.

                   Changes in version 0.99.10                       
  

SIGNIFICANT USER-VISIBLE CHANGES

• Update main vignette.

                   Changes in version 0.99.9                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Better documentation for the runRNAAncestry() function.

                   Changes in version 0.99.8                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Some examples have been updated in the documentation.

                   Changes in version 0.99.7                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• The new runRNAAncestry() function executes most steps leading to the ancestry inference call on a specific RNA profile.
• A vignette describing the content of the Reference GDS files has been created.

• More parameter names have been changed to follow the camelCase style.

                   Changes in version 0.99.6                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• The vignette now referes to the generic formatted reference GDS rather than 1KG GDS file to showcase that the software is not dependant of the 1KG GDS file. Any refence dataset can be used as long as the dataset is formatted into a GDS file.

                   Changes in version 0.99.5                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• The function documentation has been improved.

• New vignette has been created. The vignette covers the steps done by the runExomeAncestry() function.

                   Changes in version 0.99.4                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• More parameter names have been changed to follow the camelCase style.
• The function documentation has been improved.

• A wrapper function runExomeAncestry() is now available.

                   Changes in version 0.99.3                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• More parameter names have been changed to follow the camelCase style.

BUG FIXES

• The warning related to the package man page has been removed.

                   Changes in version 0.99.2                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Most parameter names have been changed to follow the camelCase style.

                   Changes in version 0.99.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• The new runExomeAncestry() function encapsulates multiple ancestry inference steps in one command.

BUG FIXES

• Ensure GDS file is closed before using stop() in the addPhase1KG2SampleGDSFromFile() function.

                   Changes in version 0.99.0                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• The number of visible functions has been limited to simplify usage.

Rarr

                     Changes in version 1.1                         

• Fixed bug when reading an array if the fill value in .zarray was null.
• Addressed bug in makevars where Rarr.so could be compiled before libblosc.a was ready. Also backported to Rarr 1.0.2. (Thanks to Michael Sumner for reporting this issue: https://github.com/grimbough/Rarr/issues/5)
• Corrected issue where fixed length string datatypes would be written with null terminators, resulting in strings that were one byte longer than the dtype value written in the .zarray metadata. Also backported to Rarr 1.0.3.
• Added support for reading and writing the fixed length Unicode datatype, and for reading variable length UTF-8 datatype.

rawrr

             Changes in version 1.9.2 (2023-10-24)                  

• Download RawFileReader DLL’s from https://github.com/thermofisherlsms/RawFileReader #66.

Rcpi

             Changes in version 1.37.1 (2023-06-27)                 

Improvements

• Migrate rcdk to a runtime soft dependency using rlang, to avoid build time issues.
• Migrate unit tests from using RUnit to testthat.
• Use GitHub Actions workflows for R CMD check and building the pkgdown website.
• Fix URLs that are broken or moved in the documentation.

recount3

                   Changes in version 1.11.2                        

SIGNIFICANT USER-VISIBLE CHANGES

• Windows users can now use http://duffel.rail.bio/recount3 again! The switch to httr::http_error() resolved the duffel access problem for Windows users.

                   Changes in version 1.11.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Switched from using RCurl::url.exists() to !httr::http_error().

RedeR

                    Changes in version 2.6.0                        

• Major code refactoring.

• Improved readability.

• Reduced code complexities.

• Improved compatibility with standard igraph attributes.

regionalpcs

             Changes in version 0.99.0 (2023-08-25)                 

NEW FEATURES

• Added compute_regional_pcs() function to compute principal components for given gene regions.

• Included gene region annotations dataset gene_annots.

IMPROVEMENTS

• Improved performance of compute_regional_pcs() by using a more efficient algorithm.

• Updated vignette with more in-depth explanations and examples.

BUG FIXES

• Fixed bug in compute_regional_pcs() that produced incorrect results for certain edge cases.

• Corrected typos in man pages.

DEPRECATED AND DEFUNCT

• Deprecated old_function_name() in favor of new_function_name().

DOCUMENTATION

• Added a detailed vignette for working with compute_regional_pcs().

• Improved man pages with runnable examples for all exported functions.

RegionalST

                   Changes in version 0.99.8                        

• Add unit tests

• Add input checking functions

                   Changes in version 0.99.2                        
  

• New package RegionalST, for regional analysis of spatial transcriptomics data.

rgoslin

                    Changes in version 1.5.0                        

Please note that this Bioconductor version is based on Goslin version 2.0.0. See the Goslin repository and Goslin C++ repository for more details.

BioConductor 3.18 - Changes in 1.5.0

Improvements

• Better handling of mediators
• Translating gangliosides into new nomenclature structure
• Updated HMDB grammar for parsing mediators in lipid names: e.g., PA(P-16:0/LTE4)
• Parsing of adducts with heavy labeled isotopes now possible

Bug Fixes

• Minor bug fixes
• Removed wrong Lyso classification for SPB, SPBP, LHexCer, LSM

rhdf5

                   Changes in version 2.46.0                        

CHANGES

• Added support for reading nullable booleans and integers from the AnnData specification. h5read() will detect these automatically an attempt to cooerce them to the appropriate R data format.

rhdf5filters

                   Changes in version 1.14.0                        

CHANGES

• The package will now test for system libraries for several compression tools and will use those libraries rather than compiling from source if they are found.

Rhdf5lib

                    Changes in version 1.24                         

Bug fixes

• Fixed compilation issue when there was a space in the library path. (thanks to Pius Martinn @albert180 for reporting this, https://github.com/grimbough/rhdf5/issues/128)

• The configure script now detect the AR and RANLIB associated with R. This fixes an issue installing the package from source when using R provided by conda. (thanks to Jim Jeffers @jimjeffers for reporting this, https://github.com/grimbough/Rhdf5lib/issues/52)

ribosomeProfilingQC

                   Changes in version 1.13.2                        

• fix the bug the estimatePsite did not pass ignore.seqlevelsStyle to assignReadingFrame function.

                   Changes in version 1.13.1                        
  

• add ignore.seqlevelsStyle parameter to provide the flexibility of seqlevels.

RNAseqCovarImpute

            Changes in version 0.99.12 (2023-10-13)                 

• limmavoom_imputed_data_list now returns results for all variables in model formula

            Changes in version 0.99.11 (2023-10-06)                 
  

• License to GPL-3

            Changes in version 0.99.10 (2023-10-06)                 
  

• No longer exports internal functions

• License to GPL-3 + file LICENSE

• Updated vignette introduction

             Changes in version 0.99.8 (2023-09-18)                 
  

• Replaced RNAseqCovarImpute_data.RData with two individual rda files for example_DGE and example_data

• Added documentation for the package (?RNAseqCovarImpute)

• Added unit test structure and some basic unit tests

             Changes in version 0.99.7 (2023-09-16)                 
  

• Parallel now implemented with BiocParallel

• Added validity tests

             Changes in version 0.99.0 (2023-04-23)                 
  

• Submitted to Bioconductor

RnBeads

                   Changes in version 2.19.0                        

• Fixed issue with logical having a length greater than 1

rols

                    Changes in version 2.29                         

CHANGES IN VERSION 2.29.1

• Fix unit tests.

CHANGES IN VERSION 2.29.0

• New devel version (Bioc 3.18)

rpx

                     Changes in version 2.9                         

rpx 2.9.1

• Remove the generated subdir in the ftp_url when creating the PXDataset object <2023-09-26 Tue> (see issue #25).

Rsubread

                   Changes in version 2.16.0                        

• Add support for ARM64 platforms.

• Add support for CBCL format in cellCounts.

RTCGAToolbox

                   Changes in version 2.32.0                        

New features

• The functions getCNGECorrelation, getDiffExpressedGenes, and getSurvival have been removed from the package.

Rvisdiff

             Changes in version 0.99.4 (2023-09-27)                 

• DESeq2 and limma packages changed from ‘Imports’ to ‘Suggests’

             Changes in version 0.99.3 (2023-09-26)                 
  

• More checks on the input data

• More arguments to provide the names of columns

• Paths constructed using file.path() to be OS-agnostic

• Added package help-(man-)page (to be viewed via ?Rvisdiff) summarizing the packages functionality

• In the vignette, added BiocStyle functions to hyperlink external packages

• In the vignette, added code-style in order to distinguish/highlight anything R-related (package/function/argument/variable name), including Rvisdiff

• implemented more comprehensive unit testing

             Changes in version 0.99.2 (2023-09-21)                 
  

• Maintainer subscribed to the Bioc-Devel mailing list

             Changes in version 0.99.1 (2023-09-21)                 
  

• R version changed

• Added readme

             Changes in version 0.99.0 (2023-08-04)                 
  

• Submitted to Bioconductor

rWikiPathways

                   Changes in version 1.22.0                        

• Reimplementation of every function, replacing web service with static JSON

• getRecentChanges now returns data.frame of pathways per last-edit date

• findPathwaysByText has new param, “field” to optionally specify which fields to search

• getPathwayHistory now opens pathway commit history in browser

• getPathwayInfo now returns all pathways if param is left NULL

• New functions:
  • listCommunities
  • getPathwaysByCommunity
  • getPathwayXXXsByCommunity
  • getCounts
  • findPathwaysByOrcid
  • getCurationStatus
• Deprecated functions:
  • getCurationTags
  • getCurationTagNames
  • getXXXByCurationTag
  • wikipathwaysAPI
  • wikipathwaysGET

S4Arrays

                    Changes in version 1.2.0                        

NEW FEATURES

• Add abind() generic + default method.

• Add drop() method and dim() setter for Array objects.

S4Vectors

                   Changes in version 0.40.0                        

NEW FEATURES

• Subscript now can be any 1D array-like object when subsetting a Vector derivative.

SIGNIFICANT USER-VISIBLE CHANGES

• Drop empty “DataFrame and DataFrameList objects” section from S4VectorsOverview.Rnw vignette.

BUG FIXES

• Fix incorrect C-level if statement in Rle_utils.c

SAIGEgds

                    Changes in version 2.2.0                        

• fix “Matrix-deprecated” when calling as(<dsCMatrix>, "dgCMatrix")

SCArray

                   Changes in version 1.10.0                        

• update for DelayedArray (>= v0.27.2)

                    Changes in version 1.8.4                        
  

• rowMeans(), rowSums(), colMeans(), colSums() with row or column names

• override S4 functions rowDiffs(), colDiffs(), rowSdDiffs(), colSdDiffs(), rowVarDiffs(), colVarDiffs(), rowLogSumExps(), colLogSumExps()

                    Changes in version 1.8.3                        
  

• progress bar in scHDF2GDS()

• update %*% with SC_GDSMatrix

• update rbind() and cbind() with SC_GDSMatrix

• runPCA() on SC_GDSMatrix

SCArray.sat

                    Changes in version 1.0.3                        

• update FoldChange.SCArrayAssay() and FindMarkers.SCArrayAssay()

• fix subset.SCArrayAssay()

• update RunICA.SCArrayAssay(), RunSPCA.SCArrayAssay(), RunLDA.SCArrayAssay(), RenameCells.SCArrayAssay(), merge.SCArrayAssay()

scBubbletree

                    Changes in version 1.3.1                        

• vignette checks, minor modification

scDesign3

             Changes in version 1.0.1 (2023-01-20)                  

• Submitted to Bioconductor

             Changes in version 0.99.5 (2023-07-15)                 
  

• Update the MVN sampling

scider

                   Changes in version 0.99.0                        

First release.

scp

                    Changes in version 1.11                         

scp 1.11.3

• feat: added readSCPfromDIANN() that creates a QFeatures object from DIANN output tables.

scp 1.11.2

• Nothing yet.

scp 1.11.2

• feat: added reportMissingValues(), jaccardIndex(), cumulativeSensitivityCurve() and predictSensitivity() to facilitate reporting missing values. The vignette is also adapted with the new functionality.
• docs: created vignette about reporting missing values in SCP
• fix failing unit test.

scp 1.11.1

• Updated citation

scp 1.11.0

• New Bioconductor 3.18 (devel) release

scPCA

             Changes in version 1.15.1 (2023-06-19)                 

• Address useNames issue in colSds() that caused tests to throw warnings.

screenCounter

                    Changes in version 1.2.0                        

• Added support for counting dual barcodes via countDualBarcodes().

• Refactored countSingleBarcodes() to support arbitrary numbers of substitutions, insertions and deletions.

• Simplified countComboBarcodes() at the expense of dropping support for edits inside variable regions.

scRNAseqApp

                   Changes in version 1.1.10                        

• Fix the download button for the explorer module.

                    Changes in version 1.1.9                        
  

• Fix the repeat retreive for reference by createAppConfig.

                    Changes in version 1.1.8                        
  

• Change the filepath for credential file.

                    Changes in version 1.1.7                        
  

• Fix the bug in scInit for datafolder.

                    Changes in version 1.1.6                        
  

• Fix the download button which download the fixed values.

• Add multiple subset buttons.

                    Changes in version 1.1.5                        
  

• List the available datasets by users privilege.

                    Changes in version 1.1.4                        
  

• Fix the bug if the data is removed where user is explorering.

                    Changes in version 1.1.3                        
  

• Fix the bug introduced by changing actionBution to checkboxInput for modBubbleHeatmap.

                    Changes in version 1.1.2                        
  

• Add multiple layer of violin plot

• Add sample order controls for stats plot

                    Changes in version 1.1.1                        
  

• Fix the bug that coverage function is not imported.

SDAMS

                   Changes in version 1.21.1                        

• update maintainer email address

sechm

             Changes in version 1.9.4 (2023-07-14)                  

• row ordering now changed in the heatmap rather than matrix

• fixed a few bugs, added a few extras

• enabled list of features as input

seqArchRplus

                    Changes in version 1.1.3                        

New

• (User-facing) Enables choosing the out device type for motif heatmaps

                    Changes in version 1.1.2                        
  

New

• (User-facing) Ability to generate HTML reports to view large combined panels for multiple processed samples as scrollable carousels

SeqArray

                   Changes in version 1.42.0                        

UTILITIES

• new option ‘write.rsid’ in seqGDS2BED()

                   Changes in version 1.40.1                        
  

BUG FIXES

• seqAddValue(gdsfile, varnm="position") works correctly

shinyMethyl

                   Changes in version 1.37.2                        

• Removing failing test

signeR

                    Changes in version 2.3.3                        

• Minor documentation fixes

                    Changes in version 2.3.2                        
  

• New function: genCountMatrixFromMAF, to generate a count matrix from a MAF file

• support for reading MAF files on signeRFlow

• support for utilizing any BSgenome on signeRFlow

                    Changes in version 2.3.1                        
  

• Moved the source repository to TojalLab

• Fixed issue when running with fixed signatures matrix

• Reduced the maxeval time in rare cases when there is no convergence

signifinder

                    Changes in version 1.4.0                        

• Add glioCellStateSign function to compute the glioblastoma cellular states defined by Neftel C. et al. Cell (2019).

• Add whichAssay argument to signature functions to allow the user to specify which assay to use for the signature computation.

• Users can now plot also other signatures not computed with signifinder when using the heatmapSignPlot, correlationSignPlot and ridgelineSignPlot functions to compare them with the signatures computed with signifinder.

                    Changes in version 1.2.1                        
  

• Add evaluationSignPlot function to show some technical information of the signatures computed.

• Add nametype argument to geneHeatmapSignPlot function to allow more gene name ID in data.

• The vignette now contains an example with a single-cell dataset and an example with a spatial transcriptomics dataset.

singleCellTK

             Changes in version 2.10.1 (2023-07-26)                 

• Added function for bubble plot
• In SCTK-QC pipeline, added support for batch processing multiple inputs
• In SCTK-QC pipeline, added support for importing and exporting AnnData objects
• In SCTK-QC pipeline, fixed a bug causing YAML output files to be empty
• Update the SCTK-QC tutorial
• Fixed bug in combineSCE causing it to create multiple copies of row or column data

SparseArray

                    Changes in version 1.2.0                        

NEW FEATURES

• Add aperm() method for SVT_SparseArray objects.

• Add abind() method for SparseArray objects.

• Add dim() setter for SVT_SparseArray objects.

• Introduce nzwhich() generic and method for SparseArray derivatives. Also provide a default method for ordinary arrays and other array-like objects.

• Implement ‘Logic’ ops on SVT_SparseArray objects.

• Implement ‘Math’/’Math2’ ops on SVT_SparseArray objects of type “double”.

• ‘Compare’ ops now support SVT_SparseArray objects of type() “raw” or “complex”.

• All matrixStats methods (except row/colMedians()) now work on multidimensional SVT_SparseArray objects and support the ‘dims’ argument, like the row/colSums() and row/colMeans() functions in base R.

• Add row/colAnys() + row/colAlls() + row/colAnyNAs() + row/colProds() methods for SVT_SparseArray objects.

SIGNIFICANT USER-VISIBLE CHANGES

• Rename nzvals() slot getter (for COO_SparseArray objects) -> nzdata(). Also reintroduce nzvals() as a fast way to get ‘x[nzwhich(x)]’ on a sparse array-like object ‘x’.

• Re-implement all matrixStats methods (except row/colMedians()) for SVT_SparseArray objects in C.

sparseMatrixStats

                    Changes in version 1.13                         

• Make sparseMatrixStats compatible with matrixStats release v1.0.0. In particular change ‘useNames’to ‘TRUE’ by default.

• Add fast path for ‘rowSums2(x, cols = logical_vector)’

• Add useNames parameter to all functions

• fix incomplete method signature of rowQuantiles

spaSim

                    Changes in version 1.3.1                        

• Added newly published paper.

                    Changes in version 1.3.0                        
  

Development version in Bioconductor 3.18

SpatialExperiment

             Changes in version 1.11.2 (2023-09-01)                 

• move DropletUtils package to Suggests

             Changes in version 1.11.1 (2023-08-21)                 
  

• add methods to rotate/mirror spatial coordinates and objects

SpatialFeatureExperiment

                    Changes in version 1.2.1                        

• Fixed bug in .check_features and .symbol2id where “symbol” column is hard coded

Spectra

                    Changes in version 1.11                         

Changes in 1.11.11

• Fix issue with filterFourierTransformArtefacts function (see issue #302). Thanks Adriano Rutz for reporting.

Changes in 1.11.10

• peaksData,MsBackendMemory returns a data.frame if additional peak variables (in addition to “mz” and “intensity”) are requested. For columns = c(“mz”, “intensity”) (the default) a list of matrix is returned.
• peaksData,Spectra returns either a matrix or data.frame and ensures the peak data is correctly subset based on the lazy evaluation processing queue.
• $,Spectra to access peak variables ensures the lazy evaluation queue is applied prior to extracting the values.
• applyProcessing correctly subsets and processes all peak variables depending on the processing queue.
• spectraData<-,Spectra throws an error if processing queue is not empty and values for peaks variables should be replaced.
• $<-,Spectra throws an error if processing queue is not empty and a peaks variable is going to be replaced.
• Add full support for additional peaks variables to MsBackendDataFrame.

Changes in 1.11.9

• Add filterPrecursorPeaks to allow filtering peaks within each spectrum with m/z values relative to the precursor m/z of the spectrum.

Changes in 1.11.8

• Add an example to the vignette describing how spectral similarity scores from the msentropy package can be used with compareSpectra.

Changes in 1.11.7

• Fix in compareSpectra to also pass parameters ppm and tolerance to the peak similarity calculation functions FUN: this allows to use custom similarity function with integrated mapping of peaks.
• Add joinPeaksNone to skip the peak matching in compareSpectra if the similarity scoring function performs its own peak matching.
• Only use parallel processing in setBackend,Spectra if both backends support it.

Changes in 1.11.6

• Add filterPrecursorMaxIntensity function.
• Add filterPrecursorIsotopes function.

Changes in 1.11.5

• Add scalePeaks function (see issue #291).

Changes in 1.11.4

• Import uniqueMsLevels from ProtGenerics.

Changes in 1.11.3

• Rename combinePeaks for lists of peak matrices into combinePeaksData.
• Add combinePeaks generics.
• Add combinePeaks,Spectra to combine peaks within each spectrum in a Spectra.

Changes in 1.11.2

• Add deisotopeSpectra and reduceSpectra functions.

Changes in 1.11.1

• Add example for filtering precursor m/z peaks from fragment spectra to the vignette.

SpectralTAD

             Changes in version 1.16.1 (2023-07-04)                 

• Adjust installation url

SPIAT

                    Changes in version 1.3.5                        

SIGNIFICANT USER-VISIBLE CHANGES

• Added a new argument margin_dist for define_structure(). Specifying the margin width with microns instead of layers of cells.

                    Changes in version 1.3.4                        
  

BUG FIXES

• Added legends to plot_cell_categories() plots when layered = TRUE.

• Added a distance parameter to fix the dimension error in calculate_spatial_autocorrelation().

                    Changes in version 1.3.3                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Fixed thresholding bug in predict_phenotypes().

NOTES

• Added Shiny App (reading data) link.

                    Changes in version 1.3.2                        
  

NOTES

• Fixed typo in citation and SPIAT overview diagram.

• Moved the following packages from Imports to Suggests: alphahull, plotly.

                    Changes in version 1.3.1                        
  

• Added citation to the newly published paper.

                    Changes in version 1.3.0                        
  

Development version on Bioconductor 3.18.

splatter

             Changes in version 1.26.0 (2023-10-25)                 

• Fixed a bug in splatSimPathDE() where DE factors were not adjusted based on the path origin (path.from parameter). This affected paths where the path origin was not the simulation origin (i.e. path.from != 0), particularly when the path DE was minimal. With this fix paths should no longer drift towards the origin.

SpliceWiz

             Changes in version 1.3.2 (2023-06-05)                  

• Bugfix: error when running featureCounts wrapper due to non-numeric assignment of single / paired end reads

             Changes in version 1.3.1 (2023-05-20)                  
  

• Bugfix: fixed - static plot coverages did not show when reverseGenomeCoords = TRUE

• Bugfix: error when running featureCounts with overwrite = TRUE

sSNAPPY

             Changes in version 1.4.4 (2023-10-09)                  

• Remove databases that are no longer supported: pathbank, panther, pharmgkb, smpdb

             Changes in version 1.4.3 (2023-07-31)                  
  

• Updated the perturbation scoring step to account for the orientiaton of topology matrices for KEGG pathways (row - Downstream genes; column - Upstream genes)

• Add prefix parameter to the weight_ss_fc function to allow user-specified prefix that are other than “ENTREZID:”

             Changes in version 1.4.2 (2023-07-12)                  
  

• Updated the permtuation strategy so that the generate_permuted_scores function now construct all possible permuted pairs by default
• Updated the plot_community function so KEGG pathways that are not assigned to categories will be ignored in community labeling

statTarget

                     Changes in version 2.0                         

NEW FEATURES

• New GUI o Mouse Hover for help information o .log file

• New Signal correction o Combat for QC-free Signal correction o QC-RFSC methods for metabolomics and proteomics data

• New feature slection o Random Forest and the Permutation based variable importance measures o new MDSplot for Random Forest o P-value based importance plot

• New data preprocessing o PQN/SUM/none normalization o center/none Scaling method

structToolbox

                   Changes in version 1.13.5                        

• improve consistency between methods in fold change computations

• better handling of NA in fold change computations

                   Changes in version 1.13.4                        
  

• fix PLSDA predicted group assignment

• add option to PLSDA to use probability for yhat for predictions

• update tests

                   Changes in version 1.13.3                        
  

• d-ratio equations changed to match Broadhurst et al (2018)

• add tests for d-ratio

• fix PCA eigenvalues calculation

                   Changes in version 1.13.2                        
  

• d-ratio filter now correctly removes features

• update descriptions/documentation for missing value filters

• add tests for d-ratio

                   Changes in version 1.13.1                        
  

• hotfix vector_norm now correctly normalises samples to length 1

• re-sync with Bioc devel

• fix broken documentation

SummarizedExperiment

                   Changes in version 1.32.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Vignette gains a new section about interactive visualization with iSEE.

SVMDO

             Changes in version 1.1.1 (2023-06-28)                  

• Removal of unnecessary variables in differential expression and classification analyses

SynExtend

                   Changes in version 1.13.8                        

• Updates to all EvoWeaver documentation files
• Fixed small bug in PhyloDistance causing Method=’JRF’ to return similarity rather than the distance

• Fixed small bug in TreeDistance.EvoWeaver resulting in an inconsistent calculation of score when using TreeMethods=’JRF’

                   Changes in version 1.13.7                        
  

• Small fixes

                   Changes in version 1.13.6                        
  

• ProtWeaver and ProtWeb have been renamed to EvoWeaver and EvoWeb, respectively
• New sequence level method for EvoWeaver

• Various small internal updates to EvoWeaver

                   Changes in version 1.13.5                        
  

• Minor changes to SelectByK and vignette

                   Changes in version 1.13.4                        
  

• New predictor PAPV.ProtWeaver to calculate p-values for presence/absence profiles.
• ContextTree now uses MirrorTree with species tree correction and p/a overlap correction

• Updates to documentation

                   Changes in version 1.13.3                        
  

• predict.ProtWeaver now supports multiple algorithms at once (ex. predict(ew, Method=c(“Jaccard”, “Hamming”)))

• Documentation for ProtWeaver and associated methods has been updated to match recent updates.

                   Changes in version 1.13.2                        
  

• FastQFromSRR function added as a convenience wrapper for the SRAtoolkit function fastq-dump.

                   Changes in version 1.13.1                        
  

• SuperTree now works directly with dist objects, providing better performance and scaling
• Updates to simMat objects
• No longer throw a warning when initialized in RStudio
• Formatting is cleaner and supports larger object names
• Updates to NVDC.ProtWeaver
• Now supports amino acid sequences using the DNAseqs=FALSE argument
• Now calculates a p-value-weighted score
• Adds MakeBlastDb function to create a BLAST database from R, plus associated documentation updates
• Smaller fixes to some ProtWeaver methods
• predict.ProtWeaver no longer returns using invisible (this was annoying and unneccessary)
• APC correction for MutualInformation.ProtWeaver removed to allow for parallelization
• MirrorTree.ProtWeaver now works correctly with MTCorrection=”speciestree”
• CorrGL.ProtWeaver now uses Fisher’s Exact Test for p-values rather than the R value of spearman correlation
• Many internal performance improvements
• ProtWeaver almost entirely uses dist objects rather than matrix, saving significantly on memory
• faster Cophenetic function implemented internally
• Copied internal .Call(‘cophenetic’) from DECIPHER to SynExtend to avoid potential namespace issues
• Small fixes to remove some notes from BiocCheck::BiocCheck()
• Variety of small updates to pass BiocCheck

syntenet

                    Changes in version 1.3.5                        

NEW FEATURES

• Added function run_last() to run alternative BLAST search. Vignette was updated accordingly.

                    Changes in version 1.3.4                        
  

BUG FIXES

                    Changes in version 1.3.3                        

                    Changes in version 1.3.2                        

BUG FIXES

• Strand information is now preserved in the output of process_input() (for users who want to plot synteny).

                    Changes in version 1.3.1                        
  

NEW FEATURES

• Added function collapse_protein_ids() to replace protein IDs in sequence names (equivalent to FASTA headers) with gene IDs. If there are multiple protein for the same gene, onlt the longest is kept. Vignette was updated accordingly.

tadar

                   Changes in version 0.99.0                        

• Submitted to Bioconductor.

TargetSearch

                    Changes in version 2.4.0                        

NEW FEATURES

• plotPeakRI: new option to plot by RT. This, however, needs the parameter dev because the relationship between RI and RT is unknown.

• FindPeaksAll: new option to search by RT. Basically this change implements the functionality of plotPeakRI.

• C code: refactor or most part of the code that deals with file parsing, in particular the text parser. The parser is now based on regular expressions, which should be more robust in detecting errors.

• Tests: though is not relevant to the user, TargetSearch include more unit testing for several internal functions.

BUG FIXES

• Add assertion that the option TS_RI_columns has three elements and that it is a character or integer vector.

TBSignatureProfiler

                   Changes in version 1.14.0                        

Bug Fixes

• Fixed bug for signatureBoxplot by removing quotations around variables. This issue was introduced with the newest ggplot2 version. Thanks to Arthur VanValkenburg for identifying the issue and solution.
• Removed Zimmer_RES_3 which was an identical signature as the previously published Sweeney_OD_3.
• Fixed error in example for compare_algs caused by the signature being used.

Minor Changes

• Added Vargas_18 and Vargas_45 signatures (doi: 10.1371/journal.pcbi.1010770)

TCGAbiolinks

                   Changes in version 2.29.1                        

• Removing support to legacy archive since it will be shutdown by GDC soon.

• When saving files we will not include folders prefix legacy/harmonized anymore

TCGAutils

                   Changes in version 1.22.0                        

Bug fixes and minor improvements

• UUIDtoBarcode returns barcodes consistent with Genomic Data Commons API update

TENxIO

                    Changes in version 1.4.0                        

Bug fixes and minor improvements

• Skip unit tests when remote H5 access is not configured.

terraTCGAdata

                    Changes in version 1.6.0                        

New features

• findTCGAworkspaces has been removed from the package.

tomoseqr

             Changes in version 1.11.1 (2022-10-25)                 

• Made the following changes: o Added 3D visualize function to imageViewer o Changed normCount and normMask options in estimate3dExpressions() to normalize option. When it is TRUE (default), the function works as if normCount = "count", normMask = TRUE. When it is FALSE, the function works as if normCount = "none", normMask = FALSE.

trackViewer

                   Changes in version 1.37.15                       

• Fix reading valid pairs typo.

                   Changes in version 1.37.14                       
  

• update the lollipopPlot documentation to fix the issue unable to find an inherited method for function ‘content’ for signature ‘response’.

                   Changes in version 1.37.13                       
  

• fix the feature legend space.

                   Changes in version 1.37.12                       
  

• add ARA function.

• fix the missleading color legend of interaction data.

• fix the bug in addInteractionAnnotation.

                   Changes in version 1.37.11                       
  

• fix the minimal font of optimized style.

                   Changes in version 1.37.10                       
  

• add function GIoperator.

                   Changes in version 1.37.9                        
  

• add function addInteractionAnnotation for Interaction data.

                   Changes in version 1.37.8                        
  

• change the filter condiction for tads annotation of Interaction data.

                   Changes in version 1.37.7                        
  

• add tads annotation for Interaction data.

                   Changes in version 1.37.6                        
  

• add lollipop_style_switch_limit for lollipop plot.

                   Changes in version 1.37.5                        
  

• add border_color for Interaction data.

                   Changes in version 1.37.4                        
  

• update the documentation for lollipopPlot for changes of the snp label.

                   Changes in version 1.37.3                        
  

• use strawr to replace the local C++ script.

                   Changes in version 1.37.2                        
  

• remove the CXX_STD = CXX11 from straw Makevars.

                   Changes in version 1.37.1                        
  

• add stop message when there is negative values for grid.pie plot.

transomics2cytoscape

                   Changes in version 1.11.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Added pbapply progress bar at the “getEdgeInfo” points.

DATA or DOCUMENT CHANGES

• Wrote the time it takes to complete the process in my environment for each use case.

treeio

                   Changes in version 1.25.4                        

• reexport as.phylo.hclust_node() to fix as.phylo.pvclust() issue (2023-8-25, Fri, #110)

                   Changes in version 1.25.3                        
  

• add find.hclust.igraph() method to hierarchical clustering graph nodes (2023-08-11, Fri, #105)
• update spt() and as.phylo.igraph() to consider edge attributes (#105)
• move tree operation methods to the ‘tidytree’ package so that this package is focus on input, output and object conversion

• fixed issue in parse BEAST file that contains negative branch length (2023-08-03, Thu, #106)

                   Changes in version 1.25.2                        
  

• spt method to find shortest path tree (2023-07-14, Fri, #102)
• update old-style ‘CITATION’ from citEntry() to bibentry() (2023-07-14, Fri, #102)
• bug fixed in as.treedata() for tbl_df object (2023-07-14, Fri, #101)
• keep.tip() method to remove all tips excepts the selected tips (2023-07-13, Thu, #100)

• better support of converting ‘igraph’ object to ‘phylo’ object (2023-07-12, Wed, #99)

                   Changes in version 1.25.1                        
  

• bug fixed in read.nhx() when metadata contains both character and numeric (e.g., AAA111) (2023-05-31, Wed, #97)

TSAR

                   Changes in version 0.99.0                        

• First Draft for BioConductor review, completed on August 15, 2023

tximeta

                   Changes in version 1.20.0                        

• Add argument to summarizeToGene(): assignRanges that takes either “range” (default) or “abundant”, and determines the ranges that are attached to the SE (rowRanges). Note that this new argument does not affect the data aggregation at all (counts and abundance are summarized to gene by tximport). The default behavior of summarizeToGene() returns ranges that correspond to the range of the isoforms of the gene, that is the leftmost basepair to the rightmost basepair of any isoform. The non-default “abundant” instead returns the range of the most abundant isoform in the data, averaging over samples. Information about the choice of range is included in mcols

• Added support for piscem-infer: type=”piscem” also auto-detected from file ending.

                   Changes in version 1.19.8                        
  

• Added support for piscem-infer: type=”piscem” also auto-detected from file ending.

                   Changes in version 1.19.6                        
  

• Fixed genome build for mouse M26 and higher to GRCm39, thanks to Charlotte Soneson.

tximport

                   Changes in version 1.30.0                        

• Support for piscem-infer: use type="piscem".

UniProt.ws

                   Changes in version 2.42.0                        

NEW FEATURES

• pageSize and n arguments added to queryUniProt to expose underlying API request defaults. It is recommended to set the pageSize to a large value e.g. 500 for large queries.

BUG FIXES AND MINOR IMPROVEMENTS

• Support for directly mapping to ‘Ensembl’ IDs with select.

• Fixed issue with pagination with large queries (over 25 results) in queryUniProt (@jdreyf, #23)

universalmotif

                   Changes in version 1.18.1                        

BUG FIXES

• Fixed compilation flags causing errors on linux.

updateObject

                    Changes in version 1.6.0                        

BUG FIXES

• Minor tweak to low-level utilities update_rds_file() and update_rda_file().

variancePartition

                    Changes in version 2.0.5                        

• May 31, 2023
• fix convergence issues
• fix initialization of lmer() fit

• use 1 OMP thread internally, then restore to original value

                    Changes in version 2.0.4                        
  

• May 30, 2023
• When running dream(), ensure model convergence using second fitting with Nelder_Mead to avoid edge cases where the approximate hessian from lmerTest::as_lmerModLT() has a negative eigenvalue
• fix issue in get_prediction() returning NA values when variables modeled as categorical and levels are omitted
• fix issue in voomWithDreamWeights() when some genes don’t converge

• retry lmer() model fit with another optimizer after it fails convergence test.

                    Changes in version 2.0.3                        
  

• May 13, 2023

• fix vcov()

                    Changes in version 2.0.2                        
  

• May 17, 2023

• add matrix argument to mvTest()

                    Changes in version 2.0.1                        
  

• May 12, 2023
• mvTest() now shrinks covariance using the Schafer-Strimmer method

• vcovSqrt() returns the matrix whose cross product gives the vcov() result from fits with dream()

                    Changes in version 2.0.0                        
  

• April 20, 2023
• Major code refactoring to:
• improve code reuse
• simplify debugging and maintaining code
• simplify addition of new features
• improve error handling
• some linear mixed model analyses are 50% faster

• enable additional features for dreamlet package that depends heavily on variancePartition.

                   Changes in version 1.31.22                       
  

• Oct 19, 2023
• fix handling of variables with missing data

• return fit$genes properly

                   Changes in version 1.31.21                       
  

• Oct 16, 2023
• handle weights properly when the linear mixed model fails for some genes
• lmFit() and
• in iterRows() set scale = FALSE as default
• in voomWithDreamWeights(), scale in input weights and weights in side fitVarPartModel()
• get weights estimated most similar to voomLmFit()

• in dream() use rescaleWeights = FALSE to get sigma estimates compatable with lmFit()

                   Changes in version 1.31.20                       
  

• Sept 26, 2023

• allow weights to be a matrix in voomWithDreamWeights()

                   Changes in version 1.31.19                       
  

• Sept 22, 2023

• add rescaleWeightsAfter argument to voomWithDreamWeights()

                   Changes in version 1.31.18                       
  

• Sept 5, 2023

• improved error handling for fitVarPartModel(), fitExtractVarPartModel(), and voomWithDreamWeights()

                   Changes in version 1.31.16                       
  

• August 18, 2023
• in dream(), if “Kenward-Roger” is specified but gives covariance matrix that has poor condition number or is not positive definite, then fall back to “Satterthwaite” for hypothesis testing in linear mixed models

• Update documentation, and reformat code

                   Changes in version 1.31.15                       
  

• August 10, 2023

• fit = dream() now returns fit$loglik (the log-likelihood for each gene), and fit$edf (the effective degreees of freedom for each gene)

                   Changes in version 1.31.13                       
  

• August 7, 2023
• fix bug in calcVarPart() where weights was ignored in some cases

• add additional tests to check this

                   Changes in version 1.31.12                       
  

• July 3, 2023

• makeContrastsDream() converts NA contrasts to NULL

                   Changes in version 1.31.11                       
  

• setting voomWithDreamWeights(…, span=”auto”) now estimates tuning parameter from data using fANCOVA::loess.as()

                   Changes in version 1.31.10                       
  

• filterInputData() now ensures EList contains a matrix

                   Changes in version 1.31.9                        
  

• Fix issue in mvTest() when specifying features with strings

                   Changes in version 1.31.8                        
  

• Fix error message when linear mixed model fails

                   Changes in version 1.31.7                        
  

• update mvTest() to run in parallel

                   Changes in version 1.31.6                        
  

• update mvTest() to include Hotelling T2 test and LS.empirical()

                   Changes in version 1.31.1                        
  

• June 4, 2023
• Rename for Bioconductor compatability

Voyager

                    Changes in version 1.3.1                        

• Removed functions and arguments deprecated in 1.2.0

                    Changes in version 1.2.6                        
  

• Fixed bug in plotColGraph when one out of multiple samples is plotted.
• Allow 16 bit images in spatial plotting functions.

• Removed adespatial from Suggests as it’s only used as a reference in unit tests and it got removed from CRAN.

                    Changes in version 1.2.5                        
  

• Use imgRaster getter rather than the S4 no-no of @image to get images to plot, as the latter will no longer work as of SFE 1.2.3 that wraps SpatRaster images when saving RDS. Reading RDS won’t unwrap so images need to be unwrapped when they’re needed.

                    Changes in version 1.2.4                        
  

• Remove useNames = NA warning when calling MULTISPATI; the warning comes from generic of colVars.
• Use algebraic eigenvalues for MULTISPATI when either nfposi or nfnega is 0

• Added bins_contour argument to moranPlot to change the number of bins in cell density contours

                    Changes in version 1.2.3                        
  

• Fix bug when plotting a feature with illegal name alongside another feature with legal name
• Make sure runBivariate and calculateBivariate use gene symbols in results even if Ensembl IDs are specified when swap_rownames is set

• Change secondary sequential palette in the light theme to YlOrRd so it’s more distinguishable from the Blues primary palette at low values

                    Changes in version 1.2.2                        
  

• Some minor bugs: runBivariate gets correct feature names when only feature1 is specified and swap_rownames is used to show gene symbol
• Correct output for cross variogram maps for only one pair of genes
• Added default_attr to localmoran_bv’s SFEMethod
• Don’t plot attribute when localResult is a vector and there’s no default attr
• When plotting multiple features, the panels follow the same order the features are specified
• Allow illegal characters in names of colData and reducedDims in plots
• Plot only one component in spatialReducedDim with the components argument
• Deprecate plotColDataBin2D and plotRowDataBin2D

weitrix

                   Changes in version 1.13.1                        

• Use read.csv rather than read_csv in vignettes, as read_csv was causing a hard-to-reproduce error when building vignettes.

xcms

                   Changes in version 3.99.6                        

• Add method to coerce a XcmsExperiment to a xcmsSet (issue #696).

• Support providing only mz or rt also for chromatogram,MsExperiment.

                   Changes in version 3.99.5                        
  

• Only mz or rt need to be provided for chromatogram.

                   Changes in version 3.99.4                        
  

• Add chromPeakChromatograms function to extract (EIC) chromatograms for chromatographic peaks.

                   Changes in version 3.99.3                        
  

• Small fixes in the direct injection vignette.

• Add parameter isolationWindowTargetMz to the chromatogram function for MsExperiment and XcmsExperiment to ensure MS2 chromatographic data is extracted from the MS2 spectra containing fragments of the compound of interest.

                   Changes in version 3.99.2                        
  

• Add the xmse data set representing an XcmsExperiment object.

• Update the compounding vignette to use the new objects.

• Add loadXcmsData to load test data objects (and fix/update paths).

• Add groupFeatures methods for XcmsExperiment.

• Fix issue in featureArea for XcmsExperiment.

• Update main vignette to use and describe the new data objects.

• Add findChromPeaksIsolationWindow method for MsExperiment and XcmsExperiment.

• Make reconstructChromPeakSpectra a method.

• Add reconstructChromPeakSpectra implementation for XcmsExperiment.

• Add filterIsolationWindow for MsExperiment and XcmsExperiment to filter spectra (and eventually chromatographic peaks) based on the isolation window.

• Update the LC-MS/MS vignette adding also an example how to deisotope SWATH MS2 spectra.

                   Changes in version 3.99.1                        
  

• featureSummary and overlappingFeatures gain support for XcmsExperiment.

• Fix in featureChromatograms to ensure a valid object is returned.

                   Changes in version 3.99.0                        
  

• Add XcmsExperiment and support for MsExperiment/Spectra: add all functionality for a full xcms processing on a MsExperiment object.

• Fix issue in refineChromPeaks with MergeNeighboringPeaksParam where a wrong apex position was considered in the evaluation whether candidate peaks should be merged (would only happen for merging of > 2 candidate peaks).

• Re-write the reconstructChromPeakSpectra for DIA data analysis to fix an issue with chromatographic peaks in overlapping SWATH isolation windows and generally to improve performance.

YAPSA

                   Changes in version 1.26.7                        

• Some URLs are reformatted in the documentations and vignettes.

• Data is only loaded into the function environment with data(..., envir = environment()).

• Namespace imports are adjusted to fixed the function name conflict.

zellkonverter

                   Changes in version 1.12.0                        

Major changes

• Add environments for anndata v0.9.2 and v0.10.2. Version 0.10.20 is now the default envrionment for the Python reader/writer.

Minor changes

• Changes for compatibility with rhdf5 v2.45.1 including enum types that simplifies reading of nullable types in the native R reader

• Dimensions are now passed correctly when converting the raw slot

• Backed sparse matrices are now converted in AnnData2SCE()

zenith

                    Changes in version 1.3.1                        

• user can specify organism

NEWS from existing Data Experiment Packages

cfToolsData

                    Changes in version 1.0.0                        

• New Package Release

• 1st version of the package

curatedTCGAData

                   Changes in version 1.24.0                        

Bug fixes and minor improvements

• Create an on-the-fly sampleMap for RNASeq2GeneNorm* data version 2.1.1. Data source has munged colnames and sample maps were not updated in the latest upload (#59, @LiNk-NY)

gDRtestData

            Changes in version 0.99.21 (2023-09-18)                 

• adjust NEWS to Bioc format

            Changes in version 0.99.20 (2023-09-04)                 
  

• update testdata

            Changes in version 0.99.19 (2023-06-23)                 
  

• BiocStyle added to dependency

            Changes in version 0.99.18 (2023-06-22)                 
  

• replaced rds files with qs

            Changes in version 0.99.17 (2023-06-15)                 
  

• switch from merge to [[

            Changes in version 0.99.16 (2023-05-29)                 
  

• update datasets

            Changes in version 0.99.15 (2023-05-24)                 
  

• format the vignette with BiocStyle

            Changes in version 0.99.14 (2023-05-15)                 
  

• fix related with data.table

            Changes in version 0.99.13 (2023-05-15)                 
  

• update testdata as per changes in excess assays

            Changes in version 0.99.12 (2023-05-11)                 
  

• update testdata as per new data model

            Changes in version 0.99.11 (2023-04-25)                 
  

• changed data.frame to data.table

            Changes in version 0.99.10 (2023-04-24)                 
  

• removing redundant files

             Changes in version 0.99.9 (2023-04-20)                 
  

• fix warning in Bioc check

             Changes in version 0.99.8 (2023-04-20)                 
  

• switch to OSI license

             Changes in version 0.99.7 (2023-04-19)                 
  

• update testdata

             Changes in version 0.99.6 (2023-04-18)                 
  

• moved wrappers to gDRcore

             Changes in version 0.99.5 (2023-04-17)                 
  

• update packages version

             Changes in version 0.99.4 (2023-04-17)                 
  

• add R 4.2 as a dependency

             Changes in version 0.99.3 (2023-04-14)                 
  

• update testdata

             Changes in version 0.99.2 (2023-04-13)                 
  

• improve documentation (Bioc compatibility)

             Changes in version 0.99.1 (2023-04-07)                 
  

• update maintainer

             Changes in version 0.99.0 (2023-03-31)                 
  

• preparing package for Bioc submission

• fix examples

HCATonsilData

                   Changes in version 0.99.0                        

New features

• Dataset access provided for final (v2) data submission

• 7 additional tonsils from young and old adults added during revision.

• Improved package vignette to document the new changes.

• Users can now download Visium data into SpatialExperiment object.

• Vignette explains how to download ATAC and Multiome datasets from Zenodo as Seurat objects.

• Glossary available for final set of cell types, with links to key references.

Other notes

• HCATonsilData is now submitted to Bioconductor!

• Users can still access data from version 1 (preprint)

msigdb

                   Changes in version 1.10.0                        

• added MSigDB v7.5.1, v2022.1, and v2023.1

• added functions to retrieve pre-computed IDFs

orthosData

                   Changes in version 0.99.4                        

• Addition of main package documentaion

                   Changes in version 0.99.3                        
  

• ASmall additions to manual and vignette

                   Changes in version 0.99.2                        
  

• Small additions to manual and vignette

                   Changes in version 0.99.1                        
  

• Update of Zenodo links

                    Changes in version 0.1.0                        
  

• Initial version

raerdata

             Changes in version 0.99.0 (2023-05-18)                 

• init

RforProteomics

                   Changes in version 1.39.2                        

• Clearn up .gitignore and .Rbuildignore (in the hope to fix the ‘figure not found error’)

                   Changes in version 1.39.1                        
  

• Change paths to figures.

                   Changes in version 1.39.0                        
  

• New Bioc devel version.

scMultiome

                    Changes in version 1.1.1                        

• renamed assay from “logcounts” to “normalizedCounts” in reprogramseq and “counts” to “normalizedCounts” in the hematopoiesis, prostate and colon datasets

• specify version number of ExperimentHub and remove version number of R

SingleCellMultiModal

                   Changes in version 1.14.0                        

New features

• The ontomap function provides a reference table of ontology IDs and cell names by data type available in the package.

• scRNAseq colData added to cord_blood and peripheral_blood datasets provided by the CITEseq function. (@drighelli)

Bug fixes and minor improvements

• When using HDF5 as format input in scMultiome, the filtering of file paths obtained from ExperimentHub has been fixed.

• Using BiocBaseUtils internally to handle assertions and checks.

smokingMouse

                   Changes in version 0.99.0                        

NEW FEATURES

• Provides access to smokingMouse project objects. Check here for the code and data generation.

spatialLIBD

                   Changes in version 1.13.4                        

NEW FEATURES

• Added fetch_data(“spatialDLPFC_Visium_example_subset”) which is a subset of 3 samples with only the lowres images that can be used for example / tutorial purposes.

                   Changes in version 1.13.2                        
  

NEW FEATURES

• Louise A. Huuki-Myers @lahuuki added a vignette explaining the spatial registration process and all related functions. See https://github.com/LieberInstitute/spatialLIBD/pull/46 for the full pull request.

TumourMethData

                   Changes in version 0.99.0                        

• Submission to Bioconductor

NEWS from existing Workflows

seqpac

                    Changes in version 1.1.1                        

• First hard release August 2021

                    Changes in version 1.0.4                        
  

• Major updates to accomodate package specific tests, and devtools/BiocCheck

• S4 compatability

• merge_lanes can now merge flowcell lanes

• make_conv can now generate conversion tables between for example UCSC, NCBI and Ensembl chromosome names

                    Changes in version 1.0.3                        
  

• Streamlined PAC generation and annotation

• Vignette update

                    Changes in version 1.0.2                        
  

• The fundation of functions for sequence-based counting and annotation is set.

                    Changes in version 1.0.1                        
  

• First github version in 2020

• Working version for constructing PAC objects (S3)

Deprecated and Defunct Packages

Thirty three software packages were removed from this release (after being deprecated in Bioc 3.17): alpine, ArrayExpressHTS, ASpediaFI, BiocDockerManager, ChIC, chromswitch, copynumber, CopywriteR, dasper, epihet, GAPGOM, GeneAccord, genotypeeval, maanova, metavizr, MethCP, MIGSA, MIMOSA, NanoStringQCPro, NBSplice, netboxr, NxtIRFcore, ODER, pkgDepTools, PrecisionTrialDrawer, proBatch, proFIA, pulsedSilac, savR, sigPathway, STAN, TarSeqQC, tscR

Please note: gcatest and lfa, previously announced as deprecated in 3.17, has been updated and remain in Bioconductor.

Forty nine software packages are deprecated in this release and will be removed in Bioc 3.19: baySeq, BGmix, bigPint, biodbMirbase, BioMM, biomvRCNS, Clonality, CSSP, deco, DeepBlueR, DMRforPairs, exomeCopy, fcoex, gaggle, GCSscore, genbankr, GISPA, GOsummaries, GRridge, HPAStainR, imageHTS, LineagePulse, logitT, LowMACA, LPEadj, macat, mAPKL, mbOmic, MEIGOR, Metab, MSstatsSampleSize, multiSight, netbiov, OmicsLonDA, PFP, plethy, pwrEWAS, qrqc, Ringo, RNAdecay, SCATE, SEPIRA, seqbias, seqCNA, SISPA, snapCGH, sscore, Travel, trena

Two experimental data packages were removed from this release (after being deprecated in BioC 3.17): alpineData, plasFIA

Ten experimental data packages are deprecated in this release and will be removed in Bioc 3.19: ccTutorial, ChIC.data, DLBCL, mAPKLData, MAQCsubsetILM, MIGSAdata, pwrEWAS.data, SCATEData, seqCNA.annot, stjudem

One annotation packages was removed from this release (after being deprecated in Bioc 3.17). MafH5.gnomAD.v3.1.1.GRCh38

No annotation packages were deprecated in this release and will be removed in Bioc 3.19.

No workflow packages were removed from this release (after being deprecated in Bioc 3.17).

No workflow packages were deprecated in this release and will be removed in 3.19.

No books were removed from this release (after being deprecated in Bioc 3.17).

No books were deprecated in this release and will be removed in 3.19.