April 26, 2023

Bioconductors:

We are pleased to announce Bioconductor 3.17, consisting of 2230 software packages, 419 experiment data packages, 912 annotation packages, 27 workflows and 3 books.

There are 79 new software packages, 7 new data experiment packages, no new annotation packages, 2 new workflows, no new books, and many updates and improvements to existing packages.

Bioconductor 3.17 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 3.17
• 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 3.17

To update to or install Bioconductor 3.17:

1. Install R 4.3. Bioconductor 3.17 has been designed expressly for this version of R.

2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 79 new software packages in this release of Bioconductor.

• AHMassBank Supplies AnnotationHub with MassBank metabolite/compound annotations bundled in CompDb SQLite databases. CompDb SQLite databases contain general compound annotation as well as fragment spectra representing fragmentation patterns of compounds’ ions. MassBank data is retrieved from https://massbank.eu/MassBank and processed using helper functions from the CompoundDb Bioconductor package into redistributable SQLite databases.

• alabaster Umbrella for the alabaster suite, providing a single-line import for all alabaster.* packages. Installing this package ensures that all known alabaster.* packages are also installed, avoiding problems with missing packages when a staging method or loading function is dynamically requested. Obviously, this comes at the cost of needing to install more packages, so advanced users and application developers may prefer to install the required alabaster.* packages individually.

• alabaster.base Save Bioconductor data structures into file artifacts, and load them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

• alabaster.bumpy Save BumpyMatrix objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

• alabaster.mae Save MultiAssayExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

• alabaster.matrix Save matrices, arrays and similar objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

• alabaster.ranges Save GenomicRanges, IRanges and related data structures into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

• alabaster.sce Save SingleCellExperiment into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

• alabaster.schemas Stores all schemas required by various alabaster.* packages. No computation should be performed by this package, as that is handled by alabaster.base. We use a separate package instead of storing the schemas in alabaster.base itself, to avoid conflating management of the schemas with code maintenence.

• alabaster.se Save SummarizedExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

• alabaster.spatial Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

• alabaster.string Save Biostrings objects to file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

• alabaster.vcf Save variant calling SummarizedExperiment to file and load them back as VCF objects. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

• AnVILWorkflow The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The main cloud-based genomics platform deported by the AnVIL project is Terra. The AnVILWorkflow package allows remote access to Terra implemented workflows, enabling end-user to utilize Terra/ AnVIL provided resources - such as data, workflows, and flexible/scalble computing resources - through the conventional R functions.

• BG2 This package is built to perform GWAS analysis for non-Gaussian data using BG2. The BG2 method uses penalized quasi-likelihood along with nonlocal priors in a two step manner to identify SNPs in GWAS analysis. The research related to this package was supported in part by National Science Foundation awards DMS 1853549 and DMS 2054173.

• BiocHail Use hail via basilisk when appropriate, or via reticulate. This package can be used in terra.bio to interact with UK Biobank resources processed by hail.is.

• BiocHubsShiny A package that allows interactive exploration of AnnotationHub and ExperimentHub resources. It uses DT / DataTable to display resources for multiple organisms. It provides template code for reproducibility and for downloading resources via the indicated Hub package.

• BSgenomeForge A set of tools to forge BSgenome data packages. Supersedes the old seed-based tools from the BSgenome software package. This package allows the user to create a BSgenome data package in one function call, simplifying the old seed-based process.

• CBNplot This package provides the visualization of bayesian network inferred from gene expression data. The networks are based on enrichment analysis results inferred from packages including clusterProfiler and ReactomePA. The networks between pathways and genes inside the pathways can be inferred and visualized.

• cfTools The cfTools R package provides methods for cell-free DNA (cfDNA) methylation data analysis to facilitate cfDNA-based studies. Given the methylation sequencing data of a cfDNA sample, for each cancer marker or tissue marker, we deconvolve the tumor-derived or tissue-specific reads from all reads falling in the marker region. Our read-based deconvolution algorithm exploits the pervasiveness of DNA methylation for signal enhancement, therefore can sensitively identify a trace amount of tumor-specific or tissue-specific cfDNA in plasma. cfTools provides functions for (1) cancer detection: sensitively detect tumor-derived cfDNA and estimate the tumor-derived cfDNA fraction (tumor burden); (2) tissue deconvolution: infer the tissue type composition and the cfDNA fraction of multiple tissue types for a plasma cfDNA sample. These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.

• chihaya Saves the delayed operations of a DelayedArray to a HDF5 file. This enables efficient recovery of the DelayedArray’s contents in other languages and analysis frameworks.

• clevRvis clevRvis provides a set of visualization techniques for clonal evolution. These include shark plots, dolphin plots and plaice plots. Algorithms for time point interpolation as well as therapy effect estimation are provided. Phylogeny-aware color coding is implemented. A shiny-app for generating plots interactively is additionally provided.

• concordexR Many analysis workflows include approximation of a nearest neighbors graph followed by clustering of the graph structure. The concordex coefficient estimates the concordance between the graph and clustering results. The package ‘concordexR’ is an R implementation of the original concordex Python-based command line tool.

• CoSIA Cross-Species Investigation and Analysis (CoSIA) is a package that provides researchers with an alternative methodology for comparing across species and tissues using normal wild-type RNA-Seq Gene Expression data from Bgee. Using RNA-Seq Gene Expression data, CoSIA provides multiple visualization tools to explore the transcriptome diversity and variation across genes, tissues, and species. CoSIA uses the Coefficient of Variation and Shannon Entropy and Specificity to calculate transcriptome diversity and variation. CoSIA also provides additional conversion tools and utilities to provide a streamlined methodology for cross-species comparison.

• CTdata Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics.

• cytofQC cytofQC is a package for initial cleaning of CyTOF data. It uses a semi-supervised approach for labeling cells with their most likely data type (bead, doublet, debris, dead) and the probability that they belong to each label type. This package does not remove data from the dataset, but provides labels and information to aid the data user in cleaning their data. Our algorithm is able to distinguish between doublets and large cells.

• CytoPipeline This package provides support for automation and visualization of flow cytometry data analysis pipelines. In the current state, the package focuses on the preprocessing and quality control part. The framework is based on two main S4 classes, i.e. CytoPipeline and CytoProcessingStep. The pipeline steps are linked to corresponding R functions - that are either provided in the CytoPipeline package itself, or exported from a third party package, or coded by the user her/himself. The processing steps need to be specified centrally and explicitly using either a json input file or through step by step creation of a CytoPipeline object with dedicated methods. After having run the pipeline, obtained results at all steps can be retrieved and visualized thanks to file caching (the running facility uses a BiocFileCache implementation). The package provides also specific visualization tools like pipeline workflow summary display, and 1D/2D comparison plots of obtained flowFrames at various steps of the pipeline.

• cytoviewer This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization and supports image downloads.

• DELocal The goal of DELocal is to identify DE genes compared to their neighboring genes from the same chromosomal location. It has been shown that genes of related functions are generally very far from each other in the chromosome. DELocal utilzes this information to identify DE genes comparing with their neighbouring genes.

• DESpace Intuitive framework for identifying spatially variable genes (SVGs) via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. The method is flexible and robust, and is faster than the most SV methods. Furthermore, to the best of our knowledge, it is the only SV approach that allows: - performing a SV test on each individual spatial cluster, hence identifying the key regions of the tissue affected by spatial variability; - jointly fitting multiple samples, targeting genes with consistent spatial patterns across replicates.

• doubletrouble doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are: i. whole-genome duplication (WGD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). If users want a simpler classification scheme, duplicates can also be classified into WGD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

• EDIRquery EDIRquery provides a tool to search for genes of interest within the Exome Database of Interspersed Repeats (EDIR). A gene name is a required input, and users can additionally specify repeat sequence lengths, minimum and maximum distance between sequences, and whether to allow a 1-bp mismatch. Outputs include a summary of results by repeat length, as well as a dataframe of query results. Example data provided includes a subset of the data for the gene GAA (ENSG00000171298). To query the full database requires providing a path to the downloaded database files as a parameter.

• escheR The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide this open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows.

• FeatSeekR FeatSeekR performs unsupervised feature selection using replicated measurements. It iteratively selects features with the highest reproducibility across replicates, after projecting out those dimensions from the data that are spanned by the previously selected features. The selected a set of features has a high replicate reproducibility and a high degree of uniqueness.

• flowGate flowGate adds an interactive Shiny app to allow manual GUI-based gating of flow cytometry data in R. Using flowGate, you can draw 1D and 2D span/rectangle gates, quadrant gates, and polygon gates on flow cytometry data by interactively drawing the gates on a plot of your data, rather than by specifying gate coordinates. This package is especially geared toward wet-lab cytometerists looking to take advantage of R for cytometry analysis, without necessarily having a lot of R experience.

• GeoTcgaData Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It’s easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.

• HiCExperiment R generic interface to Hi-C contact matrices in .(m)cool, .hic or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The HiCExperiment class stores the Hi-C contacts parsed from local contact matrix files. HiCExperiment instances can be further investigated in R using the HiContacts analysis package.

• HiCool HiCool provides an R interface to process and normalize Hi-C paired-end fastq reads into .(m)cool files. .(m)cool is a compact, indexed HDF5 file format specifically tailored for efficiently storing HiC-based data. On top of processing fastq reads, HiCool provides a convenient reporting function to generate shareable reports summarizing Hi-C experiments and including quality controls.

• IFAA This package offers a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome in an ecosystem. It can be also directly applied to relative abundance (RA) data to make inference on AA because the ratio of two RA is equal to the ratio of their AA. This algorithm can estimate and test the associations of interest while adjusting for potential confounders. The estimates of this method have easy interpretation like a typical regression analysis. High-dimensional covariates are handled with regularization and it is implemented by parallel computing. False discovery rate is automatically controlled by this approach. Zeros do not need to be imputed by a positive value for the analysis. The IFAA package also offers the ‘MZILN’ function for estimating and testing associations of abundance ratios with covariates.

• INTACT This package integrates colocalization probabilites from colocalization analysis with transcriptome-wide association study (TWAS) scan summary statistics to implicate genes that may be biologically relevant to a complex trait. The probabilistic framework implemented in this package constrains the TWAS scan z-score-based likelihood using a gene-level colocalization probability. Given gene set annotations, this package can estimate gene set enrichment using posterior probabilities from the TWAS-colocalization integration step.

• IntOMICS IntOMICS is an efficient integrative framework based on Bayesian networks. IntOMICS systematically analyses gene expression (GE), DNA methylation (METH), copy number variation (CNV) and biological prior knowledge (B) to infer regulatory networks. IntOMICS complements the missing biological prior knowledge by so-called empirical biological knowledge (empB), estimated from the available experimental data. An automatically tuned MCMC algorithm (Yang and Rosenthal, 2017) estimates model parameters and the empirical biological knowledge. Conventional MCMC algorithm with additional Markov blanket resampling (MBR) step (Su and Borsuk, 2016) infers resulting regulatory network structure consisting of three types of nodes: GE nodes refer to gene expression levels, CNV nodes refer to associated copy number variations, and METH nodes refer to associated DNA methylation probe(s).

• magpie This package aims to perform power analysis for the MeRIP-seq study. It calculates FDR, FDC, power, and precision under various study design parameters, including but not limited to sample size, sequencing depth, and testing method. It can also output results into .xlsx files or produce corresponding figures of choice.

• mariner Tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from .hic files, and visualizing the results. Designed for compatibility with plotgardener for visualization.

• mastR mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of group markers in various biological and medical applications, including cancer research and developmental biology.

• mbQTL mbQTL is a statistical R package for simultaneous 16srRNA,16srDNA (microbial) and variant, SNP, SNV (host) relationship, correlation, regression studies. We apply linear, logistic and correlation based statistics to identify the relationships of taxa, genus, species and variant, SNP, SNV in the infected host. We produce various statistical significance measures such as P values, FDR, BC and probability estimation to show significance of these relationships. Further we provide various visualization function for ease and clarification of the results of these analysis. The package is compatible with dataframe, MRexperiment and text formats.

• microSTASIS The toolkit ‘µSTASIS’, or microSTASIS, has been developed for the stability analysis of microbiota in a temporal framework by leveraging on iterative clustering. Concretely, the core function uses Hartigan-Wong k-means algorithm as many times as possible for stressing out paired samples from the same individuals to test if they remain together for multiple numbers of clusters over a whole data set of individuals. Moreover, the package includes multiple functions to subset samples from paired times, validate the results or visualize the output.

• MoleculeExperiment MoleculeExperiment contains functions to create and work with objects from the new MoleculeExperiment class. We introduce this class for analysing molecule-based spatial transcriptomics data (e.g., Xenium by 10X, Cosmx SMI by Nanostring, and Merscope by Vizgen). This allows researchers to analyse spatial transcriptomics data at the molecule level, and to have standardised data formats accross vendors.

• MsBackendSql SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint, this package thus provides an alternative MS data representation for very large or remote MS data sets.

• MsDataHub The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.

• MsQuality The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.

• MultimodalExperiment MultimodalExperiment is an S4 class that integrates bulk and single-cell experiment data; it is optimally storage-efficient, and its methods are exceptionally fast. It effortlessly represents multimodal data of any nature and features normalized experiment, subject, sample, and cell annotations, which are related to underlying biological experiments through maps. Its coordination methods are opt-in and employ database-like join operations internally to deliver fast and flexible management of multimodal data.

• OutSplice An easy to use tool that can compare splicing events in tumor and normal tissue samples using either a user generated matrix, or data from The Cancer Genome Atlas (TCGA). This package generates a matrix of splicing outliers that are significantly over or underexpressed in tumors samples compared to normal denoted by chromosome location. The package also will calculate the splicing burden in each tumor and characterize the types of splicing events that occur.

• pairedGSEA pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.

• pfamAnalyzeR Protein domains is one of the most import annoation of proteins we have with the Pfam database/tool being (by far) the most used tool. This R package enables the user to read the pfam prediction from both webserver and stand-alone runs into R. We have recently shown most human protein domains exist as multiple distinct variants termed domain isotypes. Different domain isotypes are used in a cell, tissue, and disease-specific manner. Accordingly, we find that domain isotypes, compared to each other, modulate, or abolish the functionality of a protein domain. This R package enables the identification and classification of such domain isotypes from Pfam data.

• planttfhunter planttfhunter is used to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification scheme implemented in PlantTFDB. TFs are identified using pre-built hidden Markov model profiles for DNA-binding domains. Then, auxiliary and forbidden domains are used with DNA-binding domains to classify TFs into families and subfamilies (when applicable). Currently, TFs can be classified in 58 different TF families/subfamilies.

• Rarr The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. It’s design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specifcation in R with minimal reliance on an external tools or libraries.

• RBioFormats An R package which interfaces the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata.

• Rcollectl Provide functions to obtain instrumentation data on processes in a unix environment. Parse output of a collectl run. Vizualize aspects of system usage over time, with annotation.

• retrofit RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without using external single-cell expression references. RETROFIT outperforms existing reference-based methods in estimating cell type proportions and reconstructing gene expressions in simulations with varying spot size and sample heterogeneity, irrespective of the quality or availability of the single-cell reference. RETROFIT recapitulates known cell-type localization patterns in a Slide-seq dataset of mouse cerebellum without using any single-cell data.

• ReUseData ReUseData is an R/Bioconductor software tool to provide a systematic and versatile approach for standardized and reproducible data management. ReUseData facilitates transformation of shell or other ad hoc scripts for data preprocessing into workflow-based data recipes. Evaluation of data recipes generate curated data files in their generic formats (e.g., VCF, bed). Both recipes and data are cached using database infrastructure for easy data management and reuse. Prebuilt data recipes are available through ReUseData portal (“https://rcwl.org/dataRecipes/”) with full annotation and user instructions. Pregenerated data are available through ReUseData cloud bucket that is directly downloadable through “getCloudData()”.

• rifiComparative ‘rifiComparative’ is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.

• S4Arrays The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects).

• SCArray.sat Extends the Seurat classes and functions to support Genomic Data Structure (GDS) files as a DelayedArray backend for data representation. It relies on the implementation of GDS-based DelayedMatrix in the SCArray package to represent single cell RNA-seq data. The common optimized algorithms leveraging GDS-based and single cell-specific DelayedMatrix (SC_GDSMatrix) are implemented in the SCArray package. This package introduces a new SCArrayAssay class (derived from the Seurat Assay), which wraps raw counts, normalized expressions and scaled data matrix based on GDS-specific DelayedMatrix. It is designed to integrate seamlessly with the Seurat package to provide common data analysis in the SeuratObject-based workflow. Compared with Seurat, SCArray.sat significantly reduces the memory usage and can be applied to very large datasets.

• scFeatures scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor.

• screenCounter Provides functions for counting reads from high-throughput sequencing screen data (e.g., CRISPR, shRNA) to quantify barcode abundance. Currently supports single barcodes in single- or paired-end data, and combinatorial barcodes in paired-end data.

• scRNAseqApp scRNAseqApp is a Shiny app package that allows users to visualize single cell data interactively. It was modified from ShinyCell and repackaged to a tool to show multiple data. It can visulize the data with multiple information side by side.

• scviR This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another vignette compares outputs of Chapter 12 of the OSCA book with analogous outputs based on totalVI quantifications. Future work will address other components of scvi-tools, with a focus on building understanding of probabilistic methods based on variational autoencoders.

• seq.hotSPOT seq.hotSPOT provides a resource for designing effective sequencing panels to help improve mutation capture efficacy for ultradeep sequencing projects. Using SNV datasets, this package designs custom panels for any tissue of interest and identify the genomic regions likely to contain the most mutations. Establishing efficient targeted sequencing panels can allow researchers to study mutation burden in tissues at high depth without the economic burden of whole-exome or whole-genome sequencing. This tool was developed to make high-depth sequencing panels to study low-frequency clonal mutations in clinically normal and cancerous tissues.

• seqArchRplus seqArchRplus facilitates downstream analyses of promoter sequence architectures/clusters identified by seqArchR (or any other tool/method). With additional available information such as the TPM values and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus can order the input promoter clusters by their shape (IQWs), and write the cluster information as browser/IGV track files. Provided visualizations are of two kind: per sample/stage and per cluster visualizations. Those of the first kind include: plot panels for each sample showing per cluster shape, TPM and other score distributions, sequence logos, and peak annotations. The second include per cluster chromosome-wise and strand distributions, motif occurrence heatmaps and GO term enrichments. Additionally, seqArchRplus can also generate HTML reports for easy viewing and comparison of promoter architectures between samples/stages (future).

• SGCP SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. SGC consists of multiple novel steps that enable the computation of highly enriched modules in an unsupervised manner. But unlike all existing frameworks, it further incorporates a novel step that leverages Gene Ontology information in a semi-supervised clustering method that further improves the quality of the computed modules.

• SiPSiC Infer biological pathway activity of cells from single-cell RNA-sequencing data by calculating a pathway score for each cell (pathway genes are specified by the user). It is recommended to have the data in Transcripts-Per-Million (TPM) or Counts-Per-Million (CPM) units for best results. Scores may change when adding cells to or removing cells off the data. SiPSiC stands for Single Pathway analysis in Single Cells.

• SparseArray The SparseArray package defines the SparseArray virtual class to be extended by other S4 classes that wish to represent in-memory multidimensional sparse arrays. One such extension is the SVT_SparseArray class, also defined in the package, that provides an efficient representation of the nonzero multidimensional data via a novel layout called the “SVT layout”. SVT_SparseArray objects mimic the behavior of ordinary matrices or arrays in R as much as possible. In particular, they suppport most of the “standard array API” defined in base R.

• SpatialOmicsOverlay Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.

• speckle The speckle package contains functions for the analysis of single cell RNA-seq data. The speckle package currently contains functions to analyse differences in cell type proportions. There are also functions to estimate the parameters of the Beta distribution based on a given counts matrix, and a function to normalise a counts matrix to the median library size. There are plotting functions to visualise cell type proportions and the mean-variance relationship in cell type proportions and counts. As our research into specialised analyses of single cell data continues we anticipate that the package will be updated with new functions.

• SVMDO It is an easy-to-use GUI using disease information for detecting tumor/normal sample discriminating gene sets from differentially expressed genes. Our approach is based on an iterative algorithm filtering genes with disease ontology enrichment analysis and wilk’s lambda criterion connected to SVM classification model construction. Along with gene set extraction, SVMDO also provides individual prognostic marker detection. The algorithm is designed for FPKM and RPKM normalized RNA-Seq transcriptome datasets.

• TDbasedUFE This is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. It can perform unsupervised feature extraction. It uses tensor decomposition. It is applicable to gene expression, DNA methylation, and histone modification etc. It can perform multiomics analysis. It is also potentially applicable to single cell omics data sets.

• TDbasedUFEadv This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics analyses, this package can perform more complicated and advanced features, but they are not so popularly required. Only users who require more specific features can make use of its functionality.

• TOP TOP constructs a transferable model across gene expression platforms for prospective experiments. Such a transferable model can be trained to make predictions on independent validation data with an accuracy that is similar to a re-substituted model. The TOP procedure also has the flexibility to be adapted to suit the most common clinical response variables, including linear response, binomial and Cox PH models.

• ZygosityPredictor The ZygosityPredictor allows to predict how many copies of a gene are affected by small variants. In addition to the basic calculations of the affected copy number of a variant, the Zygosity-Predictor can integrate the influence of several variants on a gene and ultimately make a statement if and how many wild-type copies of the gene are left. This information proves to be of particular use in the context of translational medicine. For example, in cancer genomes, the Zygosity-Predictor can address whether unmutated copies of tumor-suppressor genes are present. Beyond this, it is possible to make this statement for all genes of an organism. The Zygosity-Predictor was primarily developed to handle SNVs and INDELs (later addressed as small-variants) of somatic and germline origin. In order not to overlook severe effects outside of the small-variant context, it has been extended with the assessment of large scale deletions, which cause losses of whole genes or parts of them.

New Data Experiment Packages

There are 7 new data experiment packages in this release of Bioconductor.

• CoSIAdata Variance Stabilized Transformation of Read Counts derived from Bgee RNA-Seq Expression Data. Expression Data includes annotations and is across 6 species (Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans) and across more than 132 tissues. The data is represented as a RData files and is available in ExperimentHub.

• DNAZooData DNAZooData is a data package giving programmatic access to genome assemblies and Hi-C contact matrices uniformly processed by the DNA Zoo Consortium. The matrices are available in the multi-resolution .hic format. A URL to corrected genome assemblies in .fastq format is also provided to the end-user.

• fourDNData fourDNData is a data package giving programmatic access to Hi-C contact matrices uniformly processed by the 4DN consortium. The matrices are available in the multi-resolution .mcool format.

• gDNAinRNAseqData Provides access to BAM files generated from RNA-seq data produced with different levels of gDNA contamination. It currently allows one to download a subset of the data published by Li et al., BMC Genomics, 23:554,
  1. This subset of data is formed by BAM files with about 100,000 alignments with three different levels of gDNA contamination.

• marinerData Subsampled Hi-C in HEK cells expressing the NHA9 fusion with an F to S mutated IDR (“FS”) or without any mutations to the IDR (“Wildtype” or “WT”). These files are used for testing mariner functions and some examples.

• MetaScope This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is partly an R translation of the PathoScope 2.0 pipeline.

• scMultiome Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR package and presented as MultiAssayExperiment objects.

New Annotation Packages

There are no new annotation packages.

New Workflow Packages

There are 2 new workflow packages in this release of Bioconductor.

• seqpac Seqpac provides functions and workflows for analysis of short sequenced reads. It was originally developed for small RNA analysis, but can be implemented on any sequencing raw data (provided as a fastq-file), where the unit of measurement is counts of unique sequences. The core of the seqpac workflow is the generation and subsequence analysis/visualization of a standardized object called PAC. Using an innovative targeting system, Seqpac process, analyze and visualize sample or sequence group differences using the PAC object. A PAC object in its most basic form is a list containing three types of data frames. - Phenotype table (P): Sample names (rows) with associated metadata (columns) e.g. treatment. - Annotation table (A): Unique sequences (rows) with annotation (columns), eg. reference alignments. - Counts table (C): Counts of unique sequences (rows) for each sample (columns). The PAC-object follows the rule: - Row names in P must be identical with column names in C. - Row names in A must be identical with row names in C. Thus P and A describes the columns and rows in C, respectively. The targeting system, will either target specific samples in P (pheno_target) or sequences in A (anno_target) and group them according to a target column in P and A, respectively (see vignettes for more details).

• spicyWorkflow We have developed an analytical framework for analysing data from high dimensional in situ cytometry assays including CODEX, CycIF, IMC and High Definition Spatial Transcriptomics. This framework makes use of functionality from our Bioconductor packages spicyR, lisaClust, scFeatures, FuseSOM, simpleSeg and ClassifyR and contains most of the key steps which are needed to interrogate the comprehensive spatial information generated by these exciting new technologies including cell segmentation, feature normalisation, cell type identification, micro-environment characterisation, spatial hypothesis testing and patient classification. Ultimately, our modular analysis framework provides a cohesive and accessible entry point into spatially resolved single cell data analysis for any R-based bioinformatician.

New Online Books

There are no new online books.

NEWS from existing Software Packages

ADaCGH2

             Changes in version 2.39.1 (2023-04-14)                 

• Fixed “DLL requires the use of native symbols” with R-4.3.0.

affxparser

             Changes in version 1.73.0 (2023-04-25)                 

Notes

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

             Changes in version 1.72.0 (2023-04-25)                 
  

Notes

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.17 for R (>= 4.3.0).

             Changes in version 1.71.2 (2023-04-23)                 
  

Bug Fixes

• fix to src/_mingw.h provided by Tomas Kalibera.

             Changes in version 1.71.1 (2023-04-04)                 
  

Bug Fixes

• Fix two instances of “watching polymorphic type ‘class Except’ by value [-Wcatch-value=]” compiler warnings.

             Changes in version 1.71.0 (2022-11-01)                 
  

Notes

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.17 for R devel.

AHMassBank

                    Changes in version 0.99                         

AHMassBank 0.99.3

• Add package documentation.
• Increase required R version.

AHMassBanki 0.99.0

• Add metadata for MassBank 2022.12.1.

alevinQC

                   Changes in version 1.15.1                        

• Support BiocStyle::pdf_document and BiocStyle::html_document output formats (thanks to Mike Smith for insights regarding BiocStyle)

AlpsNMR

             Changes in version 4.1.6 (2023-02-16)                  

• Download improvements:
• Progress bar
• Detect user interruptions

• Sleep 3 seconds between retrying failed downloads

             Changes in version 4.1.5 (2023-02-10)                  
  

• Replace deprecated dplyr::select() calls.
• Remove workaround for mixOmics bug, bump mixOmics dependency
• Simplify implementation (same algorithm) for determining the optimal number of latent variables in the plsda models.

• Bump dplyr dependency version.

             Changes in version 4.1.4 (2022-11-08)                  
  

• Disable nested parallelization
• Update workaround Biocparallel bpmapply

• Revert bpstop to sleep

             Changes in version 4.1.3 (2022-11-07)                  
  

• Closer to the fix

             Changes in version 4.1.2 (2022-11-04)                  
  

• Try a more robust fix on palomino4 (bpstop() instead sleep)
• Use register() in an example to avoid further breakage on palomino

• Workaround performance issues on BiocParallel::bpmapply() (https://github.com/Bioconductor/BiocParallel/pull/228)

             Changes in version 4.1.1 (2022-11-02)                  
  

• Remove archive dependency
• Try fixing build on palomino4, due to race condition in R CMD check

AneuFinder

                   Changes in version 1.27.1                        

SIGNIFICANT USER-LEVEL CHANGES

• Removed parameter “classes” from clusterHMMs(). This is due to a missing dependency (the ReorderCluster package). Sorry!

• Removed parameter “reorder.by.class” from heatmapGenomewide(). This is due to a missing dependency (the ReorderCluster package). Sorry!

AnnotationForge

                   Changes in version 1.41.0                        

MODIFICATIONS

• 1.41.5 Add RUnit to Suggest

• 1.41.3 Update viableID.rda for upcoming release

• 1.41.2 Use dbExecute() instead of dbGetQuery() or dbSendQuery() to avoid warnings

ENHANCEMENT

• 1.41.4 Knoknok Optimizations and allow specification of the desired Ensembl release

• 1.41.1 James MacDonald Fixed makeOrgPackageFromNCBI to use existing downloaded files

AnnotationHub

                    Changes in version 3.7.0                        

NEW FEATURES

• (3.7.4) Suppress snapshot date unless interactive session

• (3.7.1) Add DispatchClass for keras model weights

DEPRECATED

• (3.7.2) Deprecate display in favor of BiocHubsShiny; see vignette

AnnotationHubData

                   Changes in version 1.29.0                        

NEW FEATURES

• 1.29.2 Added HIC as acceptable source type

• 1.29.1 Added CDF as acceptable source type

AnVIL

                   Changes in version 1.12.0                        

USER VISIBLE CHANGES

• (v 1.11.2) update workflow file discovery to use API, rather than ‘scraping’ google bucket. https://github.com/Bioconductor/AnVIL/issues/69

• (v 1.11.3) Gen3 services deprecated

• (v 1.11.5) Add na = to handle NA encoding in avtable() / avtable_import(). Changes default behavior. https://github.com/Bioconductor/AnVIL/issues/75

BUG FIXES

• (v 1.11.1) consistently URLencode workspace and workflow name, to allow for spaces. https://github.com/Bioconductor/AnVIL/issues/67

AnVILWorkflow

                    Changes in version 1.0.0                        

• Initial release of the ‘AnVILWorkflow’ package

aroma.light

             Changes in version 3.31.0 (2023-04-25)                 

Notes

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

             Changes in version 3.30.0 (2023-04-25)                 
  

Notes

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.17 for R (>= 4.3.0).

             Changes in version 3.29.0 (2022-11-01)                 
  

ArrayExpress

                   Changes in version 1.58.0                        

• Update to access ArrayExpress Collection at BioStudies.

ATACseqQC

                   Changes in version 1.23.1                        

• Add smooth function to TSSEscore.
• Add pseudoPausingIndex function.

ATACseqTFEA

                    Changes in version 1.1.1                        

• fix the bugs in sample_scripts.R.

atena

             Changes in version 1.6.0 (2023-04-20)                  

USER VISIBLE CHANGES

• Improvement of the accuracy of the atena expression quantification method.

• Fixed numerical instability in TEtranscripts method.

• Added function (.matchSeqinfo) to harmonize seqinfo() of object with alignments and object with feature annotations.

• Implemented ‘OneCodeToFindThemAll’ annotation parser for RepeatMasker annotations.

• Implemented ‘atena’ annotation parser for RepeatMasker annotations.

• Added examples in the vignettes of TE annotation preprocessing steps using the implemented parsers.

• Changed default value of geneFeatures to NULL in the parameters objects.

BUG FIXES

• Fixed bug for not properly paired reads.

BASiCS

             Changes in version 2.11.9 (2023-03-07)                 

• Fixes minor bug in test_denoised.R

             Changes in version 2.11.8 (2023-03-07)                 
  

• fixes conflict after merge and version bump only

             Changes in version 2.11.7 (2023-03-07)                 
  

• Updates NEWS

• version bump to trigger new build

• Fixes small bugs in tests (test_misc.R and test_divide_and_conquer.R)

• Minor changes suggested by BiocCheck

             Changes in version 2.11.6 (2023-02-07)                 
  

• Adds BASiCS_CalculateERCC() to NAMESPACE

• Creates unit test for BASiCS_CalculateERCC()

             Changes in version 2.11.5 (2023-01-04)                 
  

• Changes maintainer

• Remove unicode mu in documentation

             Changes in version 2.11.4 (2022-12-15)                 
  

• Solves bug in BASiCS_DiagPlot()

             Changes in version 2.11.3 (2022-12-15)                 
  

• Creates BASiCS_CalculateSpikeIns() to perform spike-in calculation (depends on the scRNAseq package).

• Adds extra option to plotting functions for MCMC diagnostics (e.g. BASiCS_DiagPlot())

             Changes in version 2.11.2 (2022-11-23)                 
  

• Bugfix in DetectLVG/HVG, see Issue #265; delta column in results was actually duplicated mu column.

• Change BASiCS_CorrectOffset to also alter the scale of the normalisation factors when WithSpikes=FALSE.

• Add “rhat” option to BASiCS_DiagHist and BASiCS_DiagPlot

basilisk.utils

                   Changes in version 1.12.0                        

• Added Arm64 support for Linux.

batchelor

                   Changes in version 1.16.0                        

• Bugfix to rownames of mnnCorrect() output when using correct.all=TRUE with subset.row=.

benchdamic

             Changes in version 1.5.3 (2023-04-20)                  

• Add CITATION file

• Update README.md file

• Add ORCID for authors

• Bug-fix for DA_MAST() function

             Changes in version 1.5.2 (2022-11-21)                  
  

• Correct FDR description in vignette

• Add BiocParallel support for runMocks() and runSplits() functions

• Add example for ANCOMBC based methods in parallel

             Changes in version 1.5.1 (2022-11-14)                  
  

• Add FDR computation in Type I Error Control analysis

• Add BiocParallel support for runMocks() and runSplits() functions

• Update vignette

             Changes in version 1.5.0 (2022-11-01)                  
  

• New devel version

BiocCheck

                   Changes in version 1.36.0                        

NEW FEATURES

• Include size limit checks for data files in data, inst/extdata, and data-raw folders (@lshep, @const-ae, #167, #67)

• Source package directories that include an inst/doc folder with files are now flagged with an error. doc folders are generated during R CMD build.

• The error for packages already hosted on CRAN has been converted to a warning (@lshep, #177). Any such incoming packages must be removed from CRAN before the following Bioconductor release.

BUG FIXES AND MINOR IMPROVEMENTS

• Filter out ‘package’ docTypes from ‘\value’ documentaiton checks (@grimbough, #189)

• Obtain a more complete list of deprecated packages for checkDeprecatedPkgs

• Fix issue with path seperators on Windows (‘\’ vs ‘/’) causing the unit test for getBiocCheckDir to report erroneous mismatches (@grimbough, #175)

• Fix bug where the wrong number of functions with length greater than 50 was reported (@grimbough, #182)

• biocViews term suggestions should be a scalar character (@lcolladotor, #184)

• Update email in bioc-devel subscription check (@lshep, #185)

• Handle function length checks when there is no R code (@lshep, #186)

• Edit warning text when empty or missing value sections are found in a package (@vjcitn)

• checkForValueSection re-implemented for clarity; filters out comments in value sections (@LiNk-NY)

• Correctly identify Rd comments by updating the regular expression to identify them (@LiNk-NY)

BiocFileCache

                     Changes in version 2.7                         

USER VISIBLE CHANGE

• (2.7.1) Remove rappdirs officially from package after deprecating functionality and moving to using default R tools caching location.

BUG FIX

• (2.7.2) Fix mismatch of arguments from function to generic for bfcupdate

BiocHail

                    Changes in version 1.0.0                        

• disabled mac builds in Bioconductor build system, but the package should be usable with JDK version <= 11

BiocHubsShiny

                    Changes in version 1.0.0                        

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

BiocIO

                   Changes in version 1.10.0                        

Significant user-visible changes

• All the documentation has been updated to be more user-friendly.

BiocParallel

                    Changes in version 1.34                         

NEW FEATURES

• (1.33.2) limit worker number via environment variables. https://github.com/Bioconductor/BiocParallel/issues/229

• (v1.33.3) bpmapply() does not send the whole list of arguments to all workers. Instead, it takes the arguments and slices them, passing the corresponding slice to each worker. Thanks Sergio Oller! https://github.com/Bioconductor/BiocParallel/issues/229

USER VISIBLE CHANGES

• (1.33.1) Mark BatchJobsParam, bprunMPIslave as defunct.

• (1.33.9) Change default force.GC= to FALSE in MulticoreParam(). https://github.com/Bioconductor/BiocParallel/issues/238

• (1.33.11) change content of ‘traceback’ on error to include the stack from the location of the error up to the invokation of FUN. Previously, the traceback was from FUN to the top-level of worker code, providing limited insight into nested errors.

• (1.33.12) ‘force’ function arguments to avoid consequences of lazy evaluation discussed in https://github.com/Bioconductor/BiocParallel/issues/241#issuecomment-1445006892

BUG FIXES

• (1.33.6) Restore ‘exported’ global variables in SerialParam() https://github.com/Bioconductor/BiocParallel/issues/234

• (1.33.7) ‘configure.ac’ uses C++ compiler and checks for existence of required header https://github.com/Bioconductor/BiocParallel/pull/236

• (1.33.8 / v 1.32.5) set socket idle timeout to a large value, to avoid premature worker termination and to be consistent with snow / parallel defaults. https://github.com/Bioconductor/BiocParallel/issues/237

• (1.33.10 / v 1.32.6) be sure to clean up TransientMulticoreParam state at start of each job. https://github.com/Bioconductor/BiocParallel/issues/243

BiocPkgTools

                   Changes in version 1.18.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• biocLastBuildDate has been deprecated and moved to BiocArchive.

• pkgBiocDeps returns only the Bioconductor dependencies for a given vector of packages; can be set to all dependencies.

BUG FIXES

• Use bfcdownload when a web resource needs updating. Functions that download and cache files are affected including biocBuildReport, biocDownloadStats, biocPkgRanges, and CRANstatus.

• biocPkgList throws a descriptive error when using an alternative repository to the default CRAN, e.g., RSPM where the packages.rds file does not exist.

BiocSet

                    Changes in version 1.14                         

BUG FIX

• (1.12.1 / 1.13.1) propagate metadata with map_*() functions; reexport metadata(), metadata()<- generics and methods for public use https://github.com/Bioconductor/BiocSet/issues/6

BiocStyle

                   Changes in version 2.28.0                        

BUG FIXES

• Addressed issue where, when using newer versions of Pandoc, footnotes would appear at the bottom of HTML output rather than be moved to the margin.

• Fixed problem including references in R Markdown documents when the output format was BiocStyle::pdf_document (https://github.com/Bioconductor/BiocStyle/issues/94)

biocthis

                    Changes in version 1.9.2                        

BUG FIXES

• use_bioc_github_action() now properly works again when docker = TRUE. Behind the scenes, this function now uses docker/build-docker-action@v4 instead of the deprecated docker/build-docker-action@v1. These updates were tested at https://github.com/lcolladotor/ExampleBiocWorkshop2023.

biocViews

                   Changes in version 1.67.0                        

ENHANCEMENT

• (1.67.1) Add biocViews term WorkflowManagement

• (1.67.3) Add biocViews term LongRead

biodbHmdb

             Changes in version 1.5.1 (2023-03-22)                  

• Remove R_front script.

• Define new field secondary.accessions.

biomaRt

                   Changes in version 2.56.0                        

BUG FIXES

• Fix problem when multiple cache entries with the same ID could be created. (Thanks to Hervé Pagès & Henrik Bengtsson for independent reports of this issue.)

• bmRequest() will now respect the setting in options(“timeout”)

BioNAR

                    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.

bluster

                   Changes in version 1.10.0                        

• Corrected calculation of the ratio matrix in pairwiseRand() when adjusted=TRUE, so that ratios have an upper bound of 1.

BRGenomics

                   Changes in version 1.11.1                        

• Updated the import_bam_ATAC() function with slightly revised options and operations
• Fixed broken links in documentation

BridgeDbR

                    Changes in version 2.9.2                        

NEW FEATURES

• Updated to BridgeDb 3.0.21

                    Changes in version 2.9.1                        
  

NEW FEATURES

• Updated to BridgeDb 3.0.19

BSgenomeForge

                    Changes in version 1.0.0                        

• First version of the package that is ready for general use.

CAGEr

                    Changes in version 2.6.0                        

BUG FIXES

• Re-enable the promoter shift functions (Fixes #4).
• Compute dominant TSS information for consensus clusters (Fixes #1).

NEW FEATURES

• Inter-quantile width is also computed when no sample is selected.
• Enhancer detection using a wrapper to the CAGEfighter package’s function quickEnhancers().

Cardinal

             Changes in version 3.0.1 (2022-11-14)                  

SIGNIFICANT USER-VISIBLE CHANGES

• Overwriting existing MSI files is now a warning instead of an error

BUG FIXES

• Fixed issue in ‘peakAlign()’ reference m/z’s being sort and unique

cBioPortalData

                   Changes in version 2.12.0                        

Bug fixes and minor improvements

• Update successrate thresholds and fix long tests

CBNplot

             Changes in version 0.99.5 (2023-04-13)                 

• Changed the dependency for R version

             Changes in version 0.99.4 (2023-04-07)                 
  

• Fixed the WARNINGS in package builder at bioconductor.org

             Changes in version 0.99.3 (2023-04-07)                 
  

• Fixed the problems raised in the review

             Changes in version 0.99.1 (2022-02-24)                 
  

• Fixed errors and warnings raised in pre-checking

             Changes in version 0.99.0 (2021-07-29)                 
  

• Prepared for submission to Bioconductor

celda

             Changes in version 1.14.2 (2023-01-19)                 

• Update to match Bioconductor release version

cellxgenedp

                     Changes in version 1.4                         

SIGNIFICANT USER-VISIBLE CHANGES

• (v 1.3.3) add publisher_metadata(), authors(), and links() to make access to nested ‘collections()’ data more straight-forward

CeTF

                   Changes in version 1.11.1                        

• Update for Biocondutor 3.17 release

cfDNAPro

                    Changes in version 1.5.4                        

• In addition to “bam” and “picard” files as the input, now we accept “cfdnapro” as input_type to various functions, this ‘cfdnapro’ input is exactly the output of read_bam_insert_metrics function in cfDNAPro package. It is a tsv file containing two columns, i.e., “insert_size” (fragment length) and “All_Reads.fr_count” (the count of the fragment length).

                    Changes in version 1.5.3                        
  

• added support for hg38-NCBI version, i.e. GRCh38

cfTools

                    Changes in version 1.0.0                        

• 1st version of the package

• Submitted to Bioconductor

ChIPpeakAnno

                   Changes in version 3.33.1                        

• update the documentation for enrichment analysis

• update the disjointExons to exonicParts for ensembldb

ChIPQC

                   Changes in version 1.35.1                        

• rollup bugfixes

ChIPseeker

                   Changes in version 1.35.3                        

• fixed R check by removing calling BiocStyle::Biocpkg() in vignette, instead we use yulab.utils::Biocpkg() (2023-04-11, Tue)

                   Changes in version 1.35.2                        
  

• fixed R check by adding ‘prettydoc’ to Suggests (2023-04-04, Tue)

                   Changes in version 1.35.1                        
  

• use ggplot to plot heatmap (2022-12-30, Fri, #203)
• update startup message to display the ‘Current Protocols (2022)’ paper.

ClassifyR

                    Changes in version 3.4.0                        

• Companion website with more in-depth explanation and examples.

• Default random forest classifier based on ranger now does two-step classification; one for variable importance and one for model fitting, as recommended by ranger’s developer.

• More functions use automatic parameter value selection as their defaults.

• randomSelection function to choose random sets of features in cross-validation.

• crossValidate function now permits custom parameter tuning via extraParams.

• Elastic net GLM and ordinary GLM now calculate class weights be default, so as to perform well in class-imbalanced scenarios.

• precisionPathwaysTrain and precisionPathwaysPredict functions for building tree-like models of multiple assays and their accessory functions calcCostsAndPerformance, bubblePlot, flowchart, strataPlot for model performance evaluation.

• crissCrossValidate function that takes a list of data sets with the same set of features and the same set of outcomes and does all possible pairs of training and prediction to evaluate generalisability. crissCrossPlot for visual evaluation.

clevRvis

             Changes in version 0.99.5 (2023-01-16)                 

• Fixed notes from BiocCheck

             Changes in version 0.99.4 (2023-01-04)                 
  

• Included reviewer feedback

             Changes in version 0.99.3 (2022-12-20)                 
  

• Removed R project file

             Changes in version 0.99.2 (2022-12-06)                 
  

• Information on data added to vignette

• Show method added for seaObject

             Changes in version 0.99.1 (2022-11-26)                 
  

• Initial submission to Bioconductor

clusterProfiler

                    Changes in version 4.7.1                        

• update according to the KEGG api changes (2023-03-01, Wed)

CNVfilteR

                   Changes in version 1.13.2                        

MINOR

• Fixed bug: sample name column in CNV calling file is always interpreted as character, which prevents later errors.

                   Changes in version 1.13.1                        
  

MINOR

• Vignette: genome is explicitly shown as an option in loadVCFs()

• Vignette: mutiallelic sites are not currently supported and bcftools can be used as workaround

cogeqc

                    Changes in version 1.3.1                        

CHANGES

• Added functions to explore assembly and annotation statistics in a context: assembly and annotation stats for NCBI genomes can be extracted through the Datasets API and compared with user-defined values. New functions: get_genome_stats(), compare_genome_stats(), and plot_genome_stats().

cola

                    Changes in version 2.5.4                        

• adapt the code with markdown v1.6

                    Changes in version 2.5.3                        
  

• names are automatically added if cola_opt$color_set_1 and cola_opt$color_set_2 are specific without names.

                    Changes in version 2.5.1                        
  

• In the rmarkdown, replace message = FALSE to message = NA.

• use %dorng% for paralell computing

compcodeR

                   Changes in version 1.35.1                        

• Add a function for SVA + limma differential expression analysis

ComplexHeatmap

                   Changes in version 2.15.3                        

• Legend(): legend_gp also controls line color, width and style.

• anno_mark(): labels can be duplicated.

                   Changes in version 2.15.1                        
  

• Legend(): allows NA in pch.

• SingleAnnotation(): correctly calculate the max width/height of a vector of texts.

• to_unit(): fixed a bug when the unit is negative.

• Legend(): add tick_length argument.

• Legend(): colors are correctly calculated when differences between at are not equal.

CompoundDb

                     Changes in version 1.3                         

Changes in version 1.3.3

• Add backendBpparam to define (disable) parallel processing for the MsBackendCompDb backend.

Changes in version 1.3.2

• Evaluate validity of the MsBackendCompDb using the full test suite from the Spectra package.

Changes in version 1.3.2

• Add parameter nonStop to compound_tbl_sdf that is passed to parameter skipErrors of ChemmineR::read.SDFset. Issue #110

Changes in version 1.3.0

• Bioconductor 3.17 developmental version.

concordexR

                   Changes in version 0.99.0                        

• Submitted to Biconductor.

CoSIA

                   Changes in version 0.99.0                        

• CoSIA is an R package that provides an alternative framework for cross-species transcriptomic comparison of non-diseased wild-type RNA sequencing gene expression data across tissues and species through visualization of variability, diversity, and specificity metrics. Check out the Vignette and Readme files to get more information on how to load and use CoSIA.

COTAN

                   Changes in version 1.99.3                        

Updated the vignette, README.md and NEWS.md

                   Changes in version 1.99.2                        

Dropped second vignette: will be merged in the other one…

                   Changes in version 1.99.1                        

Minor bug fixes and new function clustersMarkersHeatmapPlot()

                   Changes in version 1.99.0                        

Included new functionalities for Bioc 2.17 release:

• created a new COTAN class to replace the old scCOTAN: this class provides internal invariants along a wide host of accessors that allows users to avoid peeking inside the class

• made a new multi-core implementation of the model parameters estimations and COEX calculations that achieves much higher speeds.

• added new functionality about gene clusters starting from given markers lists

• added new functionality about uniform cell clustering based on the maximum GDI level in the cluster

• added function to get a differential expression estimation for each cluster against background

• added function to get an enrichment score for each cluster given a list of markers specific for the cells’ population

• added plots to asses data-set information at cleaning stage

crisprBase

                    Changes in version 1.3.3                        

• Added BiocStyle to Suggests.

                    Changes in version 1.3.2                        
  

• Added nuclease MAD.

crisprBowtie

                    Changes in version 1.3.2                        

• Chromosomes not found in the BSgenome object (usually extra chromosomes) are ignored.

crisprDesign

                   Changes in version 1.1.25                        

• Added a warning message when having duplicated gRNAs.

                   Changes in version 1.1.21                        
  

• Fixed intergenic annotation of alignments when non-standard chromosomes are found.

                   Changes in version 1.1.20                        
  

• flattenGuideSet is now GuideSet2DataFrames.

                   Changes in version 1.1.19                        
  

• Changed argument standard_chr_only to FALSE by default in the functions getSpacerAlignments and friends.

                   Changes in version 1.1.18                        
  

• Updated the object guideSetExampleWithAlignments to contain the latest annotations.

                   Changes in version 1.1.17                        
  

• Updated the object guideSetExampleFullAnnotation to contain the latest annotations.

                   Changes in version 1.1.12                        
  

• Refactored addGeneAnnotation.

                   Changes in version 1.1.10                        
  

• Added the function getPreMrnaSequence.

                    Changes in version 1.1.8                        
  

• Added features for non-targeting controls (addNtcs).

crisprScore

                    Changes in version 1.3.4                        

• Fixed unit testing for MIT scores.

                    Changes in version 1.3.3                        
  

• One more fix to the MIT scoring. Forgot to save sysdata last time.

                    Changes in version 1.3.1                        
  

• Fixed MIT formula. Previous calculations were erroneous.

csdR

                    Changes in version 1.5.1                        

• Fixed segfault issue which did occur in partial_argsort() when the n_elements argument was larger than the length of the input vector. In order to ensure equivalence with order(x, decreasing = TRUE)[1:n_elements], the additional elements, if any, are padded at the end of the answer as NA values.

CTdata

                    Changes in version 0.99                         

CTdata 0.99.0

• Package submission to Biocoductor.

cytofQC

             Changes in version 0.99.3 (2022-11-11)                 

• Resubmitted to Bioconductor
  • Added script to inst/script that demonstrates how extdata was created
  • Deleted doc folder and contents
  • Added a man level page for cytofQC
  • Added relavence to Bioconductor on vignette
  • Added functions tech, scores, probs, initial, and label to replace previous get functions that performed the same function to be more consistent with Bioconductor syntax
  • Added match.arg and checks for datatypes to all relavent functions
  • Removed plotInitialGuess2 and added argument to plotInitialGuess to choose if one or both graphs are plotted

  • Cleaned up warning and message statements

             Changes in version 0.99.0 (2022-09-13)                 
    

• Submitted to Bioconductor

cytomapper

             Changes in version 1.11.3 (2023-01-23)                 

• loadImages: added option to read in single-channel images to multi-channel

             Changes in version 1.11.2 (2023-02-02)                 
  

• Bug fix: measureObjects internally sets the correct channel names

             Changes in version 1.11.1 (2023-01-18)                 
  

• Bug fix: set default dodge.width = NULL for geom_quasirandom

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 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

cytoviewer

             Changes in version 0.99.3 (2023-04-18)                 

• add initial color control for cell-level

             Changes in version 0.99.2 (2023-04-13)                 
  

• image download fix

             Changes in version 0.99.1 (2023-04-12)                 
  

• code adjustments after Bioconductor approval

• included reactive image / mask reading

             Changes in version 0.99.0 (2023-03-23)                 
  

• code preparations for Bioconductor submission

dearseq

             Changes in version 1.11.1 (2023-03-16)                 

• add parallel support on Windows

deconvR

                    Changes in version 1.5.2                        

• Fixed a bug in deconvolute
• findSignatures now can construct tissue specific methylation signatures
• findSignatures now can construct tissue specific DMPs

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 0.26.0                        

• No changes in this version.

DELocal

                   Changes in version 0.99.1                        

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

DepInfeR

             Changes in version 1.3.1 (2023-04-04)                  

• Add BiocStyle dependence in the DESCRIPTION file to avoid vingette build error on Linux

DESeq2

                   Changes in version 1.39.8                        

• Changed lower=0 to lower=1e-6 in unmix(), as the lower bound of 0 was producing sqrt(negative) errors on Linux ARM64. https://support.bioconductor.org/p/9150056/

                   Changes in version 1.39.7                        
  

• Fix bug in independent filtering: with very little variation in the curve of number of rejections over threshold, and when the maximum was only reached near the end, the default filtering wouldn’t attain sufficient filtering. This has been addressed by also checking for a threshold at which 90%, or 80% of the fitted number of rejections is found. Note: IHW is the preferred method for filtering, and can easily by used by calling filterFun=ihw.

                   Changes in version 1.39.6                        
  

• Fix bug on estimateDispersionsGeneEst when niter is larger than 1 (#64 on GitHub).

                   Changes in version 1.39.5                        
  

• PR from Hendrik Weisser for lfcShrink when the results table has additional columns than those produced by results().

                   Changes in version 1.39.4                        
  

• Removing geneplotter dependency.

                   Changes in version 1.39.1                        
  

• Removing genefilter as dependency, switching to matrixStats. This should resolve gfortran issues.

DESpace

                    Changes in version 1.0.0                        

• 1st version of the package

• submitted to Bioconductor

DiffBind

                    Changes in version 3.9.4                        

• Rollover bugfixes

• add option to return ggplot in dba.plotVolcano

DNAfusion

                    Changes in version 1.3.0                        

• Added introns_ALK_EML4()
• Added find_variants()
• Updated break_position_depth()
• Updated break_position()
• Refined EML4_ALK_detection()
• Updated vignette to include new functions

• Cleaned functions for Bioconductor 3.17 release

                    Changes in version 1.1.1                        
  

• Updated example files to include ALK reads

                    Changes in version 1.1.0                        
  

• Updated DESCRIPTION

doubletrouble

                   Changes in version 0.99.3                        

BUG FIXES

• Updated functions (e.g., get_anchor_list(), collinearity2blocks()) after update in syntenet.

                   Changes in version 0.99.2                        
  

CHANGES

• Small change in coding style after Bioconductor peer-review (m:n replaced with c(m, n) and seq(m,n))

                   Changes in version 0.99.0                        
  

NEW FEATURES

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

edgeR

                   Changes in version 3.42.0                        

• New function Seurat2PB() for creating a pseudo-bulk DGEList object from a Seurat object. New case study in User’s Guide illustrating its use.

• New function normLibSizes() is now a synonym for calcNormFactors().

• Rename effectiveLibSizes() to getNormLibSizes().

• DGEList() is now an S3 generic function with a method for data.frames. The data.frame method allows users to specify which columns contain gene annotation and which contain counts. If the annotation columns are not specified, the function will check for non-numeric columns and will attempt to set the leading columns up to the last non-numeric column as annotation. ‘y’ is now a compulsory argument for DGEList(). Previously it defaulted to a matrix with zero rows and zero columns.

• New case study in User’s Guide on a transcript-level different expression analysis.

• The case study on alernative splicing in the User’s Guide has been replaced with a new data example.

enrichplot

                   Changes in version 1.19.2                        

• fix emapplot() for parameter mismatch (2023-02-20, Mon)
• fix ridgeplot for error when x@readable == TRUE and length(x@gene2Symbol) = 0 (2022-12-5, Mon)

• fix ridgeplot for error when x@readable == TRUE and length(x@gene2Symbol) = 0 (2022-12-5, Mon, #217)

                   Changes in version 1.19.1                        
  

• fix cnetplot() for node_label parameter is flipped(2022-12-04, Sun, #216)
• bug fixed in treeplot() (2022-11-18, Fri)
• enable dotplot() and autofacet() for gseaResultList object

ensembldb

                   Changes in version 2.23.2                        

• Fix SQLite database names to include also the subspecies.

                   Changes in version 2.23.1                        
  

• Remove disjointExons method.

EpiCompare

                    Changes in version 1.3.4                        

New features

• Example report:
• Delete report/ folder and upload to Releases instead: https://github.com/neurogenomics/EpiCompare/releases
• Add Rscript to replicate example report in inst/examples.
• EpiCompare
• New arg add_download_button.
• Always keep download button for post-processed peak files.

Bug fixes

• README.Rmd:

• Fix broken link to example report.

                    Changes in version 1.3.3                        
  

New features

• download_button:
• Saves and downloads files.
• prepare_blacklist:
• Auto-selects appropriate blacklist, or returns user-specified option.
• EpiCompare(blacklist=NULL) is now the default.
• prepare_genome_builds:
• Update to handle supplying builds for “peakfiles” and “reference” but not “blacklist” (so long as the blacklist arg is not a user-supplied GRanges object)
• Added mm9_blacklist
• Made more plots interactive:
• width_boxplot
• plot_enrichment
• plot_ChIPseeker_annotation
• overlap_stat_plot
• Name elements in output list.
• Change annotation arg to more informative txdb arg, and set default to NULL, which ChIPseeker functions will automatically handle.
• New function as_interactive:
• Help standardise this.
• New EpiCompare::EpiCompare arguments:
• error: keep knitting even on errors.
• tss_distance: upstream/downstream of TSS.
• quiet: knit quietly
• Rename ‘test-EpiCompare_combinations.R’ –> ‘test-EpiCompare.R’
• Separate test-generalMetrics_functions.R into function-specific test files.
• Separate test-peakOverlap_functions.R into function-specific test files.
• Make fancy header with new func:
• report_header()
• Create EpiCompare command code as text:
• report_command()
• width_boxplot:
• Make more efficient with data.table and lapply
• Update hex sticker to match custom.css palette.
• README.Rmd
• Collapse more detailed sections.

Bug fixes

• tss_plot:
• Fix examples/tests after Sera updated the arguments.
• Pass upstream/downstream to ChIPseeker::getTagMatrix
• Make interactive
• Name plots in list
• Remove unnecessary extra level of list nesting.
• Make documentation width <80 lines where possible.
• EpiCompare.Rmd
• Remove methods::show from all parts
• Name all chunks
• Make explanations more clear
• Add table of contents for main 3 sections.
• Fix header levels
• Set results=’asis’ globally instead of in each chunk header.
• Automatically number sections with yaml arg: number_sections: true
• Omit specific headers from numbering system with {-} tags.
• Add custom.css
• plot_chromHMM:
• Error in (function (classes, fdef, mtable) unable to find an inherited method for function ‘annotateWithFeatures’ for signature ‘”SimpleGRangesList”, “list”’
• Misleading error message; was actually due to chromHMM_annotation not being converted from a list to a GRangesList.

• Change yaml arg peakfile –> peakfiles to be consistent with other variables.

                    Changes in version 1.3.1                        
  

New features

• Replace badger with rworkfows:
• Use rworkflows::use_badges
• New helper functions:
• precision_recall_matrix
• report_time
• overlap_upset_plot:
• Switched out UpSetR for ComplexUpsetto show percentages.
• Moved up dep checks to beginning of function.
• Handle bug with heatmaply by checking args where it might be used:
• check_heatmap_args
• tss_plot:
• Add unit tests
• Drastically reduce example/test runtime by setting upstream=50
• compute_corr:
• Reduce example runtime by setting bin_size = 200000 (takes <2s).

Bug fixes

• Fix typo in EpiCompare docs: “hg38 blacklist dataset”
• Avoid explicitly specifying “/” in paths to help cross-platform testing.
• tss_plot:
• Use parallel::detectCores-1 by default to set workers, but set to 1 in examples/tests to meet CRAN/Bioc standards.

EpiDISH

                   Changes in version 2.15.0                        

• Add 12 blood cell-type DNAm reference matrix for 450k and EPIC arrays.

epigraHMM

                    Changes in version 1.7.2                        

• Fix callPeaks writers so that it works on Windows

                    Changes in version 1.7.1                        
  

• Fix callPeaks function to export .bed, .wig, and .bedGraph files
• Output files are now overwritten, if existing

epistack

             Changes in version 1.5.4 (2022-04-05)                  

• CITATION added

             Changes in version 1.5.3 (2022-04-04)                  
  

• plotAverageProfile’s reversed_z_order is now exposed in plotEpistack
• 95% confidence interval is now the default in plotEpistack

• plotEpistck’s legends are now also displayed as y-axis title in plotAverageProfile plots

             Changes in version 1.5.2 (2022-04-03)                  
  

• changing the default bin colors
• bin_palette in plotEpistack(), plotBoxMetric(), and plotAverageProfile(), and palette in plotBinning() can now be vectors of colors instead of palette functions

• tints now accept palette functions and list of palette functions, in addition to colors.

             Changes in version 1.5.1 (2022-03-30)                  
  

• vignette improvements (thanks to Isabelle Stevant)
• documentation improvments: multiple zlims are possible if provided as a list

erccdashboard

                   Changes in version 1.33.1                        

SIGNIFICANT USER-VISIBLE CHANGES / BUG FIX

• Vignette output showed incorrect mRNA fraction estimates and incorrect LODR estimates due to the stringsAsFactors=FALSE switch with R > 4.0. Ratio values were not being treated as factors in the loadERCCInfo function and this was causing incorrect ratio value assignments in the est_r_m.R function. The issue has been resolved by an explicit as.factor assignment in the loadERCCInfo.R function.

escheR

                   Changes in version 0.99.8                        

SIGNIFICANT USER-VISIBLE CHANGES

• Add a new argument y_reverse = TRUE to make_escheR to provide a consistent orientation between spot plot and tissue image (see Issue #13)

                   Changes in version 0.99.7                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Add default color scheme (viridis) to add_fill
• Add explicit reference to spatialLIBD in make_escheR documentation

• Add installation instruction for users whose R version is pre-R4.3

                   Changes in version 0.99.6                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Add minimium versions to dependencies and imported packages
• Import individual functions in NAMESPACE from packages
• Clean up comments in code

• Accepted by Bioconductor and will be released in Bioconductor 3.17

                   Changes in version 0.99.1                        
  

NEW FEATURES

• Added a NEWS.md file to track changes to the package.
• First full version of the package to be submitted to Bioconductor. See Bioconductor submission here.

EWCE

                    Changes in version 1.7.3                        

New features

• check_ewce_genelist_inputs/bootstrap_enrichment_test
• New arg: sctSpecies_origin lets users clarify that their data originally came from mouse even when it is currently formatted as human orthologs. This is necessary for creating the appropriate background gene lists.
• Remove grDevices as dep entirely.
• fix_celltype_names
• Add new arg make_unique to make this function easily usable for vectors where the same celltype appears multiple times.
• bootstrap_enrichment_test
• Return gene-level scores based on adaptation of code from generate_bootstrap_plots. now stored as a list element named gene_data in data.table format.
• generate_bootstrap_plots
• Revamp wrap code into reusable subfunctions.
• Avoid resampling random genes when the gene data is stored in the bootstrap results as gene_data. It will also tell you which of these options it’s using.
• Save with ggsave instead if grDevices.
• Facet by celltype instead of generating tons of separate plots.
• Let users decide cutoff threshold with new arg adj_pval_thresh
• Now returns a named list with the plots themselves (“plot”) and the paths to where they’re saved (“paths”) rather than just a higher-level directory path in which users had to search for the right files (and didn’t ever have access to the ggplot2 objects).
• Show significance with barplot fill/color instead of asterices. Much easier to see now.
• Change savePath arg to the more accurate save_dir. Expose appending BootstrapPlots to the user within the argument.
• generate_bootstrap_plots_for_transcriptome
• Change savePath arg to the more accurate save_dir. Expose appending BootstrapPlots to the user within the argument.
• Save with ggsave instead if grDevices.
• Standardise hits + hitGenes arg all to hits.
• Update hex:
• Off load large source image from DALLE to Releases instead of including it within the package.

Bug fixes

• drop_uninformative_genes / generate_celltype_data
• Pass verbose arg to matrix formatting functions.
• generate_controlled_bootstrap_geneset
• Removed combinedGenes arg as it was not being used anywhere within.
• check_args_for_bootstrap_plot_generation
• Removed unused args: ttSpecies, sctSpecies
• test-bootstrap_enrichment_test_2.R
• “monkey_ctd” tests seems to be running more smoothly than before (not just getting NAs). This might have to with orthogene databases improving.
• Reassuringly, “godzilla” tests still fail as expected :)

• Add tess/testthat/Rplots.pdf to .gitignore.

                    Changes in version 1.7.1                        
  

New features

• Use rworkflows GHA.
• Add rworkflows::use_badges to README.Rmd.
• Remove Dockerfile (no longer necessary).
• Make all 3 platforms (Linux, Mac, Windows) use Bioc dev, as ewceData (>=1.7.1) is now required, due to a fix made only in the development version of rtracklayer.
• Remove cowplot dependency.

• Replace all %>% with

  >

Bug fixes

• calc_quantiles:
• This function was only used in filter_variance_quantiles
• Compare stats::ecdf vs. dplyr::ntile methods.
• Remove from EWCE as it’s not longer used anywhere.
• bin_columns_into_quantiles:
• Rename arg matrixIn –> vec to reflect what the function actually does.
• filter_variance_quantiles:
• Change to use bin_columns_into_quantiles instead of calc_quantiles to be consistent with how quantiles are handled in the rest of EWCE.
• Updated tests in test-get_celltype_table.r to reflect that the number of genes filtered is unaffected by the normalization procedure (when quantiles are computed with stats::quantile).
• ewce_plot:
• Celltypes were producing NAs because the names in the results were not always standardized in the same way as the CTD. Now this is done internally.
• Celltypes were not ordered factors, meaning the dendrogram didn’t line up correctly.
• Switched from gridArrange/cowplot to patchwork.
• Added dedicated unit tests file: test-ewce_plot.r

New features

• Offline runs enabled with functions using reference datasets (from ewceData). These functions have the parameter localhub added to control this.

ExperimentHub

                    Changes in version 2.7.1                        

DEPRECATE

• (2.7.1) Deprecate display in favor of BiocHubsShiny

extraChIPs

                    Changes in version 1.3.9                        

• Changed labelling strategy for plotPie()

                    Changes in version 1.3.8                        
  

• Added using coverage to makeConsensus()

                    Changes in version 1.3.7                        
  

• Added plotAssayHeatmap()

• Added fitAssayDiff() and added coercion of TopTags objects

                    Changes in version 1.3.6                        
  

• Expanded arguments for plotSpliDonut()

• Added mergeByHMP() for merging overlapping windows using the harmonic mean p

                    Changes in version 1.3.5                        
  

• Added plotSplitDonut()

• Bugfix in plotAssayDensities() and plotAssayRle() along with enabling plotting by group

                    Changes in version 1.3.4                        
  

• Added mergeBySig()

FeatSeekR

                   Changes in version 0.99.1                        

• Submitted to Bioconductor

fgsea

                   Changes in version 1.25.1                        

• introduced plotEnrichmentData() function for more flexible plotting

• update GESECA plot behavior

fishpond

                    Changes in version 2.5.4                        

• As CellRanger 7 includes both spliced and unspliced counts in their count matrix, we want to mimic this behavior by adding more pre-defined output formats in the loadFry function. We added “all” and “U+S+A” to include all counts in the count matrix. Moreover, now the “scRNA” output format has an “unspliced” field, which contains the unspliced count matrix.

                    Changes in version 2.5.3                        
  

• Fix bug where salmonEC did not correct equivalence class names for going from 0-indexing to 1-indexing internally. In prior versions, to correctly link equivalence classes to gene names, users would have needed to manually add a value of 1 to the equivalence class names, which was erroneously not mentioned in the man files. After this bug fix, if the equivalence class identifier reads 1|2|8, then the equivalence class is immediatly compatible with the transcripts and their respective genes in rows 1, 2 and 8 of ‘tx2gene_matched’, without any further user intervention.

                    Changes in version 2.5.1                        
  

• Fix plotAllelicGene() so that when samples have an allele with no expression at the gene level, it doesn’t throw an error trying to divide by 0.

flowGate

             Changes in version 0.99.3 (2023-03-15)                 

• Document cleanup as part of bioconductor review

FlowSOM

                    Changes in version 2.7.9                        

• Adapted documentation of readInput and FlowSOM. It can also use a matrix with column names

                    Changes in version 2.7.8                        
  

• Added PlotOutliers and documentation

                    Changes in version 2.7.7                        
  

• Updates to TestOutliers

                    Changes in version 2.7.5                        
  

• Edited PlotManualBars so that it shows percentages of cells

• Edited PlotDimRed so that it optionally uses scattermore if it installed

                    Changes in version 2.7.4                        
  

• AggregateFlowFrames can now also resample if more cells are asked for than available in the fcs files. Default stays FALSE, taking at most the number of cells in the fcs file

                    Changes in version 2.7.2                        
  

• Version bump to align with Bioconductor

• Update for aggregateFlowFrames for nices handling of iterative aggregation (+ according visualisation in FlowSOMmary). AggregateFlowFrames will now introduce 0 values if a channel is not present in one of the fcs files. If channels is not provided as an argument, the channels of the first file are used.

• Added support for abbrevations in PlotDimRed “colorBy”.

• Return 0 instead of NA in case of an empty cluster in GetCounts/GetPercentages

flowSpecs

             Changes in version 1.13.1 (2023-04-05)                 

• +Updates to specMatCalc to work with BigFoot data.

fmrs

                    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.

gdsfmt

                   Changes in version 1.36.0                        

UTILITIES

• fix the compiler warning: sprintf is deprecated

• LZ4 updated to v1.9.4

• XZ updated to v5.2.9

• update zlib to v1.2.13

NEW FEATURES

• system.gds()$compiler.flag[1] is either “64-bit” or “32-bit” indicating the number of bits of internal data pointer

• new argument ‘use.abspath=TRUE’ in openfn.gds() and createfn.gds(): the behavior before v1.35.4 is the same as ‘use.abspath=TRUE’

                   Changes in version 1.34.1                        
  

UTILITIES

• avoid using crayon::blurred() in the display (RStudio blurs the screen output)

genbankr

                   Changes in version 1.27.1                        

BUGFIXES

• parser now correctly reads the “D-loop” feature type (#22)

GeneTonic

                    Changes in version 2.4.0                        

New features

• enhance_table() has now the possibility to plot the visual summaries as ridge lines.
• When plotting the gene expression for the selected features in the gene-geneset-graph box, it is now possible to disable the labels from being displayed (could lead to unnecessary clutter sometimes).

Other notes

• Fortified the behavior of gene_plot() to fail early when providing an invalid value to the intgroup parameter.

GenomAutomorphism

                    Changes in version 1.0.3                        

• Add new functions to work with modular matrix operations

                    Changes in version 1.0.2                        
  

• Fix error of parallel computation on Windows (12/08/2022)

                    Changes in version 1.0.1                        
  

• Expanding analyses by including aminoacid similarity based on codon distances. Three new functions are added: codon_dist, codon_dist_matrix, and aminoacid_dist. See a tutorial applying these functions at https://is.gd/oYLDK4.

GenomeInfoDb

                   Changes in version 1.36.0                        

NEW FEATURES

• Register the following NCBI assemblies:
  • the bCatUst1.alt.v2 and bCatUst1.pri.v2 assemblies
  • the felCat9.1_X and F.catus_Fca126_mat1.0 assemblies
  • the Gossypium_hirsutum_v2.1 assembly
  • the Kamilah_GGO_v0 assembly
  • the Xenopus_laevis_v2 and Xenopus_laevis_v10.1 assemblies
• Register the following UCSC genomes:
  • gorGor6 (linked to Kamilah_GGO_v0)
  • xenLae2 (linked to Xenopus_laevis_v2)

• Add Gossypium_hirsutum.txt to inst/extdata/dataFiles/ (provided by Emory Lucas bararayung123@hotmail.com)

• Add ‘organism’ argument to registered_UCSC_genomes() (contributed by Kirabo Kakopo).

SIGNIFICANT USER-VISIBLE CHANGES

• UCSC genome hg38 is now based on GRCh38.p14 instead of GRCh38.p13 (this change originated at UCSC). See commit 091b5d2.

• The submitters for NCBI assembly Dog10K_Boxer_Tasha have updated the info for the MT sequence, which is reflected in the output of getChromInfoFromNCBI(“Dog10K_Boxer_Tasha”). See commit 79a066c.

• The Accept-organism-for-GenomeInfoDb vignette was converted from Rnw to Rmd (thanks to Haleema Khan and Jen Wokaty for this conversion).

• Small improvements to low-level helper find_NCBI_assembly_ftp_dir().

GenomicAlignments

                   Changes in version 1.36.0                        

NEW FEATURES

• Add ‘strandMode’ argument to readGAlignmentsList() (contributed by Robert Castelo).

BUG FIXES

• Increase ‘cigar_buf’ size to reduce risk of buffer overflow in cigar-utils C code.

GenomicDataCommons

                   Changes in version 1.24.0                        

Bug fixes and minor improvements

• gdc_clinical handles NULL responses when diagnoses are not available for all IDs queried (#109, @zx8754).
• Minor updates to somatic mutations vignette and unit tests.

GenomicFeatures

                   Changes in version 1.52.0                        

NEW FEATURES

• Small improvement to makeTxDbFromEnsembl(): The function can now be called on the abbreviated organism, e.g. “hsapiens”, in addition to “homo sapiens”.

DEPRECATED AND DEFUNCT

• Finally remove disjointExons() (got deprecated in BioC 3.13 and defunct in BioC 3.15).

BUG FIXES

• Fix issue with order of sequences in seqinfo(makeTxDbFromUCSC()). See commit e4381bc.

GenomicRanges

                   Changes in version 1.52.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Improve documentation of findOverlaps() argument ‘minoverlap’: The man page now explains how findOverlaps() argument ‘minoverlap’ is interpreted when ‘query’ or ‘subject’ is a GRangesList object.

GeoTcgaData

                   Changes in version 0.99.2                        

• use SummarizedExperiment input (2023-1-29, Sun)
• fix return value of differential_array (2022-10-8, Sat)
• fix gene length bug in countToTpm() and countToFpkm()(2022_9_22, Tue)
• fix a bug in id_conversion (2022-8-27, Sat)
• fix a bug in differential_RNA(useTopconfects = TRUE) (2022-8-12, Fir)
• add function methydifferential_ucsc and methydifferential_limma(2021-10-24, Sun)
• update hgnc_file data(2021-10-24, Sun)
• add function differential_RNA to do difference analysis of RNA-seq data(2021-7-20, Tue)
• add data hgnc_file
• update function: id_ava()
• add functions: ann_merge(), countToFpkm(), countToTpm()

ggtree

                    Changes in version 3.7.2                        

• ggtree() supports ‘dendro’ object (ggdendro::dendro_data() output) (2023-03-02, Thu)
• update theme_dendrogram() to use ggfun::theme_noxaxis() (2022-11-21, Mon)

• using cli::cli_alert_warning() instead of warning_wrap (2022-11-10, Thu)

                    Changes in version 3.7.1                        
  

• compatible with ggplot2 v=3.4.0 (2022-11-07, Mon)
• allows setting options(clade_align = TRUE) to align geom_hilight() layer and allows setting options(clade_width_extend = 0.35) to set the amount the width extension (in y-axis) of geom_hilight(). These two features is designed for ggtreeDendro::geom_rect_subtree() layer (2022-11-06, Sun)

ggtreeDendro

                    Changes in version 1.1.3                        

• autoplot method for ‘genoMatriXeR’ and ‘multiLocalZScore’ objects (both defined in the ‘regioneReloaded’ package) (2023-02-11, Sat)

• autoplot method for ‘ClusterExperiment’ object (2022-11-28, Mon)

                    Changes in version 1.1.2                        
  

• plot_wgcna() for visualizing WGCNA dendrogram (2022-11-06, Sun)
• supports hkmeans object defined in the factoextra package (2022-11-06, Sun)

• set default options to align geom_rect_subtree() and adjust width extension.

                    Changes in version 1.1.1                        
  

• geom_rect_subtree layer to hilight subtrees (2022-11-03, Thu)
• supports bclust object (S3) output by e1071::bclust()
• supports hdbscan object

ggtreeExtra

                    Changes in version 1.9.2                        

• add limits parameter in axis.params to display the range of x axis. (2023-03-08, Wen)
• using cli to replace warning or stop. (2022-11-24, Thu)
• using rlang to transfer the geom argument. (2022-11-24, Thu)
• using pwidth to replace width when x only have one unique value with geom = geom_tile and width is not provided. (2022-11-25, Fri) - https://github.com/YuLab-SMU/ggtreeExtra/issues/11#issuecomment-873335702
• https://github.com/YuLab-SMU/ggtreeExtra/issues/12
• https://github.com/YuLab-SMU/ggtreeExtra/issues/25
• adding the messages to show how to adjust the color scale when the color aesthetic was use internal with geom=geom_boxplot etc. (2022-12-01, Thu)

• https://github.com/YuLab-SMU/ggtree/issues/551

                    Changes in version 1.9.1                        
  

• import cli to avoid warning in checking, which is used by the latest ggplot2 (2022-11-08, Tue)

glmGamPoi

              Changes in version 1.11 (2023-01-03)                  

• Breaking change: rename ‘pseudobulk_sce’ to ‘pseudobulk’

• Add a new vignette explaining how and why pseudobulking is a powerful concept for single cell data analysis

• Depcreate ‘pseudobulk_by’ argument in ‘test_de’. Use the ‘pseudobulk’ function instead.

• Add a new argument ‘max_lfc’ to to ‘test_de’ to avoid impractically large log fold changes for lowly expressed genes.

• Support rlang quosures for the contrast argument in ‘test_de’

• Add a helper function called ‘fact’ that simplifies specification of contrast for complex experimental designs

• Add ‘use_assay’ argument to ‘glm_gp’

• Add vctrs as dependency. The package is necessary to replicate the group_by behavior from dplyr.

• Add ‘size_factors = “ratio”’ to emulate the behavior of DESeq2’s size factor calculation

• Make sure that the ‘ignore_degeneracy’ argument is propagated to ‘test_de’

GRaNIE

             Changes in version 1.3.34 (2023-03-29)                 

Bugfixes

• many small bugfixes and other small improvements to homogenize the user experience due to the usage of systematic unit tests

             Changes in version 1.3.33 (2023-03-06)                 
  

New features and vignette updates

• we provide two new functions with this update:

1. getGRNSummary() that summarizes a GRN object and returns a named list, which can be used to compare different GRN objects ore easily among each other, for example.
2. plotCorrelations() for scatter plots of the underlying data for either TF-peak, peak-gene or TF-gene pairs. This can be useful to visualize specific TF-peak, peak-gene or TF-gene pairs to investigate the underlying data and to judge the reasonability of the inferred connection.

• methods vignette updates

         Changes in version 1.3.31-1.3.32 (2023-03-06)              
  

Bugfixes

• various small bugfixes that were accidentally introduced in the latest change from using the TF.ID instead of TF.name column as unique TF identifier

         Changes in version 1.3.26-1.3.30 (2023-03-06)              
  

New features and vignette updates

• added two new supported genomes: rn6/rn7 and dm6 for the rat and the Drosophila (fruit fly) genome, respectively
• added preliminary support for a new, alternative way of how to import TF and TFBS data into GRaNIE. We now additionally offer a more user-friendly way by making it possible to directly use the JASPAR2022 database. You do not need any custom files anymore for this approach! See the Package vignette for more details.

Bugfixes

• fixed a regression bug in addConnections_TF_peak (Column peak.GC.class doesn’t exist.) that was caused due to the recent GC modifications

             Changes in version 1.3.25 (2023-02-20)                 
  

New features and vignette updates

• additional significant methods vignette updates
• updates and clarifications for the workflow vignette
• a new QC plot for plotDiagnosticPlots_TFPeaks (and indirectly in addConnections_TF_peak when plotDiagnosticPlots = TRUE) on page 1 that shows the total number of connections for real and background TF-peak links as calculated and stored in the GRN object, stratified by TF-peak FDR and correlation bin. This is a similar plot as we show in the paper and helps comparing foreground and background.

Improvements

• speed improvements for plotDiagnosticPlots_TFPeaks (and indirectly in addConnections_TF_peak when plotDiagnosticPlots = TRUE) when plotAsPDF = FALSE

Bugfixes

• fixed a bug that only occurred in addConnections_TF_peak when using useGCCorrection = TRUE

             Changes in version 1.3.24 (2023-02-20)                 
  

New features and vignette updates

• significant methods vignette updates that help clarifying methods details

         Changes in version 1.3.22-1.3.23 (2023-02-15)              
  

Minor changes

• Small workflow vignette updates

Bug fixes

• we were informed that newer versions of dplyr (1.1.0) changed their default behavior for the function if_else when NULL is involved, which caused an error. We changed the implementation to accommodate for that and now avoid dplyr::if_else and use base R ifelse instead.

         Changes in version 1.3.18-1.3.21 (2023-02-07)              
  

Minor changes

• Small vignette updates and fixing typos / improved wording

Bug fixes

• due to a change from USCS that affected GenomeInfoDb::getChromInfoFromUCSC(“hg38”) (see here for more details), the minimum required version of GenomeInfoDb had to be increased to 1.34.8. If you have troubles installing at least this version, we recommend updating to the newest Bioconductor version 3.16 or (without warranties) use the following line to manually install the newest version directly from GitHub outside of Bioconductor (not recommended): BiocManager::install(“Bioconductor/GenomeInfoDb)”
• small change in addData() so that peak IDs are stored with the same name in the object in case the user-provided peak IDs have the format chr:start:end as opposed to the required chr:start-end. filterData() otherwise incorrectly discarded all peaks because of the ID mismatch caused by the two different formats.

• fixed a rare edge case in filterGRNAndConnectGenes() that caused an error when 0 TF-peak connections were found beforehand

             Changes in version 1.3.17 (2023-01-26)                 
  

New features

• We are excited to announce that we added a new vignette for how to use GRaNIE for single-cell data! We plan to update it regularly with new information. Check it out here!

             Changes in version 1.3.16 (2023-01-24)                 
  

New features

• significant updated to the package details vignette
• revisited and improved the internal logging and object history. The time when a function was called is now added to the list name, which allows the storage of multiple instances of the same function.
• new parameter in addData(): geneAnnotation_customHost to specify a custom host and overriding the default and previously hard-coded hostname when retrieving gene annotation data via biomaRt.

• the function getGRNConnections() can now also include the various additional metadata for all type parameters and not only the default type all.filtered.

             Changes in version 1.3.15 (2023-01-20)                 
  

Bug fixes

• fixed an error that appeared in rare cases when a chromosome name from either peak or RNA data could not be found in biomaRt such as GL000194.1. Peaks from chromosomes with irretrievable lengths are now automatically discarded.

• significant updates to the package details vignette

         Changes in version 1.3.13-1.3.14 (2023-01-20)              
  

New features

• the function plotDiagnosticPlots_peakGene() (which is also called indirectly from addConnections_peak_gene() when setting plotDiagnosticPlots = TRUE) now stores the plot data for the QC plots from the first page into the GRN object. It is stored in GRN@stats$peak_genes
• the columns of the result table from getGRNConnections() are now explained in detail in the R help, and we reference this from the Vignette and other places
• various significant Vignette updates

Bug fixes

• optimized the column names for the function getGRNConnections(), which now does not return duplicate columns for particular cases anymore
• improved printing in the log for the function filterData() and addData()
• the loadExampleObject() function has been optimized and should now force download an example object when requesting it.
• the package version as stored in the GRN object now works correctly.

Minor changes

• further code cleaning in light of the tidyselect changes in version 1.2.0 to eliminate deprecated warnings
• the default gene types for addConnections_peak_gene() and plotDiagnosticPlots_peakGene() have been homogenized and changed to list(c(“all”), c(“protein_coding”)). Before, the default was list(c(“protein_coding”, “lincRNA”)), but we decided to now split this into two separate lists: Once for all genes irrespective of the gene type and once for only protein-coding genes. As before, lincRNA or other gene types can of course still be selected and chosen.

• various minor changes

             Changes in version 1.3.12 (2022-12-22)                 
  

Bug fixes

• bug fix in plotCommunitiesEnrichment() that was introduced due to the tidyselect 1.2.0 changes

Minor changes

• further code cleaning in light of the tidyselect changes in version 1.2.0 to eliminate deprecated warnings

             Changes in version 1.3.11 (2022-12-16)                 
  

Major changes

• the default URL for the example GRN object in loadExampleObject() had to be changed due to changes in the IT infrastructure. The new stable default URL is now \url{https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds}, in the same Git repository that provides GRaNIE outside of Bioconductor.

Bug fixes

• fixing bugs introduced due to the tidyverse 1.2.0 related code cleaning

• other bugfix accidentally introduced in the previous commits

             Changes in version 1.3.10 (2022-12-15)                 
  

Bug fixes

• revisited the import of TADs and made the code more error-prone and fixed some bugs related to TADs. Importing TADs now works again as before.

Minor changes

• code cleaning in light of the tidyselect changes in version 1.2.0 to eliminate deprecated warnings

New features

• new argument for addConnections_peak_gene(): TADs_mergeOverlapping. See the R help for more details.

             Changes in version 1.3.9 (2022-12-14)                  
  

New features

• new argument for addConnections_peak_gene(): shuffleRNACounts. See the R help for more details.

Minor changes

• first round of code cleaning in light of the tidyselect changes in version 1.2.0 to eliminate deprecated warnings

          Changes in version 1.3.4-1.3.8 (2022-12-06)               
  

Major changes

• the topGO package is now required package and not optional anymore. The reasoning for this is that the standard vignette should run through with the default arguments, and GO annotation is the default ontology so topGO is needed for this. Despite this package still being optional from a strict workflow point of view, we feel this is a better way and improves user friendliness by not having to install another package in the middle of the workflow.

Minor changes

• in initializeGRN(), the objectMetadata argument is now checked whether it contains only atomic elements, and an error is thrown if this is not the case. As this list is not supposed to contain real data, checking this prevents the print(GRN) function to unnecessarily print the whole content of the provided object metadata, thereby breaking the original purpose.

New features

• addTFBS() got two more arguments to make it more flexible. Now, it is possible to specify the file name of the translation table to be used via the argument translationTable, which makes it more flexible than the previously hard-coded name “translationTable.csv. In addition, the column separator for this file can now be specified via the argument translationTable_sep
• Overlapping TFBS data with the peak is now more error-tolerant and does not error out in case that some chromosome or contig names from the TFBS BED files contain elements the size of which cannot be retrieved online. This was the case for some contig names with the suffix decoy, for example. If such elements are found, a warning is now thrown and they are ignored as they are usually not wanted anyway.
• in case a GRN objects contains 0 connections (e..g, because of too strict filtering), subsequent functions as well as the print function now give a more user-friendly warning / error message.

graphite

             Changes in version 1.45.1 (2023-04-19)                 

• Updated all pathway data.

hca

                     Changes in version 1.8                         

New features

• (v. 1.7.1) Implement project_title() and project_information() to retrieve summary information from project IDs.

HDF5Array

                   Changes in version 1.28.0                        

• No changes in this version.

HIBAG

                   Changes in version 1.34.1                        

• fix the compiler warning: sprintf is deprecated

• show “64-bit” correctly when run on Windows

HiCDOC

             Changes in version 1.1.1 (2022-11-30)                  

• Change the computation of selfInteraction (use diagonal only)

• review the distance normalisation (remove bias)

• Change affectation A is the higher compartment in selfInteractionRatio

HilbertCurve

                   Changes in version 1.29.1                        

• add hc_which().

hipathia

             Changes in version 2.99.0 (2022-12-01)                 

• Adding parameters uni.terms and GO.terms to hipathia, to compute functional activity within this function.

• Adding functions DAcomp, DAtop, DAsummary, DAoverview, define_colors, plotVG, DAreport.

• Modifyng structure of objects, by creating object DAdata, which includes more information than traditional hipathia results object. This includes:

  • Activity values of nodes, paths, and selected functions
  • Extra information about the paths, nodes and functions in rowData elements of the SummarizedExperiments

HPAanalyze

                    Changes in version 1.17                         

• Changes in version 1.17.0
  • Starting devel for Bioconductor 3.18
• Changes in version 1.17.1
  • Update built-in data to version 22.0.
• Changes in version 1.17.2
  • Update HPA download to correctly download new version 22.0 data.
  • Update documentation.

hpar

                    Changes in version 1.41                         

Changes in version 1.41.1

• Drop getHpa() function and use base R or tidyverse (as illustrated in the vignette).
• Repalce getHpa(type = “details”) by browseHPA().
• Serve data through ExperimentHub.
• Update to HPA release 21.1 <2022-05-31 Tue>
• New datasets added: rnaConsensusTissue, rnaHpaTissue, rnaGtexTissue, rnaFantomTissue.
• The dataset rnaGeneTissue becomes rnaGeneTissue21.0 as no longer available in version 21.1

IFAA

                   Changes in version 0.99.8                        

• Add partition algorithm in phase 1 and phase 2.

                   Changes in version 0.99.4                        
  

• Update algorithm in phase 1 to improve speed.

illuminaio

             Changes in version 0.43.0 (2023-04-25)                 

Notes

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

             Changes in version 0.42.0 (2023-04-25)                 
  

Notes

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.17 for R (>= 4.3.0).

             Changes in version 0.41.0 (2022-11-01)                 
  

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.17 for R-devel.

imcRtools

             Changes in version 1.5.5 (2023-04-20)                  

• Bug fix: in corner cases, levels of the permuted factors in the testInteractions function do not match the baseline.

• Bug fix: testInteractions now works for cells that are not ordered by grouping level

• Added explicitly message for some functions that the output is ordered by image

             Changes in version 1.5.4 (2023-04-04)                  
  

• Added option to get permutation counts returned from testInteractions

             Changes in version 1.5.3 (2023-03-23)                  
  

• Replaced merge function by left_join as safety measure

             Changes in version 1.5.2 (2022-11-23)                  
  

• Bug fix minDistToCells: return NA when all cells of an image belong to a patch

             Changes in version 1.5.1 (2022-11-22)                  
  

• fix axis.ratio to 1 in plotSpatial function and set scales = “fixed”

immunoClust

                   Changes in version 1.31.12                       

• CHANGES

  • introducing single E,M-steps

                   Changes in version 1.31.8                        
    

• CHANGES

  • bugfix in plot.immunoClust

                   Changes in version 1.31.5                        
    

• CHANGES

  • bugfix in meta.export

                   Changes in version 1.31.3                        
    

• NEW FEATURE

  • introduces meta-clustering with SON/ormalization

                   Changes in version 1.31.2                        
    

• CHANGES

  • bugfix in meta.export functions

                   Changes in version 1.31.1                        
    

• CHANGES
  • additional option thres to control meta.SubClustering process
  • code cleaning

infercnv

             Changes in version 1.15.3 (2023-03-29)                 

• Now use the first of the 2 color bars on the left side of the observations heatmap to display subclusters when they have been calculated and k_obs_groups is not used (>1) when cluster_by_groups=F is.

• Add export of infercnv subclusters to Seurat object and features file generated by add_to_seurat.

• Add write_phylo option to run() and plot_cnv() to control if a file with newick strings for the dendrogram is generated.

• Fully transfer subclustering information when running plot_per_group to each annotation’s object to take advantage of subcluster being displayed on color bars now.

• Fix for “meanvar” sim_method in hspike generation when there are no references and one of the observation annotations has only a single cell.

• Fix plot_subclusters() when using an object that was processed with cluster_by_groups=FALSE.

• Change default k_obs_groups in plot_cnv to 1 instead of 3 to use the new subclustering coloring by default.

             Changes in version 1.15.2 (2023-03-08)                 
  

• “infercnv_subclusters” plot after subclustering step in run() that displays the subclusters is now controlled by its own “inspect_subclusters” option.

             Changes in version 1.15.1 (2023-02-24)                 
  

• Add helper method plot_subclusters() to plot subclusters as the annotations to more easily check if the subclustering settings used produce good results or not, so settings can be adjusted.

• Change cluster_by_groups default to True.

             Changes in version 1.14.2 (2023-03-08)                 
  

• Add “infercnv_subclusters” plot after subclustering step in run() that displays the subclusters. Can be disabled with the exisiting no_plot argument.

             Changes in version 1.14.1 (2023-02-24)                 
  

• Fix per chromosome subclustering to use all the data and not only the data from the last annotation group when there are no outliers filtered by z_score (which would always happen when no references are defined).

• Apply per subcluster consensus on HMM predictions on the object directly when running with per chromosome subclustering enabled, rather than only running it before writting txt outputs and figure. This makes the infercnv_obj also contain the same values plotted.

• Disable per chromosome subclustering by default. The option remains available.

• Change how the subclustering is run on the hspike to avoid issues with Leiden settings tuning. Now simply keep the structure of how the fake cells are generated.

• Fix to order in which Leiden partition is made into an hclust/dendrogram to avoid issues with singleton (as long as there are non singletons).

• Fix options stored in backup infercnv objects not being updated properly updated when changing the settings on a rerun.

• Fix to properly restart past the Bayesian network step if it has already been run and only the BayesMaxPNormal filter has been changed.

INTACT

                   Changes in version 0.99.0                        

NEW FEATURES

• Pilot version

SIGNIFICANT USER-VISIBLE CHANGES

• Pilot version

InteractiveComplexHeatmap

                    Changes in version 1.7.1                        

• row_names_max_width and column_names_max_height are all passed to sub-heatmaps.

IntEREst

                   Changes in version 1.24.0                        

NEW FEATURES

• strandSpecific is a new parameter added to interest() and interest.sequential(). It indicates that IntEREst is now strand-aware. All analysis can be run whilst taking into account (or ignoring) the strand specificity of the sequencing reads.

• referencePrepare can create references (with collapsed exons) that does not ignore the strand information.

SIGNIFICANT USER-VISIBLE CHANGES

• GenomicFiles::reduceByYield function is now used instead of BiocParallel::bpiterat for improved efficiency and readability. This relates to how analysis related to different pieces of the alignment data is distributed over the parallel cores and the results are sumarized.

BUG FIXES

• In interest() and and interest.sequential() The oredr of the results of the different methods in the result matrix is corrected. Correct running of analyses using multiple methods with a single command is now possible.

IRanges

                   Changes in version 2.34.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Improve error handling in AtomicList constructors when input is too big.

ISAnalytics

             Changes in version 1.9.3 (2023-04-04)                  

ENHANCES AND REFACTORING

• The package no longer depends on magrittr
• All functionality associated with data.table now it’s completely optional and will be used internally only if the package is available
• Several packages were moved from Imports to Suggests - functions will notify when additional packages are requested for the specific functionality
• All known deprecated or superseded functions from other packages have been removed or substituted

FIXES AND GENERAL UPDATES

• Added a new tag “barcode_mux” in available_tags()
• The function HSC_population_size_estimate() now better supports the computation of estimates from different groups of cell types and tissues at the same time. The tabular output now contains an additional column “Timepoints_included” that specifies how many time points the estimate contains
• Function is_sharing() can now handle better limit cases and has the option of being parallelised provided appropriate packages are available (better performance)

DEPRECATIONS & BREAKING CHANGES

• Functions import_parallel_Vispa2Matrices_auto() and import_parallel_Vispa2Matrices_interactive() are officially defunct and will not be exported anymore starting from the next release cycle
• The argument mode of import_parallel_Vispa2Matrices() no longer accepts INTERACTIVE as a valid option and the interactive mode is considered now defunct, since the usage is very limiting and limited
• The argument association_file of import_parallel_Vispa2Matrices() no longer accepts a string representing a path. Association file import is delegated solely to its dedicated function from now on.
• The function threshold_filter() is deprecated, since its use is rather complicated instead of using standard filtering with dplyr or similar tools

MINOR CHANGES

• default_af_transform() now pads time points based on the maximum number of characters + 1 in the column

             Changes in version 1.9.2 (2023-01-26)                  
  

FIXES AND GENERAL UPDATES

• Fixed an issue with ifelse function in top_abund_tableGrob() - now the function has a new argument transform_by which is useful for controlling ordering of columns
• Updated CITATION file
• Package DT has been moved (likely temporarily) in Imports - linked to issue https://github.com/calabrialab/ISAnalytics/issues/2

• Fixed other typos and minor issues

             Changes in version 1.9.1 (2022-12-01)                  
  

• Fixed all tidyselect warnings (internal use of .data$ in selection context)
• Added bonferroni correction in gene_frequency_fisher

iSEE

                   Changes in version 2.11.4                        

• Fix bug introduced in 2.11.2.

                   Changes in version 2.11.3                        
  

• Use standard syntax to include empty icon in relevant places.

                   Changes in version 2.11.2                        
  

• Make it possible to hide the “Visual Parameters” box.

                   Changes in version 2.11.1                        
  

• Add tooltip.signif to registerAppOptions() to regulate the number of significant digits shown in the tooltip.

iSEEhub

                    Changes in version 1.1.1                        

MINOR UPDATES

• Update screenshots in vignettes.

iSEEu

                   Changes in version 1.11.2                        

• Adjusted code to correctly parse and rename KEGG pathway identifiers.

                   Changes in version 1.11.1                        
  

• Update ggplot2 imports for AggregatedDotPlot.

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 2.01.01                       
  

• 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 1.99.16                       
  

• Update type: Minor.

• Update for Bioconductor

kebabs

                   Changes in version 1.33.2                        

• fix in src/Kebabs.h in order to avoid memory problems on 32-bit architectures

                   Changes in version 1.33.1                        
  

• fixes in several help pages to avoid warnings

                   Changes in version 1.33.0                        
  

• new branch for Bioconductor 3.17 devel

limma

                   Changes in version 3.56.0                        

• Rename readSampleInfoFromGEO() to sampleInfoFromGEO().

• Add new argument p.value for topGO() and topKEGG().

• Fix a problem with inconsistent pathway names from KEGG. Due to a change on the KEGG website, pathway names from getGeneKEGGLinks() have “path:” prefixes but pathway names from getKEGGPathwayNames() do not. To make the pathway names consistent, getGeneKEGGLinks() now removes the “path:” prefix.

• eBayes() now checks whether fit is a list object before undertaking other tests.

• Revise voom.Rd to specify that y-values in voom plot are sqrt residual standard deviations.

• Update out-of-date URLs in the help pages and the User’s Guide. Convert reference URLs to DOIs.

• Convert CITATION to use the newer bibentry() instead of citEntry().

magpie

                   Changes in version 0.99.10                       

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

mariner

                   Changes in version 0.99.0                        

Bug fixes and improvements:

• Improve dispatch speed of mergePairs() by removing S4 method dispatch on all arguments to just x and radius.

• Fix bug in mergePairs() where all pairs are altered during mean of mode transformation. Now original pairs are preserved when accessed with getPairClusters().

• Set replace method for counts<- accessor for InteractionMatrix objects. Helpful for converting DelayedMatrix to matrix.

• Update pixelsToMatrix to preserve metadata columns and include some additional tests.

• Add plotMatrix() function for plotting matrix data as a heatmap. Useful for visualizing DelayedMatrices from pullHicMatrices() and aggHicMatrices(). Compatible with plotgardener package.

• Allow plotMatrix() to accept na.color

• Bug fix in mergePairs() that allows columns named “radius” and/or “method”.

• Swap “binSize” and “files” argument order in pullHicPixels and pullHicMatrices

• Allow pullHicPixels to overwrite existing HDF5 files.

• Validity checks and functions to access/update the HDF5 paths for InteractionMatrix objects, even when those paths have been broken.

• Add temporary plotBullseye function.

• Selection functions for selecting indices of a matrix:

• selectCenterPixel
• selectRadius
• selectSubmatrix
• selectCoordinates
• selectBlock
• selectTopLeft
• selectTopRight
• selectBottomRight
• selectBottomLeft
• selectCorners
• selectRows
• selectCols
• selectInner

• selectOuter

• calcLoopEnrichment function for flexibly calculating enrichment of interactions compared to their local background.

• adjustEnrichment and plotEnrichment for adjusting the loop enrichment to remove the effect of loop size on enrichment and visualize this correction across chosen parameters.

                    Changes in version 0.2.0                        
  

Methods for pulling Hi-C pixels and matrices from .hic files and storing them on-disk with HDF5Array and DelayedArray.

Overview of functionality

New or updated functions:

• snapToBins()

• “snaps” ranges in GInteractions objects to their nearest bin boundary. Allows spanning of multiple bins.

• pullHicPixels() extracts contact frequency from .hic files and returns an InteractionMatrix object containing a matrix of Hi-C interactions (rows) and samples (columns).

• Includes counts() accessor for matrix.
• Custom show() method.

• rbind() and cbind() methods.

• pullHicMatrices() extracts submatrices of contact frequency from .hic files and returns an InteractionArray object containing a 4-dimensional array of Hi-C submatrices, rownames, and colnames.

• Includes counts() accessor for submatrices.
• Custom show() method.

• rbind() and cbind() methods.

• pixelsToMatrices() takes GInteractions containing single pixels (i.e., each range represents one binSize) and expands ranges such that there is a buffer of pixels around each range.

• changePixelRes() takes a GInteractions object containing pixels of interest and is resized to the from resolution/binSize (if its not already). Then count matrices are extracted for each interaction and .hic file using the new to resolution. Count matrices are aggregated by interactions with the supplied aggFUN and a new pixel is selected with the supplied selectFUN. Allows block processing for large datasets. The object returned is a GInteractions object with the updated pixel ranges along with a column containing the aggregated min/max value for that pixel.

• calcLoopEnrichment() pulls Hi-C pixels and calculates the enrichment over background returning a DelayedMatrix of enrichment scores where rows are interactions and columns are Hi-C files.

• Accessors for GInteractions objects such as seqnames1(), start1(), end1(), seqnames2(), start2(), end2().

                    Changes in version 0.1.0                        
  

First pre-release of mariner functionality focused on manipulating, clustering, and merging paired interactions.

Overview of functionality

• Conversion of paired-range data to GInteractions with as_ginteractions/makeGInteractionsFromDataFrame

• Functions for manipulating GInteractions and GRanges objects with binPairs, binRanges, shiftRanges.

• Functions for clustering and merging lists of GInteractions objects with mergePairs.

• Extensions to GInteractions class with MergedGInteractions, and DelegatingGInteractions.

• Accessor functions for MergedGInteractions:

• aggPairMcols
• Aggregate metadata columns of clustered interactions.
• getPairClusters
• Return interactions for each cluster of interactions.
• selectionMethod
• Method used to select pairs from each cluster of interactions.
• sources
• List of names (or indices) used as input for clustering and merging.
• subsetBySource
• Return interactions unique to each source or combination of sources.

MassSpecWavelet

             Changes in version 1.65.1 (2023-04-07)                 

• Fix .Call() for R-4.3. Thanks to Steffen Neumann. Closes #5

             Changes in version 1.64.1 (2023-01-30)                 
  

• Fix undefined variable in MassSpecWavelet.Rmd

mastR

                   Changes in version 0.99.9                        

• Updated vignette for BiocStyle packages link functions.

                   Changes in version 0.99.8                        
  

• Linked external packages in vignette using BiocStyle functions, fixed the note of using paste in conditions.

                   Changes in version 0.99.7                        
  

• Improved test coverage depth, modified demo vignette and update Suggests packages.

                   Changes in version 0.99.6                        
  

• Removed paste in message().

                   Changes in version 0.99.5                        
  

• Updated R dependency, delete .Rhistory file, move all generic functions to a separate file “AllGenerics.R”.

                   Changes in version 0.99.4                        
  

• Deleted *.Rproj file to stop git track.

                   Changes in version 0.99.3                        
  

• Added *.Rproj into .gitignore.

                   Changes in version 0.99.2                        
  

• Added non-emtpy return value to man files and update pca plot function.

                   Changes in version 0.99.1                        
  

• Fixed notes in R CMD check.

                   Changes in version 0.99.0                        
  

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

MatrixQCvis

             Changes in version 1.7.7 (2023-04-20)                  

• add package statmod to Suggests

             Changes in version 1.7.6 (2023-04-19)                  
  

• add package jpeg to Suggests

             Changes in version 1.7.5 (2023-04-18)                  
  

• adjust test ERROR messages

             Changes in version 1.7.4 (2023-01-26)                  
  

• add ExperimentHub and GEOquery to NAMESPACE

             Changes in version 1.7.3 (2023-01-23)                  
  

• use TCGA RNA-seq and cell line proteomics datasets from ExperimentHub in vignette to showcase the functionality of the package

             Changes in version 1.7.2 (2022-11-24)                  
  

• replace aes_string by aes since aes_string is deprecated in newest ggplot2 version

             Changes in version 1.7.1 (2022-11-08)                  
  

• adjust errors in unit tests after updating the packages

matter

                    Changes in version 2.1.1                        

BUG FIXES

• Fixed NAMESPACE issue by importing ‘Matrix::rowSums()’ etc.

             Changes in version 2.0.1 (2022-11-16)                  
  

SIGNIFICANT USER-VISIBLE CHANGES

• Updated “User guide” vignette

BUG FIXES

• Fixed combining for matter vectors and lists

• Fixed slow ‘matter_mat()’ constructor for large # of atoms

• Fixed bug with BPPARAM not passed in ‘rowStats()’/’colStats()’

MBECS

                    Changes in version 1.3.1                        

• Included PLSDA algorithm.

• WiP requires adjustment of vignette and tests, should work though.

mbQTL

             Changes in version 0.99.6 (2023-03-30)                 

• changes made on vignette

             Changes in version 0.99.5 (2023-02-25)                 
  

• changes made based on errors of Bioconductor

             Changes in version 0.99.4 (2023-02-05)                 
  

• changes made based on errors of Bioconductor

             Changes in version 0.99.3 (2023-02-05)                 
  

• changes made based on Warnings of Bioconductor

             Changes in version 0.99.2 (2023-02-05)                 
  

• changes made based on Bioconductor team advisory

             Changes in version 0.99.1 (2023-01-19)                 
  

• corrected data loading issues in examples

             Changes in version 0.99.0 (2023-01-15)                 
  

• initiated Package and NEWS file

MEB

                   Changes in version 1.13.1                        

• Add new function scMEB().

metabCombiner

                    Changes in version 1.9.2                        

• featdata renamed to featData

• associated methods also renamed:
  • adductdata() -> adductData()
  • iddata() -> idData()
  • mzdata() -> mzData()
  • Qdata() -> QData()
  • rtdata() -> rtData()
• new method combineData():

  • merges columns from combinedTable() and featData()

                    Changes in version 1.9.1                        
    

• Changes to metabData():
  • Major changes to duplicate feature handling
  • bug fix to existing duplicate filtering code
  • duplicate argument reworked to accept a list of parameters
  • option to merge duplicate feature rows added
  • duplicate features are filtered or merged before missingness filter
  • new rowID column added to metabData objects
• new function opts.duplicate():
  • lists default parameters for duplicate feature handling in metabData()
  • new duplicate feature merging option (opts.duplicate(resolve = “merge”))
• Minor Change to evaluateParams():
  • “score” column changed to “totalScore” (for clarity)

metabinR

             Changes in version 1.2.0 (2023-04-21)                  

• Bump x.y.z version to even y prior to creation of RELEASE_3_17 branch.

             Changes in version 1.1.0 (2022-11-01)                  
  

• Bump x.y.z version to odd y following creation of RELEASE_3_16 branch.

MetaboAnnotation

                     Changes in version 1.3                         

Changes in 1.3.2

• Add mzR as suggested package to ensure package vignettes can be built.

Changes in 1.3.1

• Small changes in matchSpectra to avoid unnecessary object creation.
• Use backendBpparam to disable parallel processing of matchSpectra if the backend does not support it.

MetCirc

             Changes in version 1.29.2 (2023-04-18)                 

• replace the error message in shinyCircos test

             Changes in version 1.29.1 (2022-11-23)                 
  

• replace aes_string by aes since aes_string is deprecated in newest ggplot2 version

MetNet

             Changes in version 1.17.1 (2022-11-23)                 

• replace aes_string by aes since aes_string is deprecated in newest ggplot2 version

mia

                     Changes in version 1.7                         

• Deprecated assay_name arguments, replaced with assay.type

• Removed abund_values argument

• makePhyloseqFromTreeSE: added option for choosing a tree from multiple rowTrees

• mergeSEs: match rows based on all available taxonomy level data on rowData

• mergeSEs: fix bug related to equally named variables that are different class

• mergeSEs: option for merging multiple assays

• calculateUnifrac: option for specifying the tree from TreeSE

• transformCounts: utilize vegan package

• calculateUnifrac: subset tree based on data

• agglomerateByRank: take into account multiple trees

• loadFromBiom: name columns of rowData based on prefixes

• Deprecate transformSamples, *Features, relabundance, ZTransform, relAbundanceCounts

• mergeSEs: faster tree merging

• Faith’s index: fix bug that occurred when only one taxon is present

miaViz

             Changes in version 1.7.2 (2022-02-17)                  

• assay_name argument changed to assay.type

                     Changes in version 1.7                         
  

• Fixed plotGraph* that was broked due changes in dependencies

MicrobiotaProcess

                   Changes in version 1.11.5                        

• update ggdiffclade using the geom layer of ggtree. (2023-03-02)
• update mp_cal_dist to support storing the distance between the features with action=’add’. (2023-03-28)

• fix the special symbol in group name with mp_diff_analysis. (2023-04-11)

                   Changes in version 1.11.4                        
  

• update mp_plot_diff_res and mp_plot_diff_boxplot to support visualize the abundance (not relative abundance). (2022-12-02, Fri)
• fix the tip.label and rownames of assays when tree is provided in mp_import_dada2 (2022-12-02, Fri)
• add the message information when the differential features was filtered in the first and second test in mp_diff_analysis. (2022-12-06, Tue)

• fix the dynamic dots issue of left_join. (2022-12-15, Thu)

                   Changes in version 1.11.3                        
  

• update mp_plot_abundance to be compatible with the latest ggplot2. (2022-11-08, Tue)
• add mp_plot_diff_manhattan to visualize the different results with manhattan plot. (2022-11-21, Mon)

microSTASIS

             Changes in version 0.99.0 (2022-09-25)                 

• Submitted to Bioconductor. Previously on CRAN. Made the following changes:

• added support for TreeSumarizedExperiment objects

• changed parallelization from future to BiocParallel

• merged iterative_clustering() and stabilitas() into iterativeClustering()

• added a wrapper for automatic multiple paired time points in pairedTimes() and iterativeClustering()

• split CV_results() into mSerrorCV() and mSlinesCV()

• added apply loops instead of for and general coding implementations

• removed dependencies on other packages

• removed pre_radarPC() and radarPC()

miQC

             Changes in version 1.7.1 (2023-01-04)                  

• Added new function, get1DCutoff

mirTarRnaSeq

             Changes in version 1.7.1 (2023-04-12)                  

• fixed ubuntu error

mistyR

                     Changes in version 1.7                         

                    Changes in version 1.6.1                        

• Discontinue the use of .data due to its deprecation since tidyselect 1.2.0.
• Update minimum required versions for some tidyverse related packages due to function deprecation.

MoleculeExperiment

             Changes in version 0.99.5 (2023-04-17)                 

• Implemented review feedback for Bioconductor submission.

             Changes in version 0.99.0 (2023-03-30)                 
  

• Submitted to Bioconductor.

msa

                   Changes in version 1.31.7                        

• changes of Version 1.31.6 undone (fix did not work on Mac OS)

• update of ClustalW makefile to avoid problems arising from compiling ClustalW with C++ 17: added -std=c++14

                   Changes in version 1.31.6                        
  

• update of ClustalW makefile to avoid problems arising from compiling ClustalW with C++ 17: added -D_HAS_AUTO_PTR_ETC=1

                   Changes in version 1.31.5                        
  

• update of Muscle source code to avoid problems arising from compiling Muscle with C++ 17: renamed type ‘byte’ to ‘MByte’

                   Changes in version 1.31.4                        
  

• updated src/Muscle/subfams.cpp to avoid conflicting definitions of INFINITY on some Mac systems

                   Changes in version 1.31.3                        
  

• updated config.sub and config.guess in source code of ClustalW and ClustalOmega to solve compilation issues on aarch64 (thanks to Yikun Jiang for contributing this fix!)

                   Changes in version 1.31.2                        
  

• msa() function changed such that it also works if the package is not attached to the workspace

                   Changes in version 1.31.1                        
  

• update of gc

                   Changes in version 1.31.0                        
  

• new branch for Bioconductor 3.17 devel

MSA2dist

             Changes in version 1.3.1 (2022-11-08)                  

Major changes

Minor improvements and bug fixes

• additional Genetic Codes into base.cpp

MsBackendMassbank

                     Changes in version 1.7                         

Changes in 1.7.4

• Add backendBpparam for MsBackendMassbankSql; parallel processing of Spectra with MsBackendMassbankSql will silently disable parallel processing.

Changes in 1.7.3

• Add support for EAD parameter.

Changes in 1.7.2

• Avoid export of retention time data if not available.

Changes in 1.7.1

• Run the full test suite from the Spectra package to validate the MsBackend implementations.

MsBackendMgf

                     Changes in version 1.7                         

Changes in 1.7.5

• Support import of MS levels from MGF files.

Changes in 1.7.4

• Fix bug in import when m/z values are not sorted.

Changes in 1.7.3

• Enforce m/z values to be increasingly ordered while importing.

Changes in 1.7.2

• Run the full unit test suite from the Spectra package to check validity of the MsBackendMgf.

Changes in 1.7.1

• Use compress = FALSE for NumericList.

Changes in 1.7.0

• Bioconductor 3.17 developmental branch.

MsBackendMsp

                     Changes in version 1.3                         

Changes in 1.3.1

• Use the full unit test suite from the Spectra package to check validity of the MsBackendMsp.

MsBackendSql

                    Changes in version 0.99                         

Changes in 0.99.7

• Decrease required R version to 4.2.

Changes in 0.99.6

• Add mzR to Suggests to ensure package vignettes can be build properly.

Changes in 0.99.5

• Add MsBackendOfflineSql backend that re-connects to the database for each query.

Changes in 0.99.4

• Add backendBpparam method to ensure parallel processing is disabled for the MsBackendSql backend.

Changes in 0.99.3

• Add backendMerge method.
• Add parameter data to backendInitialize to allow creating a new MsBackendSql database and store the values from data in it. This enables the use of Spectra,setBackend to convert any backend to a MsBackendSql.
• Implement supportsSetBackend to enable setBackend,Spectra,MsBackendSql.

Changes in 0.99.2

• Evaluate validity of the MsBackendSql using the full unit test suite from the Spectra package.

Changes in 0.99.1

• Address Kayla’s package review comments.

Changes in 0.99.0

• Prepare the package for submission to Bioconductor.

                    Changes in version 0.98                         
  

Changes in 0.98.1

• Rename MsqlBackend to MsBackendSql.

Changes in 0.98.0

• Add vignette.

                     Changes in version 0.1                         
  

Changes in 0.1.0

• Add parameter blob to allow storing m/z and intensity values as BLOB data type in the database. MsBackendSql will use different functions to retrieve data from a database with this type of storage.

MsCoreUtils

                    Changes in version 1.11                         

MsCoreUtils 1.11.6

• Fix bug in impute_MinDet(MARGIN = 1) and add unit test.
• Check that package is available and namespace is loaded adding stopifnot() when calling requireNamespace().

MsCoreUtils 1.11.5

• Add function maxi to determine the maximal intensity value. This function returns NA_real_ instead of -Inf if all values are missing or if the length of the input parameter is 0.

MsCoreUtils 1.11.4

• Check if parameter y is increasingly ordered in bin: issue #108.

MsCoreUtils 1.11.3

• Add function sumi to sum intensity values with correct NA handling.

MsCoreUtils 1.11.2

• Reimplement between in C (see issue #105).
• Use symbols to call registered C methods for faster lookup (see PR #106 and Writing R extensions: Converting a package to use registration).
• Documentation improvement: explicitly mention impute_mle2() in the MLE imputation paragraph.

MsCoreUtils 1.11.1

• Add a MARGIN argument to (relevant) imputation functions to support (and make it explicit) along which dimensions (row or columns) imputation is performed.
• New impute_mle2() function that uses norm2 (see issue #100).

MsCoreUtils 1.11.0

• New Bioconductor 3.17 (devel) release

MsDataHub

                    Changes in version 0.99                         

MsDataHub 0.99.3

• Updates based on package review (see https://github.com/Bioconductor/Contributions/issues/2887#issuecomment-1463655683).

MsDataHub 0.99.2

• Fix title names with make.names() to assert that they will represent valid function names after running ExperimentHub::createHubAccessors().
• Execute chunks in vignette.

MsDataHub 0.99.1

• Run createHubAccessors() when loading the package.

MsDataHub 0.99.0

• Package submission to Biocoductor.

MsExperiment

                     Changes in version 1.1                         

MsExperiment 1.1.4

• Fix and improve show,MSnExperiment.
• New otherData setter and getter functions.

MsExperiment 1.1.3

• Fix problem in unit test.

MsExperiment 1.1.2

• Add readMsExperiment function (issue #32).

MsExperiment 1.1.1

• Use S4Vectors::findMatches in linkSampleData which improves performance, especially for larger data sets.

MsExperiment 1.1.0

• Bioconductor release 3.17 (devel).

MSnbase

                    Changes in version 2.25                         

MSnbase 2.25.2

• Fix bug in descendPeaks (see #583)

MSnbase 2.25.1

• Fix remote mztab filename.

MSnbase 2.25.0

• New devel (Bioc 3.17)

MsQuality

                    Changes in version 0.99                         

Changes in version 0.99.9 (2023-04-18)

• enable parallel processing in calculateMetricsFromSpectra.
• rename ticQuantileToQuantileLogRatio to ticQuartileToQuartileLogRatio
• rename rtOverTicQuantile to rtOverTicQuantiles
• return quartiles instead of quantiles in precursorIntensityQuartiles
• add mzR to Suggests in DESCRIPTION

Changes in version 0.99.8 (2023-09-02)

• adjust behaviour of metrics function when Spectra object of length 0 is presented, return NA values instead of raising an error

Changes in version 0.99.7 (2023-06-02)

• adjust ticQuantileToQuantileLogRatio that it adheres to Quameter calculation

Changes in version 0.99.6 (2022-11-29):

• extend section Description in DESCRIPTION
• add sections BugReports and URL in DESCRIPTION
• update dependency to R version 4.2.0
• transfer source code in R/Lee2019-data.R to inst/sources/Lee2019-data-source.R
• use partial_bundle to reduce the file size of plotly graphics

Changes in version 0.99.5 (2022-10-12):

• add section on alternative software in vignette
• simplify the vignette with regard to dealing with the RPLC and HILIC example data set and adjust the Lee2019-data.R accordingly to keep the RPLC/HILIC information in the dataOrigin slot of the Spectra object

Changes in version 0.99.4 (2022-10-11):

• add missing comma in DESCRIPTION

Changes in version 0.99.3 (2022-10-11):

• delete Maintainer field in DESCRIPTION
• add instructions to install MsQuality in vignette and README.md via remotes/BiocManager instead of devtools

Changes in version 0.99.2 (2022-09-20):

• create branch msexperiment to store infrastructure and functions for MsExperiment objects
• remove MsExperiment objects since this is still in BioC review and solely rely on Spectra objects
• adjust documentation for the implemented changes (removal of MsExperiment)

Changes in version 0.99.1 (2021-11-23)

• simplify calculateMetricsFromSpectra:
• the function does not any longer match the arguments by the formal arguments of the metric functions
• the function does not any longer combine the parameters
• the additional arguments do not take longer the parameter list of arguments but comma-separated arguments given to …
• for all metric functions the … parameter is added
• adjust the vignette and help pages
• rename functions to camel case

Changes in version 0.99.0 (2021-09-10)

• add quality metrics/functions (metrics based on HUPO-mzQC):
• rtDuration (QC:4000053),
• rtOverTICquantile (QC:4000054),
• rtOverMsQuarters (rtOverMSQuarters),
• ticQuantileToQuantileLogRatio (QC:4000057, QC:4000058),
• numberSpectra (QC:4000059, QC:4000060),
• medianPrecursorMz (QC:4000065),
• rtIQR (QC:4000072),
• rtIQRrate (QC:4000073),
• areaUnderTIC (QC:4000077),
• areaUnderTICRTquantiles (QC:4000078),
• extentIdentifiedPrecursorIntensity (QC:4000125),
• medianTICRTIQR (QC:4000130),
• medianTICofRTRange (QC:4000132),
• mzAcquisitionRange (QC:4000138),
• rtAcquisitionRange (QC:4000139),
• precursorIntensityRange (QC:4000144),
• precursorIntensityQuartiles ((QC:4000167, QC:4000228, QC:4000233),
• precursorIntensityMean (QC:4000168, QC:4000229, QC:4000234),
• precursorIntensitySD (QC:4000169, QC:4000230, QC:4000235),
• msSignal10XChange (QC:4000172, QC:4000173),
• ratioCharge1over2 (QC:4000174, QC:4000179),
• ratioCharge3over2 (QC:4000175, QC:4000180),
• ratioCharge4over2 (QC:4000176, QC:4000181),
• meanCharge (QC:4000177, QC:4000182),
• medianCharge (QC:4000178, QC:4000183)
• .rt_order_spectra (helper function)
• add the functions calculateMetricsFromSpectra, calculateMetricsFromMsExperiment to calculate the metrics based on Spectra and MsExperiment objects
• add functions plotMetric, plotMetric_tibble to visualize the metrics
• add shiny application shinyMsQuality to interactively visualize the metrics

MSstatsConvert

                    Changes in version 1.9.1                        

• Added DIA-NN converter.

MSstatsTMT

             Changes in version 2.6.1 (2023-02-26)                  

• Minor change: update PhilosophertoMSstatsTMTFormat function normalization

MultiAssayExperiment

                   Changes in version 1.26.0                        

New features

• showReplicated displays the actual colnames of technical replicates by assay and biological unit.
• The bracket replacement method [<- for MultiAssayExperiment now also replaces the names with those from the right-hand side of the operation, if any (@DarioS, #319)

Bug fixes and minor improvements

• During single assay replacement [[<-, the re-ordering of assays based on the value input was invalid when empty assays present (@danielinteractive, #322).
• Permuting assays also updates the order of names in the MultiAssayExperiment and assays in the sampleMap

MultimodalExperiment

                   Changes in version 0.99.0                        

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

MungeSumstats

                   Changes in version 1.7.18                        

New features

• Check added, ensure BP is between 1 - length of chromosome using reference chromosome.

                   Changes in version 1.7.17                        
  

New features

• extra mapping for base-pair position (BP) column added

                   Changes in version 1.7.14                        
  

Bug fix

• Fix ensembl chain file retrieval so works on all environments

                   Changes in version 1.7.13                        
  

Bug fix

• write_sumstats:
• Fix indexing issues due to incomplete genome coordinates sorting: https://github.com/neurogenomics/MungeSumstats/issues/117
• Add default NULL to ref_genome.
• Check ref_genome (only in conditions where its used).
• sort_coord:
• Renamed .R file from sort_coordinates to match current function name.
• Add multiple sort_methods, including improved/more robust data.table-native method.
• Added dedicated unit tests within test-index_tabular.R.
• New helper function: check_numeric:
• Ensures relevant sumstats cols are numeric.
• Added internally to: sort_coord, read_header
• rworkflows.yml:
• Omit Windows runner.
• Turn on run_biocheck
• to_GRanges.R / to_VRanges.R:
• Rename files to match current function names.
• Remove extra extdata files (I think these were created by accident):
• ALSvcf.vcf.bgz
• ALSvcf.vcf.bgz.bgz
• ALSvcf.vcf.bgz.bgz.tbi
• ALSvcf.vcf.bgz.tbi
• ALSvcf.vcf.gz
• Remove .DS_Store files throughout.
• Don’t check for duplicates based on RS ID with Indels, remove these first.

New features

• Implement rworkflows.
• Removed old Dockerfile (not needed anymore) and workflow yaml.

• Add drop_indels parameter so a user can decide to remove indels from sumstats.

                   Changes in version 1.7.12                        
  

Bug fix

• For downloading files use sed -E rather than sed -r as its compatible with mac which has issues with sed -r

New features

• For instances where a single column contains CHR, BP, A1 and A2. The default order has been updated to CHR:BP:A1:A2 to align with SPDI format. If your format differs and MSS doesn’t pick up on it, update the column name to the true format e.g. CHR:BP:A2:A1

                   Changes in version 1.7.11                        
  

New features

• Update to where SNP column is given by the four CHR, BP, A1, A2. Now, if A1 or A2 is also a separate column, these will be used to infer the order.

                   Changes in version 1.7.10                        
  

Bug fix

• further fix for Latex issues when rendering PDF of examples.

                    Changes in version 1.7.9                        
  

Bug fix

• fix for Latex issues when rendering PDF of examples.

                    Changes in version 1.7.3                        
  

Bug fix

• fix for offline runs and accessing chain files from 1.7.2.

                    Changes in version 1.7.2                        
  

New features

• New chain files used for lifting over the genome build from Ensembl have now been added. These will now be set as the default chain file instead of UCSC due to licensing issues. The choice to use UCSC files will still be there but the files will not be stored in the package themselves, they will instead be downloaded for use on the fly.

                    Changes in version 1.7.1                        
  

New features

• The use of the log_folder parameter in format_sumstats() has been updated. It is still used to point to the directory for the log files and the log of MungeSumstats messages to be stored. And the default is still a temporary directory. However, now the name of the log files (log messages and log outputs) are the same as the name of the file specified in the save_path parameter with the extension ‘_log_msg.txt’ and ‘_log_output.txt’ respectively.

muscat

                   Changes in version 1.12.1                        

• fixed various typos in both vignettes

• internal fixes to keep up with ‘ggplot2’ & ‘dplyr’ updates

• bug fix in ‘simDS’ computing means when one group is missing

• bug fix in ‘resDS’ until testing when ‘cpm/frq = TRUE’

mzR

                   Changes in version 2.33.1                        

• fix: update to a new PSI-MS OBO for e.g. ZenoTOF CV term Closes #278

NanoMethViz

                    Changes in version 2.6.0                        

• Added preliminary modbam file support.
• Changed rug plot to appear under other geoms. This helps with visibility of data when methylation values are close to 0.
• Changed heatmap alpha from 0.5 to 1, line width from 1.0 to 1.2 and line colour from black to darkgrey.
• Changed x-axis limits on plots to be controlled using coord_cartesian instead of scale_x_continuous. Plots should now accurately represent data around the boundaries.

NanoStringNCTools

             Changes in version 1.7.1 (2022-01-25)                  

• Parameters added for update in ggiraph calls

NanoTube

                    Changes in version 1.5.1                        

• We’re published in Bioinformatics! CITATION file updated.

ndexr

                   Changes in version 1.21.1                        

• UPDATE: Using the RCX package for working with networks.

• all function of the old RCX implementation are removed from this package

netZooR

                    Changes in version 1.3.2                        

• R implementation of SPIDER
• R implementation of DRAGON
• header argument in pandaPy

ngsReports

                    Changes in version 2.1.5                        

• Added FastpData and FastpDataList classes for working with fastp reports

                    Changes in version 2.1.4                        
  

• Added umi_tools dedup to importNgsLogs

                    Changes in version 2.1.3                        
  

• Bugfix when importing duplicationMetrics

nullranges

                   Changes in version 1.5.19                        

• Remove speedglm dependency as it was removed from CRAN (April 2023).

oncoscanR

                    Changes in version 1.1.0                        

• To simplify the workflow, the gender of the patient is not taken into account anymore. That implies that in a male sample, a gain of 3 extra copies on the X or Y chromosome is considered as a gain and not an amplification anymore. For female samples, nothing changes.
• The oncoscan coverage has been corrected to reflect only areas where there are groups of probes. Isolated probes where causing issues to identify arm-level alterations as ChAS segments where never extended to these probes and the 90% threshold could never be met (particularly on chromosomal arms 9p and Yq).
• Minor corrections in vignette

OncoSimulR

             Changes in version 4.1.4 (2023-03-08)                  

• Updated exprTk (thanks to pull request from Arash Partow).

             Changes in version 4.1.3 (2023-02-20)                  
  

• no need to specify CXX_STD = CXX14 (the default since R-4.1.0).

             Changes in version 4.1.2 (2023-02-20)                  
  

• NAMESPACE: do not import .rbind.data.table (no longer exported from data.table 1.14.8, and not needed with R >= 4.0.0).

              Changes in version 4.1 (2022-11-24)                   
  

• Faster, cleaner, and better tests of interventions.

OrganismDbi

                   Changes in version 1.41.1                        

MODIFICATIONS

• (v. 1.41.1) Convert OrganismDbi.Rnw to OrganismDbi.Rmd

orthogene

                    Changes in version 1.5.2                        

New features

• Remove unnecessary Suggests
• map_species
• get_all_orgs: When species=NULL, now returns an extra columns called “scientific_name_formatted”.
• format_species_name: New args remove_parentheses, remove_subspecies, remove_subspecies_exceptions
• report_orthologs
• Make much more efficient by only querying ref_genes once.
• Added new internal func report_orthologs_i instead of recursion to make this easier.
• Ensure that map and report get rbound separately and returned according to the return_report arg.
• format_species
• Export function that was previously named format_species_name.
• all_species:
• New exported function
• Originally implemented a version of this in EWCE::list_species, but decided to extend it and export it here.
• get_silhouettes
• Previously was internal func: gather_images.
• Now an exported function.
• plot_orthotree
• Add “Invertebrates” to default clades
• Update README to showcase more functions.

Bug fixes

• drop_non121
• New arg symbol_only to ONLY consider gene symbols (not ensemble IDs) when identifying non-121 orthologs.
• This make a drastic difference in the number of 1:1 orthologs that get dropped!
• gather_images
• Update to use newly released rphylopic 1.0.0 which uses the new phylopic API.
• Add another tryCatch for when the SVG is available but not the png.
• is_human
• Add “9606” and “homo sapiens sapiens” species ID to list of options.
• all_genes_babelgene
• Don’t filter by support when speices is human, because this column will always be NA since it’s irrelevant for humans.
• Fix unit tests:
• report_orthologs
• dMcast

• Fix stats::pass –> stats::na.pass. Weirdly, only a problem on Linux. Did base R change a fundamental function name?

                    Changes in version 1.5.1                        
  

New features

• Bumped to 1.5.1 for Bioc devel 3.17
• Merged upstream devel.
• Now using rworkflows for GHA.
• Removed Dockerfile
• Host orthogene data resources on Zenodo:
• https://doi.org/10.5281/zenodo.7315418
• Upgrade TimeTree phylogeny to v5 (2022):
• 50k+ species –> 137k+ species!

• Replace dplyr::%>% usage with

  >

• Add CITATION file

Bug fixes

• prepare_tree:
• Ignore species name case and trim “’” when filtering tree.
• map_species:
• Add trimws step to remove flanking “ “ or “’”.

OUTRIDER

                   Changes in version 1.16.1                        

• Add option to restrict FDR correction to sets of genes of interest

• Add opttion to retrieve results based on those FDR values on subsets of genes

OutSplice

             Changes in version 0.99.9 (2023-04-17)                 

• Fixed issue when assigning gene ids

             Changes in version 0.99.8 (2023-04-11)                 
  

• Fixed error that occured when no significant outliers were present

             Changes in version 0.99.7 (2023-04-07)                 
  

• Add value section to overview man page

             Changes in version 0.99.6 (2023-04-06)                 
  

• Add options to specificy row name columns

• Return function output in addition to saving output files

             Changes in version 0.99.5 (2023-03-29)                 
  

• Correct package for build report

             Changes in version 0.99.4 (2023-03-29)                 
  

• Correct error with BiocGenerics exported functions

             Changes in version 0.99.3 (2023-03-28)                 
  

• Added BiocGenerics to Description and import statements

             Changes in version 0.99.2 (2023-03-22)                 
  

• Numerous changes to address comments made during the review process

             Changes in version 0.99.1 (2023-02-27)                 
  

• Fixed Bioc-devel mailing list registration and added package to Watched Tags

             Changes in version 0.99.0 (2023-01-06)                 
  

• Submitted to Bioconductor

pairedGSEA

                   Changes in version 0.99.6                        

• Improved test coverage and depth
• Coerced paired_ora output to DataFrame from data.table

• Added value field to data man pages

                   Changes in version 0.99.5                        
  

• Remove non-exported man pages

                   Changes in version 0.99.4                        
  

• Remove filter_gene_sets option, as it is inherent in fgsea::ora
• Added test depth and coverage for paired_diff and paired_ora

• Fixed wrong storing location for splicing intermediate results

                   Changes in version 0.99.3                        
  

• Rewrote code base to remove tidyverse dependencies
• Added \code{…} and \link{…} where appropriate in documentation
• Added input parameter checks
• Reduced redundant input parameters from aggregate_pvalue
• Modularized paired_ora and plot_ora
• Added filter_gene_sets parameter to help users reduce gene set bias
• Increased test coverage and depth

• Moved data scripts to inst/script

                   Changes in version 0.99.2                        
  

• Implement limma as alternative analysis method
• Increased test coverage significantly

• Removed usage of deprecated purrr::when

                   Changes in version 0.99.1                        
  

• Updated vignette with a brief paragraph on the motivation of pairedGSEA.

• Updated NAMESPACE to include all imported packages. Suggested packages are added in notes.

                   Changes in version 0.99.0                        
  

• Submitted to Bioconductor

peakPantheR

            Changes in version 1.13.21 (2023-03-28)                 

• Update for next Bioc release

             Changes in version 1.13.1 (2022-12-11)                 
  

• Bugfix: plotHistogram changing warning message

• Bugfix: peakPantheR_plotPeakwidth issue due to ggplot2 behaviour changes for date axis

• Depreciation warning from ggplot2 ..density.. to after_stat()

pfamAnalyzeR

             Changes in version 0.99.7 (2023-04-18)                 

• Added license

             Changes in version 0.99.6 (2023-04-13)                 
  

• Updates for BioConductor review

             Changes in version 0.99.5 (2023-04-13)                 
  

• Updates for BioConductor review

             Changes in version 0.99.4 (2023-04-13)                 
  

• Updates for BioConductor review

• Main user related is a extended vignette

             Changes in version 0.99.3 (2023-03-15)                 
  

• Redbuild documentation

             Changes in version 0.99.2 (2023-03-15)                 
  

• Update of augment_pfam() to use envelope coordiantes

• Update of augment_pfam() documentation

             Changes in version 0.99.1 (2023-03-15)                 
  

• Fixed problematic annoation

             Changes in version 0.99.0 (2023-02-14)                 
  

• Version bump for Bioconductor

• Better Description

             Changes in version 0.1.0 (2022-08-12)                  
  

• Package introduced

phantasus

                   Changes in version 1.19.3                        

• Shiny GAM -> Shiny GATOM

PharmacoGx

                    Changes in version 3.3.2                        

• Debugging vignette issues on the Bioconductor build system

                    Changes in version 3.3.1                        
  

• Added new vignette documenting support for drug combination modelling new drug combination features added in PharmacoGx >=3.0

phenomis

                    Changes in version 1.1.2                        

• minor documentation update

PhosR

                    Changes in version 1.9.1                        

• Bug fixes

PhyloProfile

                   Changes in version 1.14.0                        

• option for uploading sorted taxon list

                   Changes in version 1.12.6                        
  

• fixed bug ordering gene IDs when using gene categories

                   Changes in version 1.12.5                        
  

• fixed bug multiple entries for one (super)taxon ID

                   Changes in version 1.12.4                        
  

• fixed bug download data

                   Changes in version 1.12.3                        
  

• fixed bug customized profile not showed

                   Changes in version 1.12.1                        
  

• added number of co-orthologs and number of taxa in each supertaxon

• replaced pfam link by interpro url

Pigengene

            Changes in version 1.25.16 (2023-03-22)                 

Changes in existing functions

• Constant genes are now ignored in the compute.pigengene(doWgcna=FALSE,…) function to prevent a run time error.

            Changes in version 1.25.12 (2023-03-02)                 
  

Changes in existing functions

• The default value changed in gene.mapping(leaveNA=FALSE, …).

            Changes in version 1.25.10 (2023-01-04)                 
  

Changes in existing functions

• The doWgcna option is added to the compute.pigengene function.

             Changes in version 1.25.4 (2022-12-01)                 
  

Changes in existing functions

• The get.enriched.pw function adds gene symbols in the excel file.

planttfhunter

                   Changes in version 0.99.2                        

CHANGES

• Made small changes suggested by Bioconductor reviewer.

                   Changes in version 0.99.0                        
  

NEW FEATURES

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

plotgardener

                    Changes in version 1.5.3                        

BUG FIXES

• Fixed page viewport parsing bug fixes related to R version 4.3.0 updates.

                    Changes in version 1.5.2                        
  

BUG FIXES

• annoPixels detects and annotates all pixels for plotHicRectangle plots.

                    Changes in version 1.5.1                        
  

BUG FIXES

• yscales for plotHicRectangle and plotHicTriangle reflect distance in Hi-C bins.

                    Changes in version 1.5.0                        
  

Version bump for Bioconductor 3.16 release.

PoDCall

             Changes in version 1.7.1 (2023-04-04)                  

• Suggest user to change reference well when no threshold for ch 2

podkat

                   Changes in version 1.31.1                        

• changed arguments in qqplot() method for compatibility with new version of the standard function in the ‘stats’ package (added dummy arguments to avoid errors)

• minor adaptations of help pages

                   Changes in version 1.31.0                        
  

• new branch for Bioconductor 3.17 devel

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)

pRoloc

                    Changes in version 1.39                         

Changes in version 1.39.1

• Update transfer learning vignette to use hpar 1.41.

Changes in version 1.39.0

• New devel version (Bioc 3.17)

pRolocGUI

                    Changes in version 2.9.0                        

CHANGES IN VERSION 2.9.0

• New version for Bioc 3.17

CHANGES IN VERSION 2.9.1

• Fix bugs in table selection in explore and compare app
• Fix transparency slider in explore app

protGear

             Changes in version 1.3.32 (2022-12-11)                 

• Removed kableExtra due to build error

• added the sampleID files

             Changes in version 1.3.0 (2022-11-15)                  
  

• Updated shiny app to load
• Added missing paths for launch_protGear_interactive

PSMatch

                     Changes in version 1.3                         

PSMatch 1.3.3

• New fdr variable (default is always NA_character_ for now) that defines the spectrum FDR (or any similar/relevant metric that can be used for filtering - see next item).
• New filterPsmFdr() function that filters based on the fdr variable.

PSMatch 1.3.2

• Specific Matrix::rowSums() to fix error in example.

PSMatch 1.3.1

• Fix type in vignette.

QFeatures

                     Changes in version 1.9                         

QFeatures 1.9.4

• New dropEmptyAssays() function (see issue #184).

QFeatures 1.9.3

• Minor rephrasing in vignette and README.

QFeatures 1.9.2

• feat: filterFeatures() now allows to select assays to filter (i argument)
• feat: aggregateFeatures() can now take multiple assays
• feat: impute() can now take multiple assays
• feat: processing functions (normalize, scaleTransform, logTransform, sweep) can now take multiple assays
• refactor: avoid validObject() when possible

• Use	> rather than %>%.

QFeatures 1.9.1

• fix: solved bug in selectRowData()

QFeatures 1.9.0

• New Bioconductor 3.17 (devel) release

qsea

                   Changes in version 1.25.1                        

• Bugfixes:
  • fixed issue with R4.3 (“cannot xtfrm data frames”)
  • fixed documentation
  • updated description file

qsmooth

             Changes in version 1.15.1 (2022-11-04)                 

• Removed CC BY 4.0 license and replaced with GPL-3

QuasR

                   Changes in version 1.40.0                        

USER-VISIBLE CHANGES

• count bam alignments with coordinates but flag ‘unmapped’ (e.g. generated by hisat2) as mapped, so that qCount, qQCReport and alignmentStats are consistent

RaggedExperiment

                   Changes in version 1.24.0                        

Bug fixes and minor improvements

• Use full argument names in unit tests.
• Invoke colSums from MatrixGenerics in unit tests.

Rarr

                   Changes in version 0.99.9                        

• Response it initial package review (thanks @Kayla-Morrell)
• Provided manual page examples for use_* compression filter functions.
• Add details of how example data in inst/extdata/zarr_examples was created.

• General code tidying

                   Changes in version 0.99.8                        
  

• Patch compression libraries to remove R CMD check warnings about C functions that might crash R or write to something other than the R console. Working in Linux only.

                   Changes in version 0.99.7                        
  

• Allow reading and writing chunks with GZIP compression.

• Add compression level arguments to several compression tools.

                   Changes in version 0.99.6                        
  

• Allow reading and writing chunks with no compression.
• Enable LZ4 compression for writing.
• Fix bug in blosc compression that could result in larger chunks than necessary.

• Improve speed of indexing when combining chunks into the final output array.

                   Changes in version 0.99.5                        
  

• Fixed bug when specifying nested chunks, where the chunk couldn’t be written unless the directory already existed.

                   Changes in version 0.99.4                        
  

• When writing chunks that overlap the array edge, even the undefined overhang region should be written to disk.

                   Changes in version 0.99.3                        
  

• Allow choice between column and row ordering when creating a Zarr array

                   Changes in version 0.99.2                        
  

• Catch bug when chunk files contain values outside the array extent.

• Add manual page issues identified by BBS

                   Changes in version 0.99.1                        
  

• Switch from aws.s3 to paws.storage for S3 data retrieval.

                   Changes in version 0.99.0                        
  

• Initial Bioconductor submission.

                    Changes in version 0.0.1                        
  

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

rawrr

             Changes in version 1.7.12 (2023-03-17)                 

• Replace rtinseconds by StartTime [min] as provided by the TFS assembly #60.

             Changes in version 1.7.4 (2023-03-01)                  
  

• Add rawrr::readTrailer.

Rbwa

                    Changes in version 1.3.1                        

• Now supporting Linux ARM64.

Rcollectl

Initial Submission

• This package helps measure CPU/network/storage consumption of a series of R commands.

RCy3

                   Changes in version 2.20.0                        

• Add a delay in mergeNetworks method
  • Wait for Cytoscape to finish adding annotations column to Network table
• Bug fixes:
  • ellipsis args in createNetworkFromDataFrames, #195
  • setNodeColorBypass: List of hex colors, #188

ReactomeGSA

             Changes in version 1.13.1 (2023-04-13)                 

• Fixed documentation mismatch in “plot_heatmap”

RESOLVE

                    Changes in version 1.2.0                        

• Major code refactoring.

• Package released in Bioconductor 3.17.

retrofit

             Changes in version 0.99.0 (2023-03-05)                 

• Submitted to Bioconductor

ReUseData

                   Changes in version 0.99.23                       

• ReUseData helps create data recipes for reproducible data processing, where any necessary command-line tools are managed using conda and docker.

• ReUseData has pre-built data recipes for data downloading/curation for common biomedical data resources.

• ReUseData supports cloud downloading of pre-generated curated data.

• ReUseData has recipe landing pages (https://rcwl.org/dataRecipes/) with full annotations and instructions.

rgoslin

                    Changes in version 1.4.0                        

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 3.17 - Changes in 1.4.0

Improvements

• Improved handling of Glycosphingolipids and carbohydrates
• Improved headgroup normalization for Glycosphingolipids.
• Added PMeOH.
• Added TG-EST (estolide) Estolides [GL0305].
• Added more sterol variants.

Bug Fixes

• Fixed classification of SB1a as Sulfoglycosphingolipids (sulfatides) [SP0602].
• Fixed classification of SHex2Cer as Sulfoglycosphingolipids (sulfatides) [SP0602].
• Fixed classification of SMGDG as Glycosylalkylacylglycerols [GL0502], added synonym seminolipid.
• Fixed classification of SQDG Glycosyldiacylglycerols [GL0501].
• Fixed classification of sterols.

BioConductor 3.16 - Changes in 1.2.0

• No noteworthy changes.

BioConductor 3.15 - Changes in 1.0.0

Improvements

• Reduced memory consumption.
• Added ‘ChE’ abbreviation.
• Added FG hydroperoxy to mediator nomenclature, refinement of mediators.
• Added more sphingosine and sphinganine synonyms.
• Added more ether dialects to LipidMaps grammar.
• Improved handling for SP without explicit OH description.
• Added Sa So support.
• Updated old SP shortcuts.
• Added CholE as abbreviation for cholesterol esters.
• Modifications and improvements for Windows.
• Added column of elements to functional group list and class.
• Added ‘ChoE’.
• Added functional group butylperoxy -> BOO.

Bug Fixes

• Fixed handling of LIPID MAPS SP notation.
• Fixed critical bug when parsing LIPID MAPS names.
• Fixed implicit hydroxy count.
• Fixed ACer rule for species level.
• Fixed lcb rule in LipidMaps grammar.
• Fixed S1P and Sa1P handling.
• Fixed gangliosides in Goslin grammar.
• Fixed correct handling of dummy FAs during sorting.
• Fixed segmentation fault in FA parser event handler.

Changes in 0.99.1

• The column names within the data frames returned from the parse* methods now use column names with dots instead of spaces. This makes it easier to use the column names unquoted within other R expressions.
• All parse* methods now return data frames.
• The Messages column has been added to capture parser messages. If parsing succeeds, this will contain NA and Normalized.Name will contain the normalized lipid shorthand name.
• Parser implementations have been updated to reflect the latest lipid shorthand nomenclature changes. Please see the Goslin repository for more details.
• Exceptions in the C++ part of the library are captured as warnings in R. However, if you parse multiple lipid names, exceptions will not stop the parsing process.

rGREAT

                    Changes in version 2.1.9                        

• add getKEGGGenome()

                    Changes in version 2.1.8                        
  

• add getGenomeDateFromNCBI()

                    Changes in version 2.1.4                        
  

• online great: the names of input regions are kept.

• region coordinates (1-based or zero-based) are adjusted in getRegionGeneAssociations().

rhdf5

                   Changes in version 2.44.0                        

CHANGES

• h5closeAll() now accepts objects as arguments to allow closing a set of HDF5 identifiers.

• Functions H5Teunum_create() and H5Tenum_insert() have been included.

• h5set_extent() will now test whether a dataset is chunked and inform the user if not. This uses the new function H5Dis_chunked().

• The function H5Pset_filter() is now exposed to the user.

BUG FIXES

• Modified how the constant H5S_UNLIMITED was being passed to the HDF5 library. The previous strategy was not working on the ARM64 architecture, and leading to failures when trying to change the size of a dataset.

• Resolved issue when reporting missing filters where R-to-C indexing was being applied twice, resulting in the message: “‘idx’ argument is outside the range of filters set on this property list”

rhdf5filters

                   Changes in version 1.12.0                        

USER VISIBLE CHANGES

• Compression libraries updated:
• lz4: 1.9.2 🠪 1.9.4
• Added the standalone Zstandard filter. The distributed version of Zstandard is now 1.5.5.
• Added the VBZ filter.

BUG FIXES

• Ensure ranlib is applied to the lzf library after it is compiled. This cause linking failures on some systems. (Thanks to Sergey Fedorov for the report https://github.com/grimbough/rhdf5filters/pull/18)

Rhdf5lib

                    Changes in version 1.22                         

User visible changes

• Removed pre-compiled library for 32-bit Windows as this platform is no longer supported by R.

Rhtslib

                    Changes in version 2.2.0                        

• No significant changes in this version.

ribosomeProfilingQC

                   Changes in version 1.11.1                        

• add precedence parameter to readsDistribution

rifiComparative

                   Changes in version 0.99.5                        

• Update News file

• Usage of back ticks around variable in vignettes

• deleting details e.g. “Default is” in documentation

                   Changes in version 0.99.4                        
  

• Fixing error while building the package

                   Changes in version 0.99.3                        
  

• Improve import file by indicating the functions used of soem packages

• making rifiComparative documenation accessible by using “?rifiComparative”

• Improving some naming files as in vignette

                   Changes in version 0.99.2                        
  

• Supress unecessary comments

• Bugs in vignettes are corrected

• Several typo errors are corrected

                   Changes in version 0.99.1                        
  

• Significant changes in documentation making it easier to read.

• Bugs in vignettes are corrected

• Suppress warnings in visualization is added

• Several typo errors are corrected

RnBeads

                   Changes in version 2.17.1                        

• Temporarily removed the GLAD dependency and CNV functionality

                   Changes in version 2.17.0                        
  

• Fixed bug in differential variability analysis

ROTS

                   Changes in version 1.27.1                        

• Added support for survival analysis

rpx

                     Changes in version 2.7                         

rpx 2.7.4

• Delete entries in default cache before running the unit tests. This assures that the instances matche any updates in the class definition.

rpx 2.7.3

• New px_file_types() and file_types() functions to infer mass spectrometry and proteomics file types based on their extensions.
• New pxSubmissionDate() and pxPublicationDate() accessor functions.

rpx 2.7.2

• Deprecation warning: PXDataset class/methods and PXDataset1() constructor.

rpx 2.7.1

• Don’t rely on a PRIDE project’s README.txt files anymore, as it has been discontinued (see issue #21). The files in a project are now listed from the remote ftp directory.

rrvgo

                   Changes in version 1.10.1                        

• Add citation to microPublication Biology

Rsamtools

                    Changes in version 2.16                         

NEW FEATURES

• (v 2.15.1) sortBam() gains support for sorting by tag (byTag) and using multiple threads (nThreads). (See https://github.com/Bioconductor/Rsamtools/issues/46. ; kriemo)

RTCGAToolbox

                   Changes in version 2.30.0                        

New features

• Include additional options for miRNASeqGeneType and RNAseq2Norm inputs, see ?getFirehoseData.
• The functions getCNGECorrelation, getDiffExpressedGenes, and getSurvival have been defunct and removed from the package (see ?’RTCGAToolbox-defunct’).
• The RNAseq2Norm argument in getFirehoseData allows additional options: “RSEM_normalized_log2”, “raw_counts”, “scaled_estimate” from the ‘preprocessed’ tarballs in Firehose. The “normalized_counts” default remains.

Bug fixes and minor improvements

• getFirehoseData when used with the miRNASeqGene argument was downloading read counts data rather than RPM. This has been fixed with the miRNASeqGeneType argument. “read_count” and “cross-mapped” data are still available but must be entered explicitly in miRNASeqGeneType.

S4Arrays

                    Changes in version 1.0.0                        

• First version of the package that is ready for general use.

S4Vectors

                   Changes in version 0.38.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• The RleTricks vignette was converted from Rnw to Rmd (thanks to Beryl Kanali and Jen Wokaty for this conversion).

BUG FIXES

• Improve support of DFrame objects with S3-typed columns (commit 3b83d5f).

• Fix bug in internal helper bindROWS2() (commit 05cfd3c).

SAIGEgds

                    Changes in version 2.0.0                        

NEW FEATURES

• New features to use sparse genetic relationship matrix in generalized linear mixed models (GLMMs) according to the SAIGE-GENE paper (Zhou et al., 2020)

• a new argument ‘grm.mat’ in seqFitNullGLMM_SPA(): the dense or sparse genetic relationship matrix (GRM) can be specified via ‘grm.mat’

• MAC categories for multiple variance ratios in seqFitNullGLMM_SPA(), seqAssocGLMM_SPA(), designed for rare variants

• new function seqAssocGLMM_SKAT() for the SKAT aggregate method

• new feature seqAssocGLMM_ACAT_O() to include the SKAT aggregate method for full ACAT-O tests

• faster seqSAIGE_LoadPval() when merging multiple input files

                   Changes in version 1.12.4                        
  

• fix the compiling issue on ARM64 (see https://github.com/AbbVie-ComputationalGenomics/SAIGEgds/issues/8)

                   Changes in version 1.12.1                        
  

• fix the memory issue because of using deprecated tbb::task_scheduler_init in RcppParallel

sangeranalyseR

                    Changes in version 99.1                         

• Base class: SangerReads is designed to store each forward/revers reads.

scAnnotatR

             Changes in version 1.5.3 (2023-03-19)                  

• Added paramter to “train_classifier” and “test_classifier” to set the characters that identify cells as ambiguous.

             Changes in version 1.5.2 (2023-03-05)                  
  

• Automatically include parent classifiers if only a subset of classifires is selected.

             Changes in version 1.5.1 (2023-01-17)                  
  

• Added check to ignore any classifiers / cell types for which genes are missing in the dataset.

SCArray

                    Changes in version 1.8.0                        

• new function scNumSplit()

• update the vignettes

• override S4 functions colsum, rowsum, scale, pmin2, pmax2 for SC_GDSMatrix

• new S4 generic functions row_nnzero(), col_nnzero(), scGetFiles(), scMemory(), scRowMeanVar(), scColMeanVar()

• new functions scSetMax(), scSetMin(), scSetBounds(), scReplaceNA()

• update S4 functions [, [[, names<-, dimnames<-, aperm, Ops, Math, crossprod, tcrossprod for SC_GDSArray

• override S4 functions rowSums, colSums, rowSums2, colSums2, rowProds, colProds, rowMeans, colMeans, rowMeans2, colMeans2, rowVars, colVars, rowSds, colSds, rowMins, colMins, rowMaxs, colMaxs, rowRanges, colRanges, rowAnyNAs, colAnyNAs, rowCollapse, colCollapse for SC_GDSMatrix

SCArray.sat

                   Changes in version 0.99.0                        

• initial version of SCArray.sat

scater

                   Changes in version 1.28.0                        

• Change exprs_values (and similar) to assay.type.

• Tweak colouring of violin plots.

• Fix use of block arguments in plotGroupedHeatmap.

• Add scattermore and binning support to various plots (eg plotReducedDim).

• swap_rownames works in retrieveCellInfo for altExp now as well as in the main assay.

• Add point_shape argument to plotDots and plotPlatePosition.

scBubbletree

                    Changes in version 1.1.8                        

• Manhattan distance metric implemented

• other linkage functions for clustering implemented

• tracking timestamps for clustering, bubbletree construction, end

scDblFinder

            Changes in version 1.13.10 (2023-03-23)                 

• fixed serializing error in multithreading large single samples

• computed thresholds now reported in metadata

             Changes in version 1.13.7 (2023-01-09)                 
  

• added possibility to provide the genes/features to use, updated docs

             Changes in version 1.13.4 (2022-11-21)                 
  

• fixed bug in samples reporting in split mode (doesn’t affect doublets scores)

             Changes in version 1.13.3 (2022-11-20)                 
  

• updated default parameters according to https://arxiv.org/abs/2211.00772

             Changes in version 1.13.2 (2022-11-11)                 
  

• added two-pass mode for feature aggregation

scp

                     Changes in version 1.9                         

scp 1.9.2

• Updated citation

scp 1.9.1

• Fix minor typo in readSCP() man page

scp 1.9.0

• New Bioconductor 3.17 (devel) release

scran

                    Changes in version 1.28                         

• Added a restricted= option to quickSubCluster() to enable subclustering on specific clusters.

scReClassify

                    Changes in version 1.5.1                        

• Bug fixes: handling celltypes with 1 cell in multiAdaSampling function

• Clarification in multiAdaSampling documentation for parameter label.

                    Changes in version 1.5.0                        
  

• Bioconductor 3.16 release

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.

                    Changes in version 1.0.0                        
  

• New package screenCounter, containing the barcode counting utilities previously in gp.sa.screen.

scRNAseqApp

                    Changes in version 1.1.1                        

• Fix the bug that coverage function is not imported.

                   Changes in version 0.99.27                       
  

• Fix the subtitles for scATACseq data.

                   Changes in version 0.99.25                       
  

• Fix a typo when fixing the chromsome name style for scATACseq data.

                   Changes in version 0.99.24                       
  

• Add tracks for scATACseq data.

                   Changes in version 0.99.23                       
  

• Add title for ATAC plot buttons.

                   Changes in version 0.99.22                       
  

• Fix the issue if there is no reference.

                   Changes in version 0.99.21                       
  

• Fix the typo for createDataset function.

                   Changes in version 0.99.20                       
  

• Add zoom in and out for atac track plots.

                   Changes in version 0.99.19                       
  

• Update the atac track plots.

                   Changes in version 0.99.18                       
  

• Simplify the about module.

                   Changes in version 0.99.17                       
  

• Update documentation for cellgene VIP.

                   Changes in version 0.99.16                       
  

• fix the bug for cell index for waffleplot.

                   Changes in version 0.99.15                       
  

• fix the bug if no reference can be retrieved.

                   Changes in version 0.99.14                       
  

• fix the bug if no markers can be detected.

                   Changes in version 0.99.13                       
  

• remove aes_string.

                   Changes in version 0.99.12                       
  

• fix the dropdown names issue.

                   Changes in version 0.99.11                       
  

• add check/uncheck all to subset cells.

                   Changes in version 0.99.10                       
  

• fix the multiple loading.

                   Changes in version 0.99.9                        
  

• fix the long table in vignette.

                   Changes in version 0.99.8                        
  

• add app_path to app to fix the issue of missing files.

                   Changes in version 0.99.6                        
  

• add ATAC plots.

                   Changes in version 0.99.5                        
  

• Update R version dependency from 4.2.0 to 4.3.0

• remove ‘CellChat’, ‘monocle3’ and ‘SeuratWrappers’.

• re-organize the files in extdata to script and add documentation.

• remove the eval=FALSE in vignettes and add publish_folder to scripts.

• change the parameter of cat to category for helper1 function.

• remove suppressWarnings/Messages.

• re-format the code style to fit 80 line width and 4 spaces for line indents.

• add function to save ATAC peaks.

                   Changes in version 0.99.4                        
  

• Update documentation.

                   Changes in version 0.99.3                        
  

• Fix the heatmap donwload button.

                   Changes in version 0.99.2                        
  

• Fix multiple notes.

                   Changes in version 0.99.1                        
  

• Prepare for release.

scuttle

                    Changes in version 1.10                         

• .subset2index now converts factor inputs to character vectors, rather than treating them as integers.

seq.hotSPOT

                   Changes in version 0.99.6                        

• Submitted to Bioconductor

seqArchRplus

                  Changes in version 0.99.0.10                      

New

• (User-facing) An alternative function to plot motif heatmaps using the R pkg seqPattern. Function name: plot_motif_heatmaps2()

                  Changes in version 0.99.0.7                       
  

New

• (User-facing) Now possible to perform per cluster GO term enrichment analysis via per_cluster_go_term_enrichments() when a orgDb package is available for the organism

                  Changes in version 0.99.0.6                       
  

New

• (User-facing) Examples added majority of functions using example/dummy data

                  Changes in version 0.99.0.5                       
  

Bug-fixes

• (User-facing) In per_cluster_annotations():
• Default for clusts set to NULL. This enables cleanly specifying just the BED file as input to tc_gr

• Help pages now have examples except for the curate_clusters function. Elaborate documentation for this function is available as part of the vignette

                  Changes in version 0.99.0.4                       
  

New features

• (User-facing) In write_seqArchR_cluster_track_bed():
• new argument use_q_bound to choose if you wish to use quantiles as tag cluster boundaries
• new argument use_as_names to specify any column in info_df to be used as the name column in the output track BED file of clusters
• dominant_ctss information for each tag cluster is presented as thickStart thickEnd for ease of visualising. See documentation for more details
• (User-facing) In per_cluster_annotations():
• tc_gr can now accept a bedfile to read records as a GRanges object

• Details added in documentation for ways to selectively pick clusters to annotate

                  Changes in version 0.99.0.3                       
  

Bux-fixes

• Fixed bugs in curate_clusters() function, and touch up its documentation

                  Changes in version 0.99.0.2                       
  

New features

• (User-facing) Parallelization support to speed up annotating genomic regions

                   Changes in version 0.99.0                        
  

New

• Package ready for Bioconductor submission

SeqArray

                   Changes in version 1.40.0                        

• fix the compiler warning: sprintf is deprecated

SGCP

             Changes in version 0.99.0 (2022-10-06)                 

• The first version 0.99.0 is submitted to Bioconductor

ShortRead

                    Changes in version 1.58                         

BUG FIXES

• (v 1.57.1, 1.56.1) avoid integer overflow in countFastq() https://github.com/Bioconductor/ShortRead/issues/10

signeR

                    Changes in version 2.1.1                        

• Fixed doc issues

• Fixed cpp issues

signifinder

                    Changes in version 1.1.1                        

• 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.

SimBu

             Changes in version 1.1.2 (2023-01-12)                  

• Bugfix in the dataset_seurat function, where custom names for the parameters cell_id_col and cell_type_col did not work (thanks to @orange-whale for bringing this up)

• Changed default remove_bias_in_counts parameter of function simulate_bulk to FALSE after discussion with @ZheFrench

             Changes in version 1.1.1 (2022-11-02)                  
  

• Bugfix in mirror_db scenario, where cell type fractions were not correctly annotated in the cell_fraction output (thanks to @arielah for helping out here)

simplifyEnrichment

                    Changes in version 1.9.1                        

• term_similarity_from_gmt(): previously forgot to split rows.

singleCellTK

             Changes in version 2.8.1 (2022-03-10)                  

• Added scanpy wrapper functions for use from console
• Added scanpy UI curated workflow
• Integrated scanpy to a la carte workflow
• Fixed a bug in importing fluidigm dataset
• Updated downloading features in the Shiny app
• Added error checking around Enrichr functions
• Minor tweaks to plot defaults

SiPSiC

                   Changes in version 0.99.2                        

• Removing files LICENCE and tar.gz off the package to meet Bioconductor package requirements

SNPRelate

                   Changes in version 1.34.0                        

• fix the compiler warning: sprintf is deprecated

SparseArray

                    Changes in version 1.0.0                        

• First version of the package that is ready for general use.

spaSim

                    Changes in version 1.1.2                        

BUG FIXES

• Fixed documentation of argument jitter in TIS() and simulate_background_cells().

• Fixed incorrectly plotted image in README.

                    Changes in version 1.1.1                        
  

SIGIFICANT USER CHANGE

• simulate_background_cells() added an option (method = “Even”) to simulate evenly spaced background images. This change is accompanied with addition of two parameters, method - to choose the background cell distribution and jitter

• the parameter to simulate evenly spaced background cells. Tutorials and function TIS() were modified accordingly.

SpatialExperiment

             Changes in version 1.9.5 (2023-03-02)                  

• bugfix for tissue positions read in incorrect order with read10xVisium() in datasets with multiple samples (bug introduced in version 1.7.1)

SpatialFeatureExperiment

                    Changes in version 1.1.6                        

• Read images as SpatRaster, in read10xVisiumSFE
• read10xVisiumSFE can also convert full resolution image pixels to microns based on Visium spot spacing
• read10xVisiumSFE no longer transposes output from read10xVisium so the spots would match the image by default, and to be consistent with SpatialExperiment
• Read standard Vizgen MERFISH output with readVizgen
• SpatRasterImage class inheriting from VirtualSpatialImage for SpatialExperiment compatibility
• Methods of addImg, mirrorImg, and transposeImg for SpatRasterImage and SFE
• Mirror and transpose SFE objects, operating on both geometries and images
• Images are cropped when the SFE object is cropped

• Images are also shifted when removeEmptySpace is called

                    Changes in version 1.1.4                        
  

• Store SFE package version in object and added SFE method of updateObject to pave way for a potential reimplementation of spatialGraphs.

                    Changes in version 1.1.3                        
  

• Use BiocNeighbors for k nearest neighbors and distance based neighbors, preserving distance info to avoid slow step to refind distances with sf as done in spdep.

• Added swap_rownames argument in localResult(s) getters so gene symbols from any rowData column can be used to get local results stored under Ensembl IDs.

                    Changes in version 1.0.3                        
  

• Correctly move the geometries when there are multiple samples
• Use translate = FALSE when using localResult setter for geometries

• More helpful error messages when geometries, localResult, or spatial graphs are absent

                    Changes in version 1.0.2                        
  

• Correctly move spatialCoords in removeEmptySpace
• Preserve rownames when setting colGeometry for some of all samples

spatialHeatmap

             Changes in version 2.5.4 (2023-04-14)                  

• Developed the SPHM class for storing aSVG, bulk data, single-cell data, and matching list.

• Spatial Enrichement: outlier spatial featuers in references are supported.

• Shiny App: added K-means clustering, functional enrichment, and cluster downloading, redesigned Data Mining and Spatial Enrichment.

• Updated data structures in the background (R functions, Shiny App), and data pre-processing steps in SHM.

• Co-visualization: developed a new feature of coloring each cell by its own value of a chosen biomolecule; developed a new feature of co-visualizing bulk and spatially resolved single-cell data; developed a new feature of visualizing deconvolution results.

SpatialOmicsOverlay

             Changes in version 0.99.0 (2022-04-01)                 

• Submitted to Bioconductor

speckle

                   Changes in version 0.99.7                        

• Added convertDataToList() to allow propeller to work with any proportions data
• Added unit tests
• Added minor changes for Bioconductor submission

• Update vignette to include example of analysing proportions data directly

                   Changes in version 0.99.0                        
  

• remove classifySex functions in preparation for submission to Bioconductor

• speckle only contains propeller functions

                    Changes in version 0.0.3                        
  

• Added functions to classify cells as male or female

• Change propeller transform default to logit

                    Changes in version 0.0.2                        
  

• Added functions to plot the mean variance relationship of the cell type counts and proportions
• Added functions to estimate parameters of a Beta distribution

• Added logit transformation option to propeller

                    Changes in version 0.0.1                        
  

• First version of the speckle package contains propeller functions to test for differences in cell type composition between groups of samples in single cell RNA-Seq data

Spectra

                     Changes in version 1.9                         

Changes in 1.9.15

• Fix issue in MsBackendMemory failed to return intensity or m/z values when peaks data is empty.
• Fix bug in filterPrecursorScan() (see #194 and PR #277).

Changes in 1.9.14

• Fix issue with filterMzValues that would only keep (or remove) the first matching peak instead of all matching peaks (given ppm and tolerance). Issue #274.
• Add parameter keep to filterMzRange to support keeping or removing matching peaks.

Changes in 1.9.13

• Add the backendBpparam method that allows to evaluate whether a MsBackend supports the provided (or the default) BiocParallel-based parallel processing setup.
• Minor tweaks in the internal .peaksapply function to avoid splitting/merging of data if not needed (e.g. if no parallel processing is performed).
• Minor tweaks in spectra comparison functions to avoid repeated calling of functions in loops.

Changes in 1.9.12

• Extend the list of available MsBackend backends provided by other packages (in the README and in the package vignette).

Changes in 1.9.11

• Fix headers in MsBackend vignette.

Changes in 1.9.10

• Add supportsSetBackend method for MsBackend to specify whether a backend supports setBackend,Spectra.
• setBackend checks using supportsSetBackend whether a backend supports setBackend.

Changes in 1.9.9

• Refactor setBackend to only split and merge backends if necessary and to not change dataOrigin of the original backend.
• Support setBackend with MsBackendMemory for an empty Spectra object (issue #268).
• Disable automatic detection of peak variables for MsBackendMemory (issue #269).
• Fix issue in Spectra with empty character (issue #267).

Changes in 1.9.8

• Address comments from Michele Stravs regarding the MsBackend vignette.
• Add additional tests checking for MsBackend compliance.

Changes in 1.9.7

• Add a vignette describing how to build a MsBackend from scratch (issue #262).
• Extend unit test suite to evaluate validity of MsBackend implementations.

Changes in 1.9.6

• Replace <= with between calls.

Changes in 1.9.5

• Fix bug in containsMz() when mz isn’t ordered (see #258).

Changes in 1.9.4

• Fix error when extracting spectra variables from a MsBackendMzR of length 0.

Changes in 1.9.3

• Add chunkapply function to split a Spectra into chunks and stepwise apply a function FUN to each.

Changes in 1.9.2

• combineSpectra on Spectra with read-only backends change backend to an MsBackendMemory instead of an MsBackendDataFrame.

Changes in 1.9.1

• Expand documentation on compareSpectra for GNPS-like similarity scoring.

Changes in 1.9.0

• Bioconductor 3.17 developmental version.

SpectralTAD

             Changes in version 1.15.3 (2023-03-07)                 

• SpectralTAD fixed by Kellen: “There was something in the code designed to expand the window if no TADs were detected but it was not working properly. No idea why it just started now.”

• Change example for SpectralTAD_Par(mat_list, chr= chr, labels = labels, cores = 2)

• Update authors, make DESCRIPTION current

SPIAT

                    Changes in version 1.1.6                        

BUG FIXES

• Fixed the mixing score and normalised mixing score calculation. Each reference-reference interaction is now counted once (was treated directional and counted twice) and the fraction of normalised mixing score is fixed.

                    Changes in version 1.1.5                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Return message instead of error when there are no cells of interest present in the image (identify_neighborhoods()).
• Removed the option of manually defining tumour regions in identify_bordering_cells(). Removed parameters n_of_polygons and draw.

NOTES

• Moved the following packages from Imports to Suggestions: graphics, umap, Rtsne, rlang, ComplexHeatmap and elsa. SpatialExperiment requires version >= 1.8.0. Removed xROI.

                    Changes in version 1.1.4                        
  

BUG FIXES

• Fixed error when there are only one cell in the clusters. (identify_neighborhoods()).

                    Changes in version 1.1.3                        
  

BUG FIXES

• The calculation of cell types of interest to All_cells_in_the_structure in calculate_proportions_of_cells_in_structure() was incorrect. Now fixed.

                    Changes in version 1.1.2                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Re-organised the vignettes.

                    Changes in version 1.1.1                        
  

BUG FIXES

• Fix bug when Cell.ID column is missing from the spe_object in identify_neighborhood().

                    Changes in version 1.1.0                        
  

Development version on Bioconductor 3.17.

splatter

             Changes in version 1.24.0 (2022-04-26)                 

• Fixed bugs in splatPopSimulate() where conditional group assignments were incorrect when batch effects were applied (from Christina Azodi)

• Reduced core dependencies by importing scuttle rather than scater (scater is suggested) and making ggplot2 a suggested dependency.

SpliceWiz

             Changes in version 1.1.8 (2023-04-17)                  

• Users will no longer need to specify separate folders for processBAM and collateData output. Instead, using the GUI, processBAM will output to the pbOutput subdirectory inside the specified NxtSE folder

• Buttons in the Experiment creation and loading interfaces have been streamlined

• Users can select and de-select events using lasso / box / click select tools in volcano and scatter plots (previously only select was possible for all except click)

• A unified event filtering interface has been implemented for all visualizations

• A new system for creating coverage plots has been implemented. Coverage plots are now created in a 3-step process: getCoverageData (to get coverage data!), getPlotObject (customizes data for ASE event normalization and per condition), and plotView (which actually generates the plot). This system makes it easier to refine plots without having to fetch data from the disk everytime.

• All GUI visualization can now be exported directly as pdf files

• Added internal functions to NxtSE object - row_gr() fetches EventRegion GRanges for each ASE

             Changes in version 1.1.7 (2023-03-27)                  
  

• Bugfix: t-test track plots as zero any non-finite p-values (arises when all normalized coverages are the same value)

• Bugfix: BAM2COV uses correct number of threads now

• Bugfix: fixed duplicate junc_* elements on rbind of NxtSE objects

• Feature: Add abs_deltaPSI as a column in differential analysis result (absolute value of delta-PSI)

• Feature: GO interactive plot now displays more information

• Feature: faster retrieval of makeMatrix and makeMeanPSI functions

• Feature: makeSE() now gives more verbose loading information

• Feature: improved performance in getCoverageBins()

• Feature: faster retrieval from Ensembl FTP (using rvest instead of XML)

• Feature: slight performance optimization of plotCoverage

             Changes in version 1.1.6 (2023-02-24)                  
  

• Gene ontology analysis is available! This is implemented via a wrapper to fgsea’s fora() function (over-representation analysis)

• plotCoverage improved - now exons are plotted at higher resolution, and can be plotted in isolation (i.e., by removing intronic regions) using static plots (via as_ggplot_cov()). Further plotCoverage improvements:

• better hover-info for plotly-based events

• unstranded coverage now displays unstranded junction counts

• fixed display of novel transcripts to only display those that are supported by junction counts in the display data. All annotated transcripts are still shown

• other miscellaneous bugfixes

• collateData’s output is improved. Temporary output files are removed, the reference is compressed, allowing for lower storage footprint. This facilitates file transfer among collaborators. Additionally, COV files can be copied into the NxtSE folder for file-transfer purposes

• Novel splicing - (optionally) tandem junctions can now be extrapolated from the data. Given known exons and observed junctions, “putative tandem junctions” are included among observed tandem junctions, during novel splicing event generation. This allows for better identification, especially for novel casette exon skipping.

• Introduced StrictAltSS filter - this removes A5SS/A3SS events for which the two alternate splice sites are separated by an observed intron.

• Integrated GO analysis into GUI. Heatmaps and event lists in COV can now be subsetted by top gene ontology categories. GO analysis must first be performed prior to this option being available.

• Incompatibilities with prior versions:

• buildRef in 1.1.6 now generates gene ontology annotation.

• collateData output is incompatible with prior versions

• processBAM output remains largely unchanged compared with 1.1.5

• NxtSE objects are incompatible with that of prior versions

             Changes in version 1.1.5 (2022-12-20)                  
  

• Fix vignettes not building

             Changes in version 1.1.3 (2022-12-18)                  
  

• Improved performance of SpliceWiz processBAM() in multi-sample setting

• Fixed memory leak in processBAM and BAM2COV functions

• Added edgeR-based differential ASE wrappers, including ability to construct custom model matrices to model complex experimental designs.

• Overhauled STAR wrappers, added functions to allow STAR genome reference to be generated (without GTF). A temporary STAR genome can be subsequently derived by supplying a SpliceWiz reference containing the requisite GTF file.

• Included more tandem junctions into novel splicing reference (will find more novel splicing events compared with versions <=1.1.2)

• collateData’s lowMemoryMode will now cap usage to 4 threads (instead of 1), which is expected to limit RAM usage to ~ 16-20 Gb, depending on genome size and whether novel splicing mode is on/off. To use even less memory, consider

• Slightly improved runtimes of buildRef and collateData functions

• collateData is now single-threaded on Windows (as MulticoreParam is not available)

             Changes in version 1.1.2 (2022-11-08)                  
  

• Implemented time series analysis in limma using splines

• Reduced loading time of makeSE’s overlapping intron removal

• Optimised H5 database chunking to speed up data loading times

• Added installation instructions for SpliceWiz using conda environment

• Bugfix: resolved mismatched chromosome issues in collateData

• Bugfix: fixed novel splice counts filtering

• Bugfix: Depth calculation in collateData fixed to properly reflect maximum splicing across junction

• Bugfix: Fixed plotCoverage / plotGenome by coordinates

SpotClean

                    Changes in version 1.1.2                        

• Fixed a bug in vignettes for column sum on sparse matrix.

                    Changes in version 1.0.1                        
  

• Fixed a bug due to updated slots in SpatialExperiment objects

standR

                    Changes in version 1.3.9                        

• Add function prepareSpatialDecon to help using R package SpatialDecon after using standR to preprocess GeoMx data.

• New RUV-4: now using the RUV-4 from standR allow you to perform rank-based analysis such as gene-set scoring with the RUV-4-normalised count.

• New vignette - A quick start guide to the standR package.

• Many bugs fixed.

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

                   Changes in version 1.29.4                        
  

• Remove the GUI

• Remove the QCRLSC

stJoincount

                    Changes in version 1.1.1                        

• Update description and introduction

SummarizedExperiment

                   Changes in version 1.30.0                        

DEPRECATED AND DEFUNCT

• Finally remove readKallisto() (got deprecated in BioC 3.12 and defunct in BioC 3.15).

surfaltr

             Changes in version 1.5.1 (2022-08-12)                  

• Fixed warning

SVMDO

            Changes in version 0.99.24 (2023-04-22)                 

• Fixing problems in NEWS file invisibility

            Changes in version 0.99.23 (2023-04-18)                 
  

• Acceptance of package for nightly devel build by Bioconductor

             Changes in version 0.99.0 (2022-12-29)                 
  

• Sending reopen request for bioconductor submission of updated package

• Reopening of package submission issue

synapsis

           Changes in version 2021-07-02 (2021-07-02)               

Changes:

• Added this news file

SynExtend

                   Changes in version 1.11.8                        

• Fixes various small bugs in MoransI
• Adds some multiprocessing support (more will be added in the future)
• Slight rework to species trees and their interaction with ProtWeaver objects
• ProtWeaver has new attribute speciesTree, can be initialized with a dendrogram object
• New method SpeciesTree to get species tree from a ProtWeaver object (or compute one, if it doesn’t exist)
• Various internal improvements for Bioc style consistency

• Various documentation updates

                   Changes in version 1.11.7                        
  

• Adds new optimized dendrapply implementation (overloads stats::dendrapply)
• AddsHungarianAlgorithm for optimal solving of the linear assignment problem (O(n^3) complexity)
• Adds new C code for fast computation of Pearson’s R and p-value
• Adds new Ancestral.ProtWeaver algorithm for calculating coevolution from correlated residue changes
• Supporting code and documentation for Ancestral.ProtWeaver
• Other new internal methods
• Various updates and optimizations to internal methods and documentations
• Updates GRF method to be called CI (for Clustering Information Distance)

• Method=”CI” in PhyloDistance now calculates an approximate p-value using simulated data from Smith (2020)

                   Changes in version 1.11.6                        
  

• Adds new Residue method NVDT using gene sequence Natural Vector with Dinucleotide and Trinucleotide frequency
• Adds some new C methods to speed up calculation of NVDT
• Fixes .Call() not using PACKAGE=”SynExtend”

• Updates to documentation

                   Changes in version 1.11.5                        
  

• Adds new colocalization algorithm ColocMoran, uses Coloc with MoransI to correct for phylogenetic signal
• Adds new colocalization algorithm TranscripMI, uses mutual information of transcriptional direction
• Adds new corrections/checks to allow for transcriptional direction to be in labels
• Various bugfixes to support new four number labelling scheme
• Various documentation updates

• Adds new function MoransI to calculate Moran’s I for a set of spatially distributed signals

                   Changes in version 1.11.4                        
  

• Internal code refactor
• ShuffleC now supports reproducibility using R’s set.seed

• ShuffleC now support sampling with replacement, performance is around 2.25x faster than sample

                   Changes in version 1.11.3                        
  

• Internal bugfixes for JRF Distance–previous commit was incorrectly calculating values
• Adds new TreeDistance predictor for ProtWeaver, incorporating all tree distance metrics; these metrics are bundled due to some backend optimizations that improve performance
• Bugfixes for PhyloDistance
• Adds Random Projection for MirrorTree predictor to solve memory problems and increase accuracy
• New internal random number generator using xorshift, significantly faster than sample()
• HammingGL changed to CorrGL, now uses Pearson’s R weighted by p-value
• Refactors internal predictors to reduce size of codebase and remove redundancies
• Internal ShuffleC function to replicate sample functionality with 2-6x speedup
• Method GainLoss now uses bootstrapping to estimate a p-value

• Updates to documentation files

                   Changes in version 1.11.2                        
  

• Adds KF Distance for trees
• Adds Jaccard Robinson Foulds Distance for trees
• Reworks tree distances into PhyloDistance function
• Numerous new documentation pages

• Updates internal functions to use rapply instead of dendrapply to avoid stack overflow issues due to R recursion

                   Changes in version 1.11.1                        
  

• Minor bugfix to RF distance

• updates gitignore for workflows

                   Changes in version 1.10.1                        
  

• Memory leak bugfix

synlet

                   Changes in version 1.99.0                        

NEW FEATURES

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

• Drop doBy, reshape2, dplyr dependency.

• Added data.table support.

syntenet

                    Changes in version 1.1.6                        

BUG FIXES

• Added a check for which IQ-TREE version is installed. If IQ-TREE2 is installed (and not IQ-TREE), arguments and call are modified accordingly, because IQ-TREE developers changed some parameters (e.g., -bb is now -B).

NEW FEATURES

• Added a parameter as to parse_collinearity() that allows the extraction on synteny block information from .collinearity files. The vignette was updated accordingly.

                    Changes in version 1.1.5                        
  

BUG FIXES

• Fixed species ID retrieval by adding an exported function named create_species_id_table() that correctly creates unique species IDs (3-5 characters), even when the first 5 characters are equal.

• intraspecies_synteny() and interspecies_synteny() (originally unexported) now take the same output of process_input(), which makes them consistent with the entire package.

NEW FEATURES

• To make it easier for users who want to run DIAMOND from the command line, I added the functions export_sequences() and read_diamond(), which write processed sequences to FASTA files and read the DIAMOND output, respectively. An example code on how to run DIAMOND from the command line has been added to the vignette.

• Included a section in the vignette on how to use syntenet as a synteny detection program (i.e., to find synteny within a single genome or between two genomes).

                    Changes in version 1.1.4                        
  

BUG FIXES

• Replaced sprintf calls with snprintf calls in C++ code to address warnings in the devel branch of Bioc

UPDATES

• Added CITATION file with reference to published paper

                    Changes in version 1.1.3                        
  

BUG FIXES

• Tidy evaluation with aes_() was deprecated in ggplot 3.0.0, and testthat now returns warnings for it. Replaced aes_() with aes() and .data from the rlang package.

                    Changes in version 1.1.2                        
  

NEW FEATURES

• Added parameters clust_function and clust_params in cluster_network() to let users pass any igraph::cluster_* function to cluster the synteny network.

• Added parameters clust_function and clust_params in plot_profiles() to let users have more control on the method used to cluster the distance matrix (columns in phylogenomic profiles).

• Updated vignette to reflect the changes mentioned above and included an FAQ item with instructions on how to update the R PATH variable.

                    Changes in version 1.1.1                        
  

NEW FEATURES

• Ward’s clustering of synteny clusters is now performed prior to plotting in plot_profiles(), not in phylogenomic_profile(). As a consequence, phylogenomic_profile() now returns only a matrix of profiles, not a list containing the matrix and an hclust object.

• Added an option to handle names in vector cluster_species as new names for display in the heatmap. This way, species abbreviations can be easily replaced with species’ full names to make plots look better.

• Added parameters dist_function and dist_params to allow users to specify function and parameters to calculate the distance matrix that will be passed to Ward’s clustering.

systemPipeShiny

                   Changes in version 1.9.04                        

Major Change

• Add video tutorials to main page and all modules.

Minor Change

• Replace the major icons on welcome page, now it has 3 circles instead of 3, reflecting the 3 major functionalities of SPS, workflow, visualization, and canvas.
• Changed some namings in workflow creation options
• empty: Start from scratch
• existing: upload custom workflows

Bug Fix

• Fix FontAwesome 6.0 introduced name changes

• One would also need to install develop version of spsComps and drawer.

• Fix not working tab link on welcome page.

• Fix empty icon problems.

• Fix bug where RNAseq module is always disabled

TargetSearch

                    Changes in version 2.2.0                        

BUG FIXES

• C code: Refactor the function get_line due to failures in files with CR line terminators, commonly found in MacOS systems.

TBSignatureProfiler

                   Changes in version 1.92.0                        

Bug Fixes

• Fixed the tableAUC bootstrapped confidence interval to be the 2.5 and 97.5 percentiles instead of the 5 and 95 percentiles
• Fixed the upper CI value for the pROC/DeLong AUC CI method in the bootstrapAUC function

Major Changes

• Changed tableAUC confidence interval default to bootstrapped instead of DeLong (pROC argument)

Minor Changes

• Updated the github and website introductions.
• Added Natarajan_7, Kaul_3 signatures
• Added Francisco_OD_2, Kwan_186 signatures
• Shortened some example run times

TCGAutils

                   Changes in version 1.20.0                        

New features

• makeSummarizedExperimentFromGISTIC and splitAssays are now defunct.

TDbasedUFE

                   Changes in version 0.99.7                        

• Bugfix

• selectFeaureVectorLarge,selectFeaureVectorSmall

                    Changes in version 0.1.0                        
  

• Replacing menu with shiny and spell check
• Added a NEWS.md file to track changes to the package.

TDbasedUFEadv

            Changes in version 0.99.21 (2023-04-14)                 

• Correction to DESCRIPTION:

• Correct wrong format of DESCRIPTION

            Changes in version 0.99.20 (2023-04-12)                 
  

• Correction to DESCRIPTION:

• modify DESCRIPTION so as to be disrtnct from the previous packpage, TDbasedUFE

            Changes in version 0.99.19 (2023-03-28)                 
  

• Addressing reviews comments:

• Removing some “«-“s in test.

            Changes in version 0.99.18 (2023-03-27)                 
  

• Addressing reviews comments:

• Fragmenting testthat toward individual functions

            Changes in version 0.99.17 (2023-03-25)                 
  

• Addressing reviews comments:
• Replace as.integer with L
• Add link to TDbasedUFE in vignettes

• Correct testthat (with using test_that())

            Changes in version 0.99.16 (2023-03-23)                 
  

• Addressing reviews comments:
• Renaming class
• Removing one “for” loop
• Adding comment to GUI

• Adding explanation of data in inst/extdata

            Changes in version 0.99.15 (2023-03-21)                 
  

• Addressing reviews comments:
• Adding argument check
• adding test functions
• Rename and merge vignettes
• and so on

TENxIO

                    Changes in version 1.2.0                        

New features

• TENxTSV class has been added to handle compressed and uncompressed TSV files.

Bug fixes and minor improvements

• The import method for TENxFileList was returning a nested SummarizedExperiment within the SingleCellExperiment. The counts and assay(…, i=”counts”) methods should only return the bare Matrix rather than the embedded SummarizedExperiment (@dgastn, #2).

terraTCGAdata

                    Changes in version 1.4.0                        

New features

• findTCGAworkspaces is defunct. Use selectTCGAworkspace instead.

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.

             Changes in version 1.3.2 (2022-11-29)                  
  

• Updated tomo-seq data from Junker et al., 2014.

TPP

                   Changes in version 3.27.1                        

• Fixed bugs and warnings after dplyr update

trackViewer

                   Changes in version 1.35.5                        

• use straw for hic import.

                   Changes in version 1.35.4                        
  

• handel label.parameter.draw for labels.

                   Changes in version 1.35.3                        
  

• Add documentation for selected labels for mutations.

                   Changes in version 1.35.2                        
  

• Add support for node label parameters.

                   Changes in version 1.35.1                        
  

• Add support for single resolution cooler file.

treeio

                   Changes in version 1.23.1                        

• supports converting dendro object (output of ggdendro::dendro_data()) to a phylo object (2023-03-02, Thu, #95)
• add inner_join() method to allows appending data of a variable
• use nested data structure and tidyr::unnest can extract and convert the data to a simple tibble data frame (#93)
• update full_join method (#92)
• support standard dplyr UI of by = c( ‘columnX’ = ‘cloumnY’)
• drop data from external data.frame that are not presented in the tree
• use nested column if duplicated rows exist

tRNA

             Changes in version 1.17.1 (2022-12-19)                 

• bugfix for gettRNAstructureSeqs

tximeta

                   Changes in version 1.17.2                        

• Up to GENCODE 43 (H.s.), M32 (M.m), and Ensembl 109

tximport

                   Changes in version 1.27.1                        

• Changing license from GPL to LGPL.

UniProt.ws

                   Changes in version 2.40.0                        

USER VISIBLE CHANGES

• Convert vignette from RSweave to web-based RMarkdown

BUG FIXES AND MINOR IMPROVEMENTS

• Increase fault tolerance of unit tests
• Add examples to mapUniProt documentation

universalmotif

                   Changes in version 1.18.0                        

NEW FEATURES

• read_meme(readsites.meta.tidy): New option to tidy the output of the readsites.meta option into a single data.frame.

MINOR CHANGES

• create_motif(): More robust argument checking.

• The rowMeans, colMeans, rowSums, and colSums generics are now imported from the MatrixGenerics package instead of BiocGenerics.

BUG FIXES

• Clean up output of argument checks internal to exported functions.

• Delete a reference in IntroductionToSequenceMotifs vignette to a non-exported function.

• Delete outdated in MotifManipulation vignette regarding convert_motifs function.

updateObject

                    Changes in version 1.4.0                        

• No changes in this version.

variancePartition

                   Changes in version 1.28.9                        

• March 14, 2023
• fix rounding error in makeContrastsDream()

• add Pearson residuals to residuals()

                   Changes in version 1.28.8                        
  

• March 8, 2023

• add mvTest() with features as list

                   Changes in version 1.28.7                        
  

• March 7, 2023

• Fix bug in makeContrastsDream() by adding droplevels()

                   Changes in version 1.28.6                        
  

• March 1, 2023

• diffVar() now fits contrasts estimated in first step

                   Changes in version 1.28.5                        
  

• Feb 24, 2023

• Fix error in vcov() when samples are dropped due to covariate having NA value

                   Changes in version 1.28.4                        
  

• Feb 2, 2023

• Improve documentation for contrasts

                   Changes in version 1.28.3                        
  

• Jan 19, 2023

• Improve checking and documentation for contrasts

                   Changes in version 1.28.2                        
  

• Jan 13, 2023
• canCorPairs() now allows random effects in formula

• but won’t change results

                   Changes in version 1.28.1                        
  

• Jan 04, 2023
• bug fixes

velociraptor

                    Changes in version 1.9.2                        

• Remove column names from reduced dimension matrix in gridVectors().

Voyager

                   Changes in version 1.1.12                        

• Plot image behind geometries in all functions that plot geometries

• Added dark theme support for functions that plot geometries

                   Changes in version 1.1.11                        
  

• Added MULTISPATI PCA
• Added multivariate local Geary’s C from Anselin 2019
• Added calculateMultivariate as a unified user interface to multivariate spatial analyses
• Variogram and variogram map with gstat and related plotting functions

• Allow non-standard names for local results in plotLocalResult

                   Changes in version 1.1.10                        
  

• Record parameters used to get spatial results

• Force users to use a new name when running the same method with different parameters

                    Changes in version 1.1.9                        
  

• Deprecated show_symbol argument, replacing with swap_rownames to be consistent with scater

                    Changes in version 1.1.7                        
  

• Added bbox argument to spatial plotting functions to zoom in with a bounding box

weitrix

                   Changes in version 1.11.1                        

• Don’t import colSums, rowSums, which have disappeared from BiocGenerics.

xcms

                   Changes in version 3.21.5                        

• Fix issue in chromatogram after filtering a result object (issue #511).

                   Changes in version 3.21.4                        
  

• Move multtest from Suggests to Imports in dependencies

                   Changes in version 3.21.3                        
  

• Only fixes in the long running tests

                   Changes in version 3.21.2                        
  

• 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.

                   Changes in version 3.21.1                        
  

• Fix error with fillChromPeaks on sparse data (many empty spectra) and peak detection performed with MatchedFilterParam (issue #653).

• Update to newer function names in the rgl package (issue #654).

zellkonverter

                   Changes in version 1.10.0                        

Major changes

• Add compatibility with the anndata v0.8 H5AD format to the the native R writer (By @jackkamm and @mtmorgan)

• Add functions for converting pandas arrays used by anndata when arrays have missing values

Minor changes

• Add Robrecht Cannoodt and Jack Kamm as contributors!

• Minor adjustments to tests to match reader changes

zenith

                    Changes in version 1.1.2                        

• April 20, 2023

• fix warnings for limma

                    Changes in version 1.1.1                        
  

• fix warnings

                    Changes in version 1.0.7                        
  

• update docs

                    Changes in version 1.0.6                        
  

• in zenith() set inter.gene.cor=0.01 to be default to be consistent with limma::camera

                    Changes in version 1.0.5                        
  

• bug fix in zenith() when progressbar=FALSE

                    Changes in version 1.0.3                        
  

• fix issue with corInGeneSet() when some residuals are NA

                    Changes in version 1.0.2                        
  

• add zenithPR_gsa()

• flag to disable correlation in zenith()

                    Changes in version 1.0.1                        
  

• fixes to Bioconductor

• improve documentation
• get_GeneOntology() uses getGenesets(…,hierarchical=TRUE)

ZygosityPredictor

             Changes in version 0.99.0 (2023-02-22)                 

• Submitted to Bioconductor

NEWS from existing Data Experiment Packages

CoSIAdata

New Package Release

• CoSIAdata includes Variance Stabilized Transformation of Read Counts from Bgee RNA-Seq Expression Data across six species (Homo sapiens, Mus musculus, Rattus norvegicius, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans) and more than 132 tissues. Each species has its own independent data frame with its unique set of tissue and gene specific expression data.

• CoSIAdata is meant to be integrated into the CoSIA Package, a visualization tool for cross species comparison of expression metrics. However, it can be used to conduct independent species, tissue, and gene-specific expression analysis.

curatedTCGAData

                   Changes in version 1.22.0                        

Bug fixes and minor improvements

• When the assays argument was RNASeq2Gene, curatedTCGAData would incorrectly include RNASeq2GeneNorm assays. Users who want to return both assay types should enter RNASeq2Gene* instead (with an asterisk).

gDNAinRNAseqData

                    Changes in version 1.0.0                        

USER VISIBLE CHANGES

• Submission of the first version to the Bioconductor project on March 30th, 2023.

imcdatasets

             Changes in version 1.7.3 (2023-02-26)                  

• Added HochSchulz_2022_Melanoma dataset.

             Changes in version 1.7.2 (2023-02-25)                  
  

• Added IMMUcan_2022_CancerExample dataset.

• Using the IMMUcan_2022_CancerExample dataset in the vignette.

             Changes in version 1.7.1 (2023-01-31)                  
  

• Added full dataset (masks and single cell data) for the JacksonFischer dataset.

• Added “Zurich” cohort for the JacksonFischer dataset.

• Added full datasets (masks and single cell data) for the Damond… dataset.

• Make deprecated functions (DamondPancreas2019Data, JacksonFischer2020Data, and ZanotelliSpheroids2020Data) defunct.

marinerData

                   Changes in version 0.99.0                        

NEW FEATURES

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

SIGNIFICANT USER-VISIBLE CHANGES

• Your main changes to a function foo() or parameter param.

BUG FIXES

• Your bug fixes. See more details at http://bioconductor.org/developers/package-guidelines/#news.

MetaScope

                   Changes in version 0.99.0                        

• Pre-Release version of MetaScope Bug Fixes

• Fixed check error message about data.table::fread for reading .gz files by adding R.utils to imports. Major Changes

• Submitted to Bioconductor Minor Changes

microRNAome

                   Changes in version 1.21.1                        

• Updated microRNAome data to the latest published version (v3) processed with the latest version of miRge.

pRolocdata

                   Changes in version 1.37.1                        

• add data from Moloney et al. (2023)

• update syntax in the author field of description

• remove redundant alias for itzhak2016

                   Changes in version 1.37.0                        
  

• new devel version for Bioc

scMultiome

                   Changes in version 0.99.5                        

NEWS.md setup

• added NEWS.md

SFEData

                    Changes in version 1.2.0                        

• Added seqFISH mouse gastrulation data

• Corrected Xenium dataset format

SingleCellMultiModal

                   Changes in version 1.12.0                        

Bug fixes and minor improvements

• Added Ludwig Geistlinger as author (@lgeistlinger) for contributing the GTseq dataset.

spatialLIBD

                   Changes in version 1.11.13                       

SIGNIFICANT USER-VISIBLE CHANGES

• The vignette now has a section describing the data from the spatialDLFPC, Visium_SPG_AD, and locus-c projects that were done by members of the Keri Martinowich, Kristen R. Maynard, and Leonardo Collado-Torres LIBD teams as well as our collaborators.

                   Changes in version 1.11.12                       
  

SIGNIFICANT USER-VISIBLE CHANGES

• fetch_data(“Visium_SPG_AD_Visium_wholegenome_spe””), fetch_data(“Visium_SPG_AD_Visium_targeted_spe”), fetch_data(“Visium_SPG_AD_Visium_wholegenome_pseudobulk_spe”), and fetch_data(“Visium_SPG_AD_Visium_wholegenome_modeling_results”) have been added. Use this to access data from the https://github.com/LieberInstitute/Visium_SPG_AD project.

                   Changes in version 1.11.11                       
  

SIGNIFICANT USER-VISIBLE CHANGES

• fetch_data(“spatialDLPFC_snRNAseq”) now works if you want to download the snRNA-seq data used in http://research.libd.org/spatialDLPFC/.

                   Changes in version 1.11.10                       
  

BUG FIXES

• read10xVisiumAnalysis() now supports spaceranger version 2023.0208.0 (internal 10x Genomics version) output files that store analysis CSVs under the outs/analysis_csv directory instead of outs/analysis and also use the gene_expression_ prefix for each of the analysis directories. This was tested with @heenadivecha on files from https://github.com/LieberInstitute/spatial_DG_lifespan/blob/main/code/02_build_spe/01_build_spe.R.

                   Changes in version 1.11.9                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• gene_set_enrichment() now internally uses fisher.test(alternative = “greater”) to test for odds ratios greater than 1. Otherwise odds ratios of 0 could be significant.

                   Changes in version 1.11.4                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Several changes were made to the default plotting aspect of vis_gene(), vis_clus() and related plotting functions. This was done with input from @lahuuki and @nick-eagles and is described in more detail at https://github.com/LieberInstitute/spatialLIBD/commit/8fa8459d8fa881d254824d43e52193bf2c3021c0. Most noticeably, the aspect ratio is no longer stretched to fill the plotting area, the NA values will be shown with a light grey that has alpha blending, and the position of the legends has been made consistent between the plots.

                   Changes in version 1.11.3                        
  

NEW FEATURES

• Added the function frame_limits() and introduced the auto_crop argument to vis_clus(), vis_gene() and all related functions. This new function enables automatically cropping the image and thus adjusting the plotting area which is useful in cases where the image is not centered and is not a square. This was based on work by @lahuuki at https://github.com/LieberInstitute/spatialDLPFC/blob/2dfb58db728c86875a86cc7b4999680ba1f34c38/code/analysis/99_spatial_plotting/01_get_frame_limits.R and https://github.com/LieberInstitute/spatialDLPFC/blob/ef2952a5a0098a36b09488ebd5e36a902bb11b48/code/analysis/99_spatial_plotting/vis_gene_crop.R.

NEWS from existing Workflows

seqpac

• Initial Bioconductor submission

Deprecated and Defunct Packages

Thirty two software packages were removed from this release (after being deprecated in Bioc 3.16): AffyCompatible, BAC, BitSeq, BrainSABER, bridge, cellTree, coexnet, conclus, ctgGEM, CytoTree, DEComplexDisease, flowCL, flowUtils, gaia, gpart, inveRsion, IsoGeneGUI, iteremoval, MACPET, PoTRA, rama, Rcade, RNASeqR, scAlign, scMAGeCK, sojourner, TCGAbiolinksGUI, TDARACNE, TimeSeriesExperiment, TraRe, tspair, XCIR

Please note: coMET, previously announced as deprecated in 3.16, has been updated and remain in Bioconductor.

Thirty five software packages are deprecated in this release and will be removed in Bioc 3.18: alpine, ArrayExpressHTS, ASpediaFI, BiocDockerManager, ChIC, chromswitch, copynumber, CopywriteR, dasper, epihet, GAPGOM, gcatest, GeneAccord, genotypeeval, lfa, maanova, metavizr, MethCP, MIGSA, MIMOSA, NanoStringQCPro, NBSplice, netboxr, NxtIRFcore, ODER, pkgDepTools, PrecisionTrialDrawer, proBatch, proFIA, pulsedSilac, savR, sigPathway, STAN, TarSeqQC, tscR

Two experimental data packages were removed from this release (after being deprecated in BioC 3.16): gatingMLData, RNASeqRData

Two experimental data packages are deprecated in this release and will be removed in Bioc 3.18: alpineData, plasFIA

No annotation packages were removed from this release (after being deprecated in Bioc 3.16).

No annotation packages were deprecated in this release and will be removed in Bioc 3.18.

No workflow package was removed from this release (after being deprecated in Bioc 3.16).

No workflow packages were deprecated in this release and will be removed in 3.18.