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.
To update to or install Bioconductor 3.17:
Install R 4.3. Bioconductor 3.17 has been designed expressly for this version of R.
Follow the instructions at Installing Bioconductor.
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.
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.
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.
There are no new annotation 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.
There are no new online books.
Changes in version 2.39.1 (2023-04-14)
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
Changes in version 0.99
AHMassBank 0.99.3
AHMassBanki 0.99.0
Changes in version 1.15.1
Changes in version 4.1.6 (2023-02-16)
Sleep 3 seconds between retrying failed downloads
Changes in version 4.1.5 (2023-02-10)
Bump dplyr dependency version.
Changes in version 4.1.4 (2022-11-08)
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)
Workaround performance issues on BiocParallel::bpmapply() (https://github.com/Bioconductor/BiocParallel/pull/228)
Changes in version 4.1.1 (2022-11-02)
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!
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
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
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
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
Changes in version 1.0.0
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)
Changes in version 1.58.0
Changes in version 1.23.1
Changes in version 1.1.1
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
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
Changes in version 1.12.0
Changes in version 1.16.0
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
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)
Changes in version 2.7
USER VISIBLE CHANGE
BUG FIX
Changes in version 1.0.0
Changes in version 1.0.0
Changes in version 1.10.0
Significant user-visible changes
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
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.
Changes in version 1.14
BUG FIX
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)
Changes in version 1.9.2
BUG FIXES
Changes in version 1.67.0
ENHANCEMENT
(1.67.1) Add biocViews term WorkflowManagement
(1.67.3) Add biocViews term LongRead
Changes in version 1.5.1 (2023-03-22)
Remove R_front script.
Define new field secondary.accessions.
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”)
Changes in version 1.2.1
Changes in version 1.10.0
Changes in version 1.11.1
Changes in version 2.9.2
NEW FEATURES
Updated to BridgeDb 3.0.21
Changes in version 2.9.1
NEW FEATURES
Changes in version 1.0.0
Changes in version 2.6.0
BUG FIXES
NEW FEATURES
Changes in version 3.0.1 (2022-11-14)
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
Changes in version 2.12.0
Bug fixes and minor improvements
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
Changes in version 1.14.2 (2023-01-19)
Changes in version 1.4
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.11.1
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
Changes in version 1.0.0
1st version of the package
Submitted to Bioconductor
Changes in version 3.33.1
update the documentation for enrichment analysis
update the disjointExons to exonicParts for ensembldb
Changes in version 1.35.1
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
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.
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
Changes in version 4.7.1
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
Changes in version 1.3.1
CHANGES
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
Changes in version 1.35.1
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.
Changes in version 1.3
Changes in version 1.3.3
Changes in version 1.3.2
Changes in version 1.3.2
Changes in version 1.3.0
Changes in version 0.99.0
Changes in version 0.99.0
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
Changes in version 1.3.3
Added BiocStyle to Suggests.
Changes in version 1.3.2
Added nuclease MAD.
Changes in version 1.3.2
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).
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.
Changes in version 1.5.1
Changes in version 0.99
CTdata 0.99.0
Changes in version 0.99.3 (2022-11-11)
Cleaned up warning and message statements
Changes in version 0.99.0 (2022-09-13)
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
Changes in version 3.11
API Changes
Fixes/internal changes
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:
compare.counts -> gs_compare_cytobank_counts
Renaming of classes:
flowJoWorkspace -> flowjo_workspace
Fixes/internal changes
Changes in version 0.99
CytoPipeline 0.99.6
CytoPipeline 0.99.5
CytoPipeline 0.99.4
CytoPipeline 0.99.3
CytoPipeline 0.99.2
CytoPipeline 0.99.1
CytoPipeline 0.99.0
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
Changes in version 1.11.1 (2023-03-16)
Changes in version 1.5.2
Changes in version 1.99.3 (2013-07-25)
Updates
A few changes to shearwater vignette
Renamed arguments pi.gene and pi.backgr in makePrior()
Bugfixes
Fixed bug in bf2Vcf() when no variant is called
Changes in version 1.99.2 (2013-07-11)
Updates
Updated CITATION
Added verbose option to bam2R to suppress output
Changed mode() to “integer” for value of loadAllData()
Bugfixes
Fixed bug when only one variant is called in bf2Vcf()
Changes in version 1.99.1 (2013-06-25)
Updates
Using knitr for prettier vignettes
Including shearwater vignette
Bugfixes
fixed issues with deletions in bf2Vcf()
makePrior() adds background on all sites
Changes in version 1.99.0 (2013-04-30)
Updates
New shearwater algorithm
Including VCF output through summary(deepSNV, value=”VCF”)
Changes in version 0.26.0
Changes in version 0.99.1
Changes in version 1.3.1 (2023-04-04)
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.
Changes in version 1.0.0
1st version of the package
submitted to Bioconductor
Changes in version 3.9.4
Rollover bugfixes
add option to return ggplot in dba.plotVolcano
Changes in version 1.3.0
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
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
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.
Changes in version 1.19.2
fix ridgeplot for error when x@readable == TRUE and length(x@gene2Symbol) = 0 (2022-12-5, Mon, #217)
Changes in version 1.19.1
Changes in version 2.23.2
Fix SQLite database names to include also the subspecies.
Changes in version 2.23.1
Remove disjointExons method.
Changes in version 1.3.4
New features
Bug fixes
Fix broken link to example report.
Changes in version 1.3.3
New features
Bug fixes
Change yaml arg peakfile –> peakfiles to be consistent with other variables.
Changes in version 1.3.1
New features
Bug fixes
Changes in version 2.15.0
Changes in version 1.7.2
Fix callPeaks writers so that it works on Windows
Changes in version 1.7.1
Changes in version 1.5.4 (2022-04-05)
CITATION added
Changes in version 1.5.3 (2022-04-04)
plotEpistck’s legends are now also displayed as y-axis title in plotAverageProfile plots
Changes in version 1.5.2 (2022-04-03)
tints now accept palette functions and list of palette functions, in addition to colors.
Changes in version 1.5.1 (2022-03-30)
Changes in version 1.33.1
SIGNIFICANT USER-VISIBLE CHANGES / BUG FIX
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 installation instruction for users whose R version is pre-R4.3
Changes in version 0.99.6
SIGNIFICANT USER-VISIBLE CHANGES
Accepted by Bioconductor and will be released in Bioconductor 3.17
Changes in version 0.99.1
NEW FEATURES
Changes in version 1.7.3
New features
Bug fixes
Add tess/testthat/Rplots.pdf to .gitignore.
Changes in version 1.7.1
New features
Replace all %>% with | > |
Bug fixes
New features
Changes in version 2.7.1
DEPRECATE
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 fitAssayDiff() and added coercion of TopTags objects
Changes in version 1.3.6
Added mergeByHMP() for merging overlapping windows using the harmonic mean p
Changes in version 1.3.5
Bugfix in plotAssayDensities() and plotAssayRle() along with enabling plotting by group
Changes in version 1.3.4
Changes in version 0.99.1
Changes in version 1.25.1
introduced plotEnrichmentData() function for more flexible plotting
update GESECA plot behavior
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.
Changes in version 0.99.3 (2023-03-15)
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
Changes in version 1.13.1 (2023-04-05)
Changes in version 2.0.0
IMPROVEMENTS SINCE LAST RELEASE
BUG FIXES
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
crayon::blurred()
in the display (RStudio blurs the
screen
output) Changes in version 1.27.1
BUGFIXES
Changes in version 2.4.0
New features
Other notes
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.
Changes in version 1.36.0
NEW FEATURES
Add Gossypium_hirsutum.txt to inst/extdata/dataFiles/ (provided by Emory Lucas bararayung123@hotmail.com)
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().
Changes in version 1.36.0
NEW FEATURES
BUG FIXES
Changes in version 1.24.0
Bug fixes and minor improvements
Changes in version 1.52.0
NEW FEATURES
DEPRECATED AND DEFUNCT
BUG FIXES
Changes in version 1.52.0
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 0.99.2
Changes in version 3.7.2
using cli::cli_alert_warning() instead of warning_wrap (2022-11-10, Thu)
Changes in version 3.7.1
Changes in version 1.1.3
autoplot method for ‘ClusterExperiment’ object (2022-11-28, Mon)
Changes in version 1.1.2
set default options to align geom_rect_subtree() and adjust width extension.
Changes in version 1.1.1
Changes in version 1.9.2
https://github.com/YuLab-SMU/ggtree/issues/551
Changes in version 1.9.1
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’
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
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
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
Improvements
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
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
Bug fixes
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
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
significant updates to the package details vignette
Changes in version 1.3.13-1.3.14 (2023-01-20)
New features
Bug fixes
Minor changes
various minor changes
Changes in version 1.3.12 (2022-12-22)
Bug fixes
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
Bug fixes
other bugfix accidentally introduced in the previous commits
Changes in version 1.3.10 (2022-12-15)
Bug fixes
Minor changes
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
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
Minor changes
New features
Changes in version 1.45.1 (2023-04-19)
Changes in version 1.8
New features
Changes in version 1.28.0
Changes in version 1.34.1
fix the compiler warning: sprintf is deprecated
show “64-bit” correctly when run on Windows
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
Changes in version 1.29.1
hc_which()
. 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:
Changes in version 1.17
Changes in version 1.41
Changes in version 1.41.1
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.
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.
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”
Changes in version 1.31.12
introducing single E,M-steps
Changes in version 1.31.8
bugfix in plot.immunoClust
Changes in version 1.31.5
bugfix in meta.export
Changes in version 1.31.3
introduces meta-clustering with SON/ormalization
Changes in version 1.31.2
bugfix in meta.export functions
Changes in version 1.31.1
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.
Changes in version 0.99.0
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.7.1
row_names_max_width
and column_names_max_height
are all passed to
sub-heatmaps. 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
BUG FIXES
Changes in version 2.34.0
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.9.3 (2023-04-04)
ENHANCES AND REFACTORING
FIXES AND GENERAL UPDATES
DEPRECATIONS & BREAKING CHANGES
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 other typos and minor issues
Changes in version 1.9.1 (2022-12-01)
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.
Changes in version 1.1.1
MINOR UPDATES
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.
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
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
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().
Changes in version 0.99.10
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:
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).
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.
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:
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
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.
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
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
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()’
Changes in version 1.3.1
Included PLSDA algorithm.
WiP requires adjustment of vignette and tests, should work though.
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
Changes in version 1.13.1
Changes in version 1.9.2
featdata renamed to featData
merges columns from combinedTable() and featData()
Changes in version 1.9.1
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.
Changes in version 1.3
Changes in 1.3.2
Changes in 1.3.1
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
Changes in version 1.17.1 (2022-11-23)
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
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
Changes in version 1.11.5
fix the special symbol in group name with mp_diff_analysis. (2023-04-11)
Changes in version 1.11.4
fix the dynamic dots issue of left_join. (2022-12-15, Thu)
Changes in version 1.11.3
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()
Changes in version 1.7.1 (2023-01-04)
Changes in version 1.7.1 (2023-04-12)
Changes in version 1.7
Changes in version 1.6.1
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.
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
Changes in version 1.3.1 (2022-11-08)
Major changes
Minor improvements and bug fixes
Changes in version 1.7
Changes in 1.7.4
Changes in 1.7.3
Changes in 1.7.2
Changes in 1.7.1
Changes in version 1.7
Changes in 1.7.5
Changes in 1.7.4
Changes in 1.7.3
Changes in 1.7.2
Changes in 1.7.1
Changes in 1.7.0
Changes in version 1.3
Changes in 1.3.1
Changes in version 0.99
Changes in 0.99.7
Changes in 0.99.6
Changes in 0.99.5
Changes in 0.99.4
Changes in 0.99.3
Changes in 0.99.2
Changes in 0.99.1
Changes in 0.99.0
Prepare the package for submission to Bioconductor.
Changes in version 0.98
Changes in 0.98.1
Changes in 0.98.0
Add vignette.
Changes in version 0.1
Changes in 0.1.0
Changes in version 1.11
MsCoreUtils 1.11.6
MsCoreUtils 1.11.5
MsCoreUtils 1.11.4
MsCoreUtils 1.11.3
MsCoreUtils 1.11.2
MsCoreUtils 1.11.1
MsCoreUtils 1.11.0
Changes in version 0.99
MsDataHub 0.99.3
MsDataHub 0.99.2
MsDataHub 0.99.1
MsDataHub 0.99.0
Changes in version 1.1
MsExperiment 1.1.4
MsExperiment 1.1.3
MsExperiment 1.1.2
MsExperiment 1.1.1
MsExperiment 1.1.0
Changes in version 2.25
MSnbase 2.25.2
MSnbase 2.25.1
MSnbase 2.25.0
Changes in version 0.99
Changes in version 0.99.9 (2023-04-18)
Changes in version 0.99.8 (2023-09-02)
Changes in version 0.99.7 (2023-06-02)
Changes in version 0.99.6 (2022-11-29):
Changes in version 0.99.5 (2022-10-12):
Changes in version 0.99.4 (2022-10-11):
Changes in version 0.99.3 (2022-10-11):
Changes in version 0.99.2 (2022-09-20):
Changes in version 0.99.1 (2021-11-23)
Changes in version 0.99.0 (2021-09-10)
Changes in version 1.9.1
Changes in version 2.6.1 (2023-02-26)
Changes in version 1.26.0
New features
Bug fixes and minor improvements
Changes in version 0.99.0
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
New features
Add drop_indels parameter so a user can decide to remove indels from sumstats.
Changes in version 1.7.12
Bug fix
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
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’
Changes in version 2.33.1
Changes in version 2.6.0
Changes in version 1.7.1 (2022-01-25)
Changes in version 1.5.1
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
Changes in version 1.3.2
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
Changes in version 1.5.19
Changes in version 1.1.0
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.
Changes in version 1.41.1
MODIFICATIONS
Changes in version 1.5.2
New features
Bug fixes
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
Replace dplyr::%>% usage with | > |
Bug fixes
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
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
Changes in version 0.99.6
Added value field to data man pages
Changes in version 0.99.5
Remove non-exported man pages
Changes in version 0.99.4
Fixed wrong storing location for splicing intermediate results
Changes in version 0.99.3
Moved data scripts to inst/script
Changes in version 0.99.2
Removed usage of deprecated purrr::when
Changes in version 0.99.1
Updated NAMESPACE to include all imported packages. Suggested packages are added in notes.
Changes in version 0.99.0
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()
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
Changes in version 1.19.3
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
Changes in version 1.1.2
Changes in version 1.9.1
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
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
Changes in version 0.99.2
CHANGES
Made small changes suggested by Bioconductor reviewer.
Changes in version 0.99.0
NEW FEATURES
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.
Changes in version 1.7.1 (2023-04-04)
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
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)
Changes in version 1.39
Changes in version 1.39.1
Changes in version 1.39.0
Changes in version 2.9.0
CHANGES IN VERSION 2.9.0
CHANGES IN VERSION 2.9.1
Changes in version 1.3.32 (2022-12-11)
added the sampleID files
Changes in version 1.3.0 (2022-11-15)
Changes in version 1.3
PSMatch 1.3.3
PSMatch 1.3.2
PSMatch 1.3.1
Changes in version 1.9
QFeatures 1.9.4
QFeatures 1.9.3
QFeatures 1.9.2
Use | > rather than %>%. |
QFeatures 1.9.1
QFeatures 1.9.0
Changes in version 1.25.1
Changes in version 1.15.1 (2022-11-04)
Changes in version 1.40.0
USER-VISIBLE CHANGES
Changes in version 1.24.0
Bug fixes and minor improvements
Changes in version 0.99.9
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
Add compression level arguments to several compression tools.
Changes in version 0.99.6
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
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
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.
Changes in version 1.3.1
Initial Submission
Changes in version 2.20.0
Changes in version 1.13.1 (2023-04-13)
Changes in version 1.2.0
Major code refactoring.
Package released in Bioconductor 3.17.
Changes in version 0.99.0 (2023-03-05)
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.
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
Bug Fixes
BioConductor 3.16 - Changes in 1.2.0
BioConductor 3.15 - Changes in 1.0.0
Improvements
Bug Fixes
Changes in 0.99.1
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()
.
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”
Changes in version 1.12.0
USER VISIBLE CHANGES
BUG FIXES
Changes in version 1.22
User visible changes
Changes in version 2.2.0
Changes in version 1.11.1
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
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
Changes in version 1.27.1
Changes in version 2.7
rpx 2.7.4
rpx 2.7.3
rpx 2.7.2
rpx 2.7.1
Changes in version 1.10.1
Changes in version 2.16
NEW FEATURES
Changes in version 2.30.0
New features
Bug fixes and minor improvements
Changes in version 1.0.0
Changes in version 0.38.0
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
Improve support of DFrame objects with S3-typed columns (commit 3b83d5f).
Fix bug in internal helper bindROWS2() (commit 05cfd3c).
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
Changes in version 99.1
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.
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
Changes in version 0.99.0
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.
Changes in version 1.1.8
Manhattan distance metric implemented
other linkage functions for clustering implemented
tracking timestamps for clustering, bubbletree construction, end
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
Changes in version 1.9
scp 1.9.2
scp 1.9.1
scp 1.9.0
Changes in version 1.28
Changes in version 1.5.1
Clarification in multiAdaSampling documentation for parameter label.
Changes in version 1.5.0
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.
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.
Changes in version 1.10
Changes in version 0.99.6
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
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
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
Changes in version 1.40.0
Changes in version 0.99.0 (2022-10-06)
Changes in version 1.58
BUG FIXES
Changes in version 2.1.1
Fixed doc issues
Fixed cpp issues
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.
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)
Changes in version 1.9.1
term_similarity_from_gmt()
: previously forgot to split rows. Changes in version 2.8.1 (2022-03-10)
Changes in version 0.99.2
Changes in version 1.34.0
Changes in version 1.0.0
Changes in version 1.1.2
BUG FIXES
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.
Changes in version 1.9.5 (2023-03-02)
Changes in version 1.1.6
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
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
More helpful error messages when geometries, localResult, or spatial graphs are absent
Changes in version 1.0.2
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.
Changes in version 0.99.0 (2022-04-01)
Changes in version 0.99.7
Update vignette to include example of analysing proportions data directly
Changes in version 0.99.0
speckle only contains propeller functions
Changes in version 0.0.3
Change propeller transform default to logit
Changes in version 0.0.2
Added logit transformation option to propeller
Changes in version 0.0.1
Changes in version 1.9
Changes in 1.9.15
Changes in 1.9.14
Changes in 1.9.13
Changes in 1.9.12
Changes in 1.9.11
Changes in 1.9.10
Changes in 1.9.9
Changes in 1.9.8
Changes in 1.9.7
Changes in 1.9.6
Changes in 1.9.5
Changes in 1.9.4
Changes in 1.9.3
Changes in 1.9.2
Changes in 1.9.1
Changes in 1.9.0
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
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
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.
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.
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
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
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.
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
Changes in version 1.1.1
Changes in version 1.30.0
DEPRECATED AND DEFUNCT
Changes in version 1.5.1 (2022-08-12)
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
Changes in version 2021-07-02 (2021-07-02)
Changes:
Changes in version 1.11.8
Various documentation updates
Changes in version 1.11.7
Method=”CI” in PhyloDistance now calculates an approximate p-value using simulated data from Smith (2020)
Changes in version 1.11.6
Updates to documentation
Changes in version 1.11.5
Adds new function MoransI to calculate Moran’s I for a set of spatially distributed signals
Changes in version 1.11.4
ShuffleC now support sampling with replacement, performance is around 2.25x faster than sample
Changes in version 1.11.3
Updates to documentation files
Changes in version 1.11.2
Updates internal functions to use rapply instead of dendrapply to avoid stack overflow issues due to R recursion
Changes in version 1.11.1
updates gitignore for workflows
Changes in version 1.10.1
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.
Changes in version 1.1.6
BUG FIXES
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
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.
Changes in version 1.9.04
Major Change
Minor Change
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
Changes in version 2.2.0
BUG FIXES
Changes in version 1.92.0
Bug Fixes
Major Changes
Minor Changes
Changes in version 1.20.0
New features
Changes in version 0.99.7
selectFeaureVectorLarge,selectFeaureVectorSmall
Changes in version 0.1.0
Changes in version 0.99.21 (2023-04-14)
Correct wrong format of DESCRIPTION
Changes in version 0.99.20 (2023-04-12)
modify DESCRIPTION so as to be disrtnct from the previous packpage, TDbasedUFE
Changes in version 0.99.19 (2023-03-28)
Removing some “«-“s in test.
Changes in version 0.99.18 (2023-03-27)
Fragmenting testthat toward individual functions
Changes in version 0.99.17 (2023-03-25)
Correct testthat (with using test_that())
Changes in version 0.99.16 (2023-03-23)
Adding explanation of data in inst/extdata
Changes in version 0.99.15 (2023-03-21)
Changes in version 1.2.0
New features
Bug fixes and minor improvements
Changes in version 1.4.0
New features
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.
Changes in version 3.27.1
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.
Changes in version 1.23.1
Changes in version 1.17.1 (2022-12-19)
Changes in version 1.17.2
Changes in version 1.27.1
Changes in version 2.40.0
USER VISIBLE CHANGES
BUG FIXES AND MINOR IMPROVEMENTS
mapUniProt
documentation Changes in version 1.18.0
NEW FEATURES
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.
Changes in version 1.4.0
Changes in version 1.28.9
add Pearson residuals to residuals()
Changes in version 1.28.8
add mvTest() with features as list
Changes in version 1.28.7
Fix bug in makeContrastsDream() by adding droplevels()
Changes in version 1.28.6
diffVar() now fits contrasts estimated in first step
Changes in version 1.28.5
Fix error in vcov() when samples are dropped due to covariate having NA value
Changes in version 1.28.4
Improve documentation for contrasts
Changes in version 1.28.3
Improve checking and documentation for contrasts
Changes in version 1.28.2
but won’t change results
Changes in version 1.28.1
Changes in version 1.9.2
Changes in version 1.1.12
Added dark theme support for functions that plot geometries
Changes in version 1.1.11
Allow non-standard names for local results in plotLocalResult
Changes in version 1.1.10
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
Changes in version 1.11.1
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).
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
Changes in version 1.1.2
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
Changes in version 0.99.0 (2023-02-22)
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.
Changes in version 1.22.0
Bug fixes and minor improvements
Changes in version 1.0.0
USER VISIBLE CHANGES
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.
Changes in version 0.99.0
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
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
Changes in version 1.21.1
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
Changes in version 0.99.5
NEWS.md setup
Changes in version 1.2.0
Added seqFISH mouse gastrulation data
Corrected Xenium dataset format
Changes in version 1.12.0
Bug fixes and minor improvements
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
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.