October 27, 2021
Bioconductors:
We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books.
There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow, no new books, and many updates and improvements to existing packages; Bioconductor 3.14 is compatible with R 4.1.1, and is supported on Linux, 32- and 64-bit Windows, and Intel 64-bit macOS 10.13 (High Sierra) or higher. We do not currently support arm64 so arm64 Mac users who wish to install Bioconductor Mac binary packages must install the Intel 64-bit build of R available on CRAN. This release will include updated Bioconductor Docker containers.
Thank you to everyone for your contribution to Bioconductor
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Bioconductor used Microsoft Azure VMs during our 3.14 release process for a critical part of our branching process for software packages. These VMs are available to Bioconductor through our collaboration with the Microsoft Genomics team.
To update to or install Bioconductor 3.14:
Install R 4.1.1. Bioconductor 3.14 has been designed expressly for this version of R.
Follow the instructions at Installing Bioconductor.
There are 89 new software packages in this release of Bioconductor.
atena Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification function with this object and getting a SummarizedExperiment object as output container of the quantified expression profiles. The implementation allows one to quantify TEs and gene transcripts in an integrated manner.
benchdamic Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method’s distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.
BindingSiteFinder Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.
biodbChebi The biodbChebi library provides access to the ChEBI Database, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name, mass or other fields.
biodbHmdb The biodbHmdb library is an extension of the biodb framework package that provides access to the HMDB Metabolites database. It allows to download the whole HMDB Metabolites database locally, access entries and search for entries by name or description. A future version of this package will also include a search by mass and mass spectra annotation.
biodbKegg The biodbKegg library is an extension of the biodb framework package that provides access to the KEGG databases Compound, Enzyme, Genes, Module, Orthology and Reaction. It allows to retrieve entries by their accession numbers. Web services like “find”, “list” and “findExactMass” are also available. Some functions for navigating along the pathways have also been implemented.
biodbLipidmaps The biodbLipidmaps library provides access to the Lipidmaps Structure Database, using biodb package framework. It allows to retrieve entries by their accession number, and run web the services lmsdSearch and lmsdRecord.
biodbUniprot The biodbUniprot library is an extension of the biodb framework package. It provides access to the UniProt database. It allows to retrieve entries by their accession number, and run web service queries for searching for entries.
BioPlex The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data.
bugsigdbr The bugsigdbr package implements convenient access to bugsigdb.org from within R/Bioconductor. The goal of the package is to facilitate import of BugSigDB data into R/Bioconductor, provide utilities for extracting microbe signatures, and enable export of the extracted signatures to plain text files in standard file formats such as GMT.
BUSseq BUSseq R package fits an interpretable Bayesian hierarchical model—the Batch Effects Correction with Unknown Subtypes for scRNA seq Data (BUSseq)—to correct batch effects in the presence of unknown cell types. BUSseq is able to simultaneously correct batch effects, clusters cell types, and takes care of the count data nature, the overdispersion, the dropout events, and the cell-specific sequencing depth of scRNA-seq data. After correcting the batch effects with BUSseq, the corrected value can be used for downstream analysis as if all cells were sequenced in a single batch. BUSseq can integrate read count matrices obtained from different scRNA-seq platforms and allow cell types to be measured in some but not all of the batches as long as the experimental design fulfills the conditions listed in our manuscript.
cageminer This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments.
CellBarcode This package performs Cellular DNA Barcode (genetic lineage tracing) analysis. The package can handle all kinds of DNA barcodes, as long as the barcode within a single sequencing read and has a pattern which can be matched by a regular expression. This package can handle barcode with flexible length, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing of some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing and meta genome data.
Cepo Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression.
cfDNAPro cfDNA fragment size metrics are important features for utilizing liquid biopsy in tumor early detection, diagnosis, therapy personlization and monitoring. Analyzing and visualizing insert size metrics could be time intensive. This package intends to simplify this exploration process, and it offers two sets of functions for data characterization and data visualization.
cliProfiler An easy and fast way to visualize and profile the high-throughput IP data. This package generates the meta gene profile and other profiles. These profiles could provide valuable information for understanding the IP experiment results.
Cogito Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis.
csdR This package contains functionality to run differential gene co-expression across two different conditions. The algorithm is inspired by Voigt et al. 2017 and finds Conserved, Specific and Differentiated genes (hence the name CSD). This package include efficient and variance calculation by bootstrapping and Welford’s algorithm.
CyTOFpower This package is a tool to predict the power of CyTOF experiments in the context of differential state analyses. The package provides a shiny app with two options to predict the power of an experiment: i. generation of in-sicilico CyTOF data, using users input ii. browsing in a grid of parameters for which the power was already precomputed.
cytoKernel cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression data. In this R package, we implement functions that compute the feature-wise p values and their corresponding adjusted p values. Additionally, it also computes the feature-wise shrunk effect sizes and their corresponding shrunken effect size. Further, it calculates the percent of differentially expressed features and plots user-friendly heatmap of the top differentially expressed features on the rows and samples on the columns.
deconvR This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.
DelayedTensor DelayedTensor operates Tensor arithmetic directly on DelayedArray object. DelayedTensor provides some generic function related to Tensor arithmetic/decompotision and dispatches it on the DelayedArray class. DelayedTensor also suppors Tensor contraction by einsum function, which is inspired by numpy einsum.
Dino Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis. The approach produces a matrix of corrected expression for which the dependency between sequencing depth and the full distribution of normalized expression; many existing methods aim to remove only the dependency between sequencing depth and the mean of the normalized expression. This is particuarly useful in the context of highly sparse datasets such as those produced by 10X genomics and other uninque molecular identifier (UMI) based microfluidics protocols for which the depth-dependent proportion of zeros in the raw expression data can otherwise present a challenge.
dStruct dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al, Genome Biology, 2019 for the underlying method.
easier This package provides a workflow for the use of EaSIeR tool, developed to assess patients’ likelihood to respond to ICB therapies providing just the patients’ RNA-seq data as input. We integrate RNA-seq data with different types of prior knowledge to extract quantitative descriptors of the tumor microenvironment from several points of view, including composition of the immune repertoire, and activity of intra- and extra-cellular communications. Then, we use multi-task machine learning trained in TCGA data to identify how these descriptors can simultaneously predict several state-of-the-art hallmarks of anti-cancer immune response. In this way we derive cancer-specific models and identify cancer-specific systems biomarkers of immune response. These biomarkers have been experimentally validated in the literature and the performance of EaSIeR predictions has been validated using independent datasets form four different cancer types with patients treated with anti-PD1 or anti-PDL1 therapy.
enhancerHomologSearch Get ENCODE data of enhancer region via H3K4me1 peaks and search homolog regions for given sequences. The candidates of enhancer homolog regions can be filtered by distance to target TSS. The top candidates from human and mouse will be aligned to each other and then exported as multiple alignments with given enhancer.
epistack The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest.
FindIT2 This package implements functions to find influential TF and target based on different input type. It have five module: Multi-peak multi-gene annotaion(mmPeakAnno module), Calculate regulation potential(calcRP module), Find influential Target based on ChIP-Seq and RNA-Seq data(Find influential Target module), Find influential TF based on different input(Find influential TF module), Calculate peak-gene or peak-peak correlation(peakGeneCor module). And there are also some other useful function like integrate different source information, calculate jaccard similarity for your TF.
FLAMES Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.
genomicInstability This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of sets of contiguous genes (loci-blocks) on the gene expression profiles and estimates the Genomic Instability Score (GIS) for each analyzed cell.
GeoDiff A series of statistical models using count generating distributions for background modelling, feature and sample QC, normalization and differential expression analysis on GeoMx RNA data. The application of these methods are demonstrated by example data analysis vignette.
GEOexplorer GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of gene expression analysis on microarray gene expression datasets held on the GEO database. The outputs are interactive graphs that enable users to explore the results of the analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).
ggmsa A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using ‘ggplot2’. Multiple sequence alignment can easily be combined with other ‘ggplot2’ plots, such as phylogenetic tree Visualized by ‘ggtree’, boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.
ggspavis Visualization functions for spatially resolved transcriptomics datasets stored in SpatialExperiment format. Includes functions to create several types of plots for data from from spot-based (e.g. 10x Genomics Visium) and molecule-based (e.g. seqFISH) technological platforms.
HPiP HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data unavailability for HP-PPI network reconstructions. Moreover, establishing computational frameworks in that regard will reveal mechanistic insights into infectious diseases and suggest potential HP-PPI targets, thus narrowing down the range of possible candidates for subsequent wet-lab experimental validations.
imcRtools This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.
iPath iPath is the Bioconductor package used for calculating personalized pathway score and test the association with survival outcomes. Abundant single-gene biomarkers have been identified and used in the clinics. However, hundreds of oncogenes or tumor-suppressor genes are involved during the process of tumorigenesis. We believe individual-level expression patterns of pre-defined pathways or gene sets are better biomarkers than single genes. In this study, we devised a computational method named iPath to identify prognostic biomarker pathways, one sample at a time. To test its utility, we conducted a pan-cancer analysis across 14 cancer types from The Cancer Genome Atlas and demonstrated that iPath is capable of identifying highly predictive biomarkers for clinical outcomes, including overall survival, tumor subtypes, and tumor stage classifications. We found that pathway-based biomarkers are more robust and effective than single genes.
m6Aboost This package can help user to run the m6Aboost model on their own miCLIP2 data. The package includes functions to assign the read counts and get the features to run the m6Aboost model. The miCLIP2 data should be stored in a GRanges object. More details can be found in the vignette.
MAI A two-step approach to imputing missing data in metabolomics. Step 1 uses a random forest classifier to classify missing values as either Missing Completely at Random/Missing At Random (MCAR/MAR) or Missing Not At Random (MNAR). MCAR/MAR are combined because it is often difficult to distinguish these two missing types in metabolomics data. Step 2 imputes the missing values based on the classified missing mechanisms, using the appropriate imputation algorithms. Imputation algorithms tested and available for MCAR/MAR include Bayesian Principal Component Analysis (BPCA), Multiple Imputation No-Skip K-Nearest Neighbors (Multi_nsKNN), and Random Forest. Imputation algorithms tested and available for MNAR include nsKNN and a single imputation approach for imputation of metabolites where left-censoring is present.
metapone The package conducts pathway testing from untargetted metabolomics data. It requires the user to supply feature-level test results, from case-control testing, regression, or other suitable feature-level tests for the study design. Weights are given to metabolic features based on how many metabolites they could potentially match to. The package can combine positive and negative mode results in pathway tests.
methylclock This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath’s clock, Hannum’s clock, BNN, Horvath’s skin+blood clock, PedBE clock and Wu’s clock. Gestational DNAm age : Knight’s clock, Bohlin’s clock, Mayne’s clock and Lee’s clocks. Biological DNAm clocks : Levine’s clock and Telomere Length’s clock.
miaSim Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell’s Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to SummarizedExperiment or TreeSummarizedExperiment objects.
microbiomeMarker To date, a number of methods have been developed for microbiome marker discovery based on metagenomic profiles, e.g. LEfSe. However, all of these methods have its own advantages and disadvantages, and none of them is considered standard or universal. Moreover, different programs or softwares may be development using different programming languages, even in different operating systems. Here, we have developed an all-in-one R package microbiomeMarker that integrates commonly used differential analysis methods as well as three machine learning-based approaches, including Logistic regression, Random forest, and Support vector machine, to facilitate the identification of microbiome markers.
MicrobiomeProfiler This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.
mitoClone2 This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context.
monaLisa Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided.
mosbi This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract bicluster communities from the similarity network, which can then be converted to ensemble biclusters. Additionally, MoSBi includes several network visualization methods to give an intuitive and scalable overview of the results. MoSBi comes with several biclustering algorithms, but can be easily extended to new biclustering algorithms.
MsBackendRawFileReader implements a MsBackend for the Spectra package using Thermo Fisher Scientific’s NewRawFileReader .Net libraries. The package is generalizing the functionality introduced by the rawrr package (Kockmann T. et al. (2020) <doi:10.1101/2020.10.30.362533>) Methods defined in this package are supposed to extend the Spectra Bioconductor package.
MSstatsLiP Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.
NanoTube NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable interoperability with other Bioconductor NanoString data analysis packages.
netOmics netOmics is a multi-omics networks builder and explorer. It uses a combination of network inference algorithms and and knowledge-based graphs to build multi-layered networks. The package can be combined with timeOmics to incorporate time-course expression data and build sub-networks from multi-omics kinetic clusters. Finally, from the generated multi-omics networks, propagation analyses allow the identification of missing biological functions (1), multi-omics mechanisms (2) and molecules between kinetic clusters (3). This helps to resolve complex regulatory mechanisms.
NeuCA NeuCA is is a neural-network based method for scRNA-seq data annotation. It can automatically adjust its classification strategy depending on cell type correlations, to accurately annotate cell. NeuCA can automatically utilize the structure information of the cell types through a hierarchical tree to improve the annotation accuracy. It is especially helpful when the data contain closely correlated cell types.
nullranges Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.
NxtIRFcore Interactively analyses Intron Retention and Alternative Splicing Events (ASE) in RNA-seq data. NxtIRF quantifies ASE events in BAM files aligned to the genome using a splice-aware aligner such as STAR. The core quantitation algorithm relies on the IRFinder/C++ engine ported via Rcpp for multi-platform compatibility. In addition, NxtIRF provides convenient pipelines for downstream analysis and publication-ready visualisation tools.
ODER The aim of ODER is to identify previously unannotated expressed regions (ERs) using RNA-sequencing data. For this purpose, ODER defines and optimises the definition of ERs, then connected these ERs to genes using junction data. In this way, ODER improves gene annotation. Gene annotation is a staple input of many bioinformatic pipelines and a more complete gene annotation can enable more accurate interpretation of disease associated variants.
orthogene orthogene is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date interspecies gene ortholog mappings across 700+ organisms. It also provides various utility functions to map common objects (e.g. data.frames, gene expression matrices, lists) onto 1:1 gene orthologs from any other species.
pairkat PaIRKAT is model framework for assessing statistical relationships between networks of metabolites (pathways) and an outcome of interest (phenotype). PaIRKAT queries the KEGG database to determine interactions between metabolites from which network connectivity is constructed. This model framework improves testing power on high dimensional data by including graph topography in the kernel machine regression setting. Studies on high dimensional data can struggle to include the complex relationships between variables. The semi-parametric kernel machine regression model is a powerful tool for capturing these types of relationships. They provide a framework for testing for relationships between outcomes of interest and high dimensional data such as metabolomic, genomic, or proteomic pathways. PaIRKAT uses known biological connections between high dimensional variables by representing them as edges of ‘graphs’ or ‘networks.’ It is common for nodes (e.g. metabolites) to be disconnected from all others within the graph, which leads to meaningful decreases in testing power whether or not the graph information is included. We include a graph regularization or ‘smoothing’ approach for managing this issue.
pengls Combine generalised least squares methodology from the nlme package for dealing with autocorrelation with penalised least squares methods from the glmnet package to deal with high dimensionality. This pengls packages glues them together through an iterative loop. The resulting method is applicable to high dimensional datasets that exhibit autocorrelation, such as spatial or temporal data.
plotgardener Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.
ProteoDisco ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.
rGenomeTracks rGenomeTracks package leverages the power of pyGenomeTracks software with the interactivity of R. pyGenomeTracks is a python software that offers robust method for visualizing epigenetic data files like narrowPeak, Hic matrix, TADs and arcs, however though, here is no way currently to use it within R interactive session. rGenomeTracks wrapped the whole functionality of pyGenomeTracks with additional utilites to make to more pleasant for R users.
RiboCrypt R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots. The package is still under development.
RLSeq RLSeq is a toolkit for analyzing and
evaluating R-loop mapping datasets. RLSeq serves two primary
purposes:
(1) to facilitate the evaluation of dataset quality
(2) to enable R-loop analysis in the context of publicly-available
data sets from RLBase. The package is intended to provide a simple
pipeline, called with the RLSeq()
function, which performs all
main analyses. Individual functions are also accessible and provide
custom analysis capabilities. Finally an HTML report is generated
with report()
.
rmspc The rmspc package runs MSPC (Multiple Sample Peak Calling) software using R. The analysis of ChIP-seq samples outputs a number of enriched regions (commonly known as “peaks”), each indicating a protein-DNA interaction or a specific chromatin modification. When replicate samples are analyzed, overlapping peaks are expected. This repeated evidence can therefore be used to locally lower the minimum significance required to accept a peak. MSPC uses combined evidence from replicated experiments to evaluate peak calling output, rescuing peaks, and reduce false positives. It takes any number of replicates as input and improves sensitivity and specificity of peak calling on each, and identifies consensus regions between the input samples.
scanMiR A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3’ alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).
scanMiRApp A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.
scAnnotatR The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs.
scatterHatch The objective of this package is to efficiently create scatterplots where groups can be distinguished by color and texture. Visualizations in computational biology tend to have many groups making it difficult to distinguish between groups solely on color. Thus, this package is useful for increasing the accessibility of scatterplot visualizations to those with visual impairments such as color blindness.
scReClassify A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique. The current version of scReClassify supports Support Vector Machine and Random Forest as a base classifier.
scShapes We present a novel statistical framework for identifying differential distributions in single-cell RNA-sequencing (scRNA-seq) data between treatment conditions by modeling gene expression read counts using generalized linear models (GLMs). We model each gene independently under each treatment condition using error distributions Poisson (P), Negative Binomial (NB), Zero-inflated Poisson (ZIP) and Zero-inflated Negative Binomial (ZINB) with log link function and model based normalization for differences in sequencing depth. Since all four distributions considered in our framework belong to the same family of distributions, we first perform a Kolmogorov-Smirnov (KS) test to select genes belonging to the family of ZINB distributions. Genes passing the KS test will be then modeled using GLMs. Model selection is done by calculating the Bayesian Information Criterion (BIC) and likelihood ratio test (LRT) statistic.
scTreeViz scTreeViz provides classes to
support interactive data aggregation and visualization of single
cell RNA-seq datasets with hierarchies for e.g. cell clusters at
different resolutions. The TreeIndex
class provides methods to
manage hierarchy and split the tree at a given resolution or across
resolutions. The TreeViz
class extends SummarizedExperiment
and
can performs quick aggregations on the count matrix defined by
clusters.
segmenter Chromatin segmentation analysis transforms ChIP-seq data into signals over the genome. The latter represents the observed states in a multivariate Markov model to predict the chromatin’s underlying states. ChromHMM, written in Java, integrates histone modification datasets to learn the chromatin states de-novo. The goal of this package is to call chromHMM from within R, capture the output files in an S4 object and interface to other relevant Bioconductor analysis tools. In addition, segmenter provides functions to test, select and visualize the output of the segmentation.
sparrow Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.
spatialDE SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.
spatzie Identifies motifs that are significantly co-enriched from enhancer-promoter interaction data. While enhancer-promoter annotation is commonly used to define groups of interaction anchors, spatzie also supports co-enrichment analysis between preprocessed interaction anchors. Supports BEDPE interaction data derived from genome-wide assays such as HiC, ChIA-PET, and HiChIP. Can also be used to look for differentially enriched motif pairs between two interaction experiments.
spiky spiky implements methods and model generation for cfMeDIP (cell-free methylated DNA immunoprecipitation) with spike-in controls. CfMeDIP is an enrichment protocol which avoids destructive conversion of scarce template, making it ideal as a “liquid biopsy,” but creating certain challenges in comparing results across specimens, subjects, and experiments. The use of synthetic spike-in standard oligos allows diagnostics performed with cfMeDIP to quantitatively compare samples across subjects, experiments, and time points in both relative and absolute terms.
surfaltr Cell surface proteins form a major fraction of the druggable proteome and can be used for tissue-specific delivery of oligonucleotide/cell-based therapeutics. Alternatively spliced surface protein isoforms have been shown to differ in their subcellular localization and/or their transmembrane (TM) topology. Surface proteins are hydrophobic and remain difficult to study thereby necessitating the use of TM topology prediction methods such as TMHMM and Phobius. However, there exists a need for bioinformatic approaches to streamline batch processing of isoforms for comparing and visualizing topologies. To address this gap, we have developed an R package, surfaltr. It pairs inputted isoforms, either known alternatively spliced or novel, with their APPRIS annotated principal counterparts, predicts their TM topologies using TMHMM or Phobius, and generates a customizable graphical output. Further, surfaltr facilitates the prioritization of biologically diverse isoform pairs through the incorporation of three different ranking metrics and through protein alignment functions. Citations for programs mentioned here can be found in the vignette.
svaNUMT svaNUMT contains functions for detecting NUMT events from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies NUMTs by nuclear-mitochondrial breakend junctions. The main function reports candidate NUMTs if there is a pair of valid insertion sites found on the nuclear genome within a certain distance threshold. The candidate NUMTs are reported by events.
svaRetro svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported by events and annotated with information of the inserted transcripts.
synapsis Synapsis is a Bioconductor software package for automated (unbiased and reproducible) analysis of meiotic immunofluorescence datasets. The primary functions of the software can i) identify cells in meiotic prophase that are labelled by a synaptonemal complex axis or central element protein, ii) isolate individual synaptonemal complexes and measure their physical length, iii) quantify foci and co-localise them with synaptonemal complexes, iv) measure interference between synaptonemal complex-associated foci. The software has applications that extend to multiple species and to the analysis of other proteins that label meiotic prophase chromosomes. The software converts meiotic immunofluorescence images into R data frames that are compatible with machine learning methods. Given a set of microscopy images of meiotic spread slides, synapsis crops images around individual single cells, counts colocalising foci on strands on a per cell basis, and measures the distance between foci on any given strand.
tanggle Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. ‘ggtree’ and using functions from ‘ape’ and ‘phangorn’. It extends the ‘ggtree’ package [@Yu2017] to allow the visualization of phylogenetic networks using the ‘ggplot2’ syntax. It offers an alternative to the plot functions already available in ‘ape’ Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and ‘phangorn’ Schliep (2011) <doi:10.1093/bioinformatics/btq706>.
TargetDecoy A first step in the data analysis of Mass Spectrometry (MS) based proteomics data is to identify peptides and proteins. With this respect the huge number of experimental mass spectra typically have to be assigned to theoretical peptides derived from a sequence database. Search engines are used for this purpose. These tools compare each of the observed spectra to all candidate theoretical spectra derived from the sequence data base and calculate a score for each comparison. The observed spectrum is then assigned to the theoretical peptide with the best score, which is also referred to as the peptide to spectrum match (PSM). It is of course crucial for the downstream analysis to evaluate the quality of these matches. Therefore False Discovery Rate (FDR) control is used to return a reliable list PSMs. The FDR, however, requires a good characterisation of the score distribution of PSMs that are matched to the wrong peptide (bad target hits). In proteomics, the target decoy approach (TDA) is typically used for this purpose. The TDA method matches the spectra to a database of real (targets) and nonsense peptides (decoys). A popular approach to generate these decoys is to reverse the target database. Hence, all the PSMs that match to a decoy are known to be bad hits and the distribution of their scores are used to estimate the distribution of the bad scoring target PSMs. A crucial assumption of the TDA is that the decoy PSM hits have similar properties as bad target hits so that the decoy PSM scores are a good simulation of the target PSM scores. Users, however, typically do not evaluate these assumptions. To this end we developed TargetDecoy to generate diagnostic plots to evaluate the quality of the target decoy method.
transformGamPoi Variance-stabilizing transformations help with the analysis of heteroskedastic data (i.e., data where the variance is not constant, like count data). This package provide two types of variance stabilizing transformations: (1) methods based on the delta method (e.g., ‘acosh’, ‘log(x+1)’), (2) model residual based (Pearson and randomized quantile residuals).
traviz traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in reduced dimension, as well as averge gene expression smoothers as a function of pseudotime. Asides from general utility functions, traviz also allows plotting trajectories estimated by Slingshot, as well as smoothers estimated by tradeSeq. Furthermore, it allows for visualization of Slingshot trajectories using ggplot2.
TRESS This package is devoted to analyzing MeRIP-seq data. Current functionality is for detection of transcriptome-wide m6A methylation regions. The method is based on hierarchical negative binomial models.
tripr TRIP is a software framework that provides analytics services on antigen receptor (B cell receptor immunoglobulin, BcR IG | T cell receptor, TR) gene sequence data. It is a web application written in R Shiny. It takes as input the output files of the IMGT/HighV-Quest tool. Users can select to analyze the data from each of the input samples separately, or the combined data files from all samples and visualize the results accordingly.
txcutr Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment stage, as well as in downstream analysis. This package implements some convenience methods for readily generating such truncated annotations and their corresponding sequences.
VAExprs A fundamental problem in biomedical research is the low number of observations, mostly due to a lack of available biosamples, prohibitive costs, or ethical reasons. By augmenting a few real observations with artificially generated samples, their analysis could lead to more robust and higher reproducible. One possible solution to the problem is the use of generative models, which are statistical models of data that attempt to capture the entire probability distribution from the observations. Using the variational autoencoder (VAE), a well-known deep generative model, this package is aimed to generate samples with gene expression data, especially for single-cell RNA-seq data. Furthermore, the VAE can use conditioning to produce specific cell types or subpopulations. The conditional VAE (CVAE) allows us to create targeted samples rather than completely random ones.
veloviz VeloViz uses each cell’s current observed and predicted future transcriptional states inferred from RNA velocity analysis to build a nearest neighbor graph between cells in the population. Edges are then pruned based on a cosine correlation threshold and/or a distance threshold and the resulting graph is visualized using a force-directed graph layout algorithm. VeloViz can help ensure that relationships between cell states are reflected in the 2D embedding, allowing for more reliable representation of underlying cellular trajectories.
There are 13 new data experiment packages in this release of Bioconductor.
curatedTBData The curatedTBData is an R package that provides standardized, curated tuberculosis(TB) transcriptomic studies. The initial release of the package contains 49 studies. The curatedTBData package allows users to access tuberculosis trancriptomic efficiently and to make efficient comparison for different TB gene signatures across multiple datasets.
easierData Access to internal data required
for the functional performance of easier package and exemplary
bladder cancer dataset with both processed RNA-seq data and
information on response to ICB therapy generated by Mariathasan et
al. “TGF-B attenuates tumour response to PD-L1 blockade by
contributing to exclusion of T cells”, published in Nature, 2018
doi:10.1038/nature25501. The
data is made available via
IMvigor210CoreBiologies
package under the CC-BY license.
GSE103322 Single cell RNA-Seq data for 5902 cells from 18 patients with oral cavity head and neck squamous cell carcinoma available as GEO accession GSE103322. GSE103322 data have been parsed into a SincleCellExperiment object available in ExperimentHub.
GSE159526 19 term and 9 first trimester placental chorionic villi and matched cell-sorted samples ran on Illumina HumanMethylationEPIC DNA methylation microarrays. This data was made available on GEO accession GSE159526. Both the raw and processed data has been made available on \code{ExperimentHub}. Raw unprocessed data formatted as an RGChannelSet object for integration and normalization using minfi and other existing Bioconductor packages. Processed normalized data is also available as a DNA methylation \code{matrix}, with a corresponding phenotype information as a \code{data.frame} object.
nullrangesData Provides datasets for the nullranges package vignette, in particular example datasets for DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF genomic interactions. These are used to demonstrate generation of null hypothesis feature sets, either through block bootstrapping or matching, in the nullranges vignette. For more details, see the data object man pages, and the R scripts for object construction provided within the package.
NxtIRFdata NxtIRFdata is a companion package for NxtIRF, which is an IRFinder- based R package for Intron Retention and Alternative Splicing quantitation for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains a synthetic genome reference and example BAM files used to test NxtIRF. BAM files are based on 6 samples from the Leucegene dataset provided by NCBI Gene Expression Omnibus under accession number GSE67039.
plotgardenerData This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes.
RLHub | RLHub provides a convenient interface to the processed data provided within RLSuite, a tool-chain for analyzing R-loop-mapping data sets. The primary purpose of RLHub is to serve the processed data sets required by the RLSeq R package and the RLBase web service. Additionally, RLHub provides a stand-alone R interface to these data, benefiting users who are addressing questions related to R-loop regions (RL-Regions), R-loop-binding proteins (RLBPs), R-loop co-localizing factors, and the differences between R-loop-mapping methods. The full data-generating protocol is found here: https://github.com/Bishop-Laboratory/RLBase-data.
scanMiRData This package contains
companion data to the scanMiR package. It contains KdModel
(miRNA
12-mer binding affinity models) collections corresponding to all
human, mouse and rat mirbase miRNAs. See the scanMiR package for
details.
scATAC.Explorer This package provides a tool to search and download a collection of publicly available single cell ATAC-seq datasets and their metadata. scATAC-Explorer aims to act as a single point of entry for users looking to study single cell ATAC-seq data. Users can quickly search available datasets using the metadata table and download datasets of interest for immediate analysis within R.
spatialDmelxsim Spatial allelic expression counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object. This package contains data of allelic expression counts of spatial slices of a fly embryo, a Drosophila melanogaster x Drosophila simulans cross. See the CITATION file for the data source, and the associated script for how the object was constructed from publicly available data.
TabulaMurisSenisData This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects.
tuberculosis The tuberculosis R/Bioconductor package features tuberculosis gene expression data for machine learning. All human samples from GEO that did not come from cell lines, were not taken postmortem, and did not feature recombination have been included. The package has more than 10,000 samples from both microarray and sequencing studies that have been processed from raw data through a hyper-standardized, reproducible pipeline.
There are 10 new annotation packages in this release of Bioconductor.
chromhmmData Annotation files of the formatted genomic annotation for ChromHMM. Three types of text files are included the chromosome sizes, region coordinates and anchors specifying the transcription start and end sites. The package includes data for two versions of the genome of humans and mice.
CTCF Genomic coordinates of predicted CTCF binding sites with motif MA0139.1 (Jaspar), in BED format. With strand orientation (directionality of binding). Human (hg19, hg38) and mouse (mm9, mm10) genomes. The binding sites were detected using the FIMO tool of the MEME suite using default settings. Extra columns include motif name (MA0139.1), score, p-value, q-value, and the motif sequence.
excluderanges Genomic coordinates of problematic genomic regions that should be avoided when working with genomic data. GRanges of exclusion regions (formerly known as blacklisted), centromeres, telomeres, known heterochromatin regions, etc. (UCSC ‘gap’ table data). Primarily for human and mouse genomes, hg19/hg38 and mm9/mm10 genome assemblies.
GeneSummary This package provides long description of genes collected from the RefSeq database. The text in “COMMENT” section started with “Summary” is extracted as the description of the gene. The long text descriptions can be used for analysis such as text mining.
ontoProcData This package manages rda files of multiple ontologies that are used in the ontoProc package. These ontologies were originally downloaded as owl or obo files and converted into Rda files. The files were downloaded at various times but most of them were downloaded on June 22 2021.
rGenomeTracksData rGenomeTracksData is a collection of data from pyGenomeTracks project. The purpose of this data is testing and demonstration of rGenomeTracks. This package include 14 sample file from different genomic and epigenomic file format.
scAnnotatR.models Pretrained models for scAnnotatR package. These models can be used to automatically classify several (immune) cell types in human scRNA-seq data.
synaptome.data The package provides access to the copy of the Synaptic proteome database. It was designed as an accompaniment for Synaptome.DB package. Database provides information for specific genes and allows building the protein-protein interaction graph for gene sets, synaptic compartments, and brain regions.
synaptome.db The package contains local copy of the Synaptic proteome database. On top of this it provide a set of utility R functions to query and analyse its content. It allows extraction of information for specific genes and building the protein-protein interaction graph for gene sets, synaptic compartments, and brain regions.
TxDb.Athaliana.BioMart.plantsmart51 Exposes an annotation databases generated from BioMart by exposing these as TxDb objects. This package is for Arabidopsis thaliana (taxID: 3702). The BioMart plantsmart release number is 51.
There is 1 new workflow package in this release of Bioconductor.
There are no new online books.
Changes in version 1.41.1
Changes in version 1.65.3 (2021-09-22)
SOFTWARE QUALITY
Making sure all pathnames are of length 100 or shorter.
Changes in version 1.65.2 (2021-09-22)
SOFTWARE QUALITY
Now properly registering native routines.
Changes in version 1.65.1 (2021-09-09)
BUG FIXES
Changes in version 3.3.4 (2021-09-16)
Changes in version 1.3.2 (2021-08-05)
Add rmarkdown to the suggests field
Changes in version 1.3.1 (2021-08-05)
Add warnings for small sample size.
Changes in version 3.1.0
MAJOR UPDATES
USER-VISIBLE MODIFICATIONS
(3.1.1) If there is a duplicate entry in the hub cache for a resource, hub code will no longer produce an ERROR. If the duplicate resource was not requested the duplicate is ignored. If the duplicate resource is requested, produce a warning for corrupt cache and continue with first found entry.
(3.1.3) Fix typo in message display
(3.1.5) Deprecate the display,Hub-method
BUG CORRECTION
Changes in version 1.6.0
NEW FEATURES
(v. 1.5.5) add repository() to return the binary repository location, if available.
(v. 1.5.7) drs_stat() and drs_cp() support signed URLs
USER VISIBLE CHANGES
(v. 1.5.2) drs_stat() uses multiple cores (on non-Windows) to enhance performance
(v. 1.5.6) install() delegates to BiocManager::install(), providing more flexibility (e.g., installing from GitHub) and robustness.
(v. 1.5.7) drs_stat() returns fields more selectively.
Changes in version 1.4.0
New Features
Changes in version 1.7.3 (2021-08-01)
Fixed the typo in vignettes.
Changes in version 1.7.2 (2021-07-31)
Fixed the issues of using 3’most bam file (generate using ThreeMostPairBam) in PASEXP_IPA.
Changes in version 1.7.1 (2021-07-09)
Fixed the missing SS column issues in PAS2GEF.
Changes in version 3.23.1 (2021-08-19)
DOCUMENTATION
Changes in version 1.10.2 (2021-07-13)
Bug fix affecting {artmsAnalysisQuantifications()}
Allow {artmsAnalysisQuantifications()} to process previous versions of artMS
Change Extension of {artms_sessionInfo_quantification} file from {.txt} to {.log}
Change default parameters of the configuration files: less verbose
Changes in version 1.10.1 (2021-06-30)
External packages used exclusively by the {artmsAnalysisQuantifications} function are not required. Those packages will have to be installed before running this function.
{artmsAvgIntensityRT}: argument {species} is not longer required
Changes in version 2.3.1
BUG FIXES
Changes in version 1.17.1
Changes in version 0.99.36 (2021-08-01)
USER VISIBLE CHANGES
Changes in version 2.5.7 (2021-10-05)
Fix tests for BiocParallel behaviour.
Changes in version 2.5.6 (2021-10-05)
Revert 2.5.5 changes; add expectation to empty tests.
Changes in version 2.5.5 (2021-08-24)
Bugfix tests with change in BiocParallel behaviour
Changes in version 2.5.4 (2021-08-24)
Ensure ordering of genes in chains is consistent with input data when using divide and conquer
Changes in version 2.5.3 (2021-08-11)
Add GeneExponent and CellExponent settings for divide and conquer.
Changes in version 2.5.2 (2021-08-11)
Add better spacing around EFDR message.
Fix ggplot2 guide=FALSE
warnings
Remove an errant browser() call
Changes in version 2.5.1 (2021-05-19)
Add error condition for unnamed cells.
Changes in version 1.3.1
Minor improvements and fixes
Update documentation for getRDS(), mcmcChain(), and spatialEnhance().
Changes in version 1.3.0
Minor improvements and fixes
Changes in version 0.99.4 (2021-10-15)
Changed stats::coef to stats4::coef
Changes in version 0.99.3 (2021-10-15)
Added the plotIt = FALSE option for plotRMSE function
Added some more explanations into the “Goodness of Fit” chapter
fitNB, fitZINB, fitHURDLE, fitZIG, and fitDM functions now work with both phyloseq object or count matrices
Changes in version 0.99.2 (2021-10-11)
Changed dependency from R 4.0.0 to 4.1.0
Added example for iterative_ordering() function
Removed the usage of @ to access object’s slot in the vignette
Removed a suppressMessages() and a suppressWarnings() from createTIEC()
Added verbosity to createTIEC() function
Added NEWS file
Changes in version 0.99.1 (2021-10-04)
Removed unnecessary files
Changes in version 0.99.0 (2021-09-29)
Bumped version for submission to Bioconductor
Added README.md file
Changes in version 2.18.1
Possibility to retrieve single cell full length RNA-Seq from Bgee 15.0 and after
Possibility to filter data based on sex and strain for Bgee 15.0 and after
Possibility to filter on cellTypeId for single cell full length RNA-Seq for Bgee 15.0 and after
Added pValue in the download files
Changes in version 0.99.10
coverageOverRanges() now supports mean and sum as combination method. Dpending on the returnOption, mean/ sum are computed over ranges or replicates.
Changes in version 0.99.9
BSFDataSet() and BSFDataSetFromBigWig() now check the path to the bigwig files in the meta data for potential duplicates
coverageOverRanges() now supports also ranges with different width,
if
returnOption = merge_positions_keep_replicates
Fix bug in makeBindingSites(); The minWidth parameter is now implemented as true lower boundary (>= instead of >). The default has changed from 2 to 3.
Fix description in makeBindingSites(); The minCrosslinks parameter describes the number of positions covered by crosslink events, instead of the total number of crosslinks.
Updated color scheme in rangeCoveragePlot(); and changed position of indicator box
Updated visual of reproducibiliyCutoffPlot() function
Changes in version 0.99.8
Updated coverageOverRange(), Function now does support different output formats, summarizing the coverage differently over range, replicates and condition
Changes in version 0.99.1
Fix bugs for Bioconductor submission
Changes in version 0.99.0 (2021-05-15)
Submitted to Bioconductor
Changes in version 1.29
NEW FEATURES
(1.29.10) Check for Sys.setenv
and
suppressWarnings
/suppressMessages
(1.29.8) Check for sessionInfo
/ session_info
in vignette code.
(1.29.5) Check for installation calls in vignette code.
(1.29.1) Check for install()
function calls in R code.
BUG FIXES
(1.29.14) Various internal improvements to the codebase.
(1.29.12) Checks on class membership code now include is() ==
grammar.
(1.29.6) Use appropriate input (pkgdir
) to internal checking
functions.
(1.29.3) Add unit tests for legacy function searches.
(1.29.2) rename internal function from checkIsPackageAlreadyInRepo to checkIsPackageNameAlreadyInUse
Changes in version 2.1
MAJOR UPDATES
Changes in version 1.28
USER VISIBLE CHANGES
(v 1.27.3) Setting progressbar = TRUE
for SnowParam() or
MulticoreParam() changes the default value of tasks
from 0 to
.Machine$integer.max
, so that progress on each element of X
is
reported.
(v 1.27.3) tasks
greater than length(X)
are set to
length(X)
. Thus .Machine$integer.max
, for instance, assures
that each element of X
is a separate task.
(v 1.27.5) Use of random numbers is robust to the distribution of jobs across tasks for SerialParam(), SnowParam(), and MulticoreParam(), for both bplapply() and bpiterate(), using the RNGseed= argument to each *Param(). The change is NOT backward compatible – users wishing to exactly reproduce earlier results should use a previous version of the package.
(v 1.27.8) Standardize SerialParam() construct to enable setting additional fields. Standardize coercion of other BiocParallelParam types (e.g., SnowParam(), MulticoreParam()) to SerialParam() with as(., “SerialParam”).
(v. 1.27.9) By defualt, do not only run garbage collection after every call to FUN(), except under MulticoreParam(). R’s garbage collection algorithm only fails to do well when forked processes (i.e., MulticoreParam) assume that they are the only consumers of process memory.
(v 1.27.11) Developer-oriented functions bploop.*() arguments changed.
(v 1.27.12) Ignore set.seed() and never increment the global random number stream. This reverts a side-effect of behavior introduced in v. 1.27.5 to behavior more consistent with version 1.26.
(v 1.27.16) Better BPREDO support for previously started BPPARAM, and ‘transient’ BPPARAM without RNGseed.
BUG FIXES
Changes in version 1.12.0
NEW FEATURES
biocRevDepEmail
sends an email to several downstream maintainers to
notify them of a deprecated package.
biocBuildEmail
allows deprecation notices using the template in the
inst
folder. Use templatePath()
to see available templates by
their
location.
PackageStatus
indicates whether a package is slated for
‘Deprecation’ by checking the meat-index.dcf
file.
pkgDownloadStats
provides the download statistics table for a
particular package.
BUG FIXES
biocDownloadStats
includes all types of Bioconductor packages
biocBuildReport
improved to work on old-rel, release, and devel
Bioconductor versions
Changes in version 2.22.0
USER-VISIBLE CHANGES
BUG FIXES AND IMPROVEMENTS TO HTML STYLE
Improved navigation for screen readers by adding role=’link’ and tabindex=’0’ to elements in the table of contents. TOC navigation can also be followed by pressing “Enter” when selected in addition to clicking with the cursor.
Addressed further styling issues for code blocks, introduced by changes in rmarkdown. This time re-introducing padding around <pre> tags.
Changes in version 1.3.8
SIGNIFICANT USER-VISIBLE CHANGES
use_bioc_github_action() has been updated to match as much as possible the changes in r-lib/actions up to the latest commit https://github.com/r-lib/actions/commit/630f4c9d8b813f45d0327a2fc20eb264fd518450.
Changes in version 1.3.4
NEW FEATURES
use_bioc_github_action() is now more robust in preventing tcltk errors thanks to this pull request by Ben Laufer https://github.com/lcolladotor/biocthis/pull/19.
Changes in version 1.3.2
NEW FEATURES
Changes in version 1.61.0
ENHANCEMENT
Changes in version 1.1.16 (2021-10-19)
Update documentation.
Add ORCID for Alexis.
Changes in version 1.1.15 (2021-10-18)
Correct getUrlContent() to handle binary files.
Changes in version 1.1.14 (2021-10-17)
Factorize RCurl calls into global functions.
Disable warnings in calls to readLines() when using base::url().
Catch errors when trying to set locale.
Correct some tests.
Changes in version 1.1.13 (2021-10-12)
Make custom persistent the cache the default, following slowness with BiocFileCache in biodbHmdb.
Remove useless bib refs in vignettes/references.bib.
Add session info in vignettes.
Add ORCID, URL and BugReports.
Add an install section in main vignette.
Changes in version 1.1.12 (2021-10-09)
Switch back to custom implementation of persistent cache, following errors with BiocFileCache on Windows and also slowness with HMDB.
Changes in version 1.1.11 (2021-10-07)
Decompose test test.collapseRows() because of error on Bioconductor not reproduced on local computer.
Changes in version 1.1.10 (2021-09-30)
Disable UniProt request test: it fails (result is NA) for reason unknown only on Bioconductor Linux server during “R CMD check”. Works fine on local computer.
Changes in version 1.1.9 (2021-09-28)
Correct handling of wrong URL with base::url().
Changes in version 1.1.8 (2021-09-28)
Correct bug of UniProt request on Windows.
Changes in version 1.1.7 (2021-09-23)
Ignore build folder when building package.
Update documentation.
Correct setting of R_ENVIRON_USER when building.
Changes in version 1.1.6 (2021-09-14)
Update documentation.
Changes in version 1.1.5 (2021-09-13)
Correct bug in return type of BiodbRequestScheduler::sendRequest().
Correct encoding of test reference filenames.
Changes in version 1.1.4 (2021-09-12)
Allow to set the test reference folder directly into runGenericTests(). This is now necessary for running generic tests in extension packages.
Changes in version 1.1.3 (2021-09-12)
Set package name when calling runGenericTests() in order to find test ref files the correct way, by calling system.file().
Changes in version 1.1.2 (2021-09-09)
Use BiocFileCache for the persistent cache system.
Switch to R6.
Define do…() private methods to be redefined in subclasses, instead of redefining public methods defined inside super class.
Use now local entry files for testing parsing of entry fields.
Changes in version 1.1.1 (2021-06-10)
Allow skipping of some fields when testing searchForEntries().
Move test reference entries folder from tests/testthat/res to inst/testref.
Move long tests folder from tests/long to longtests and enable Bioconductor long tests.
Changes in version 1.0.4 (2021-06-09)
Bug fix: correct call to logger in BiodbPersitentCache class.
Changes in version 1.0.3 (2021-05-26)
Bug fix: correct generic test of searchForEntries(), allowing testing with NA value.
Changes in version 1.0.2 (2021-05-23)
Bug fix: correct return type of searchForEntries(), which now returns always a character vector and never NULL.
Changes in version 1.0.1 (2021-05-20)
Bug fix: correct some calls to logging functions that raised a warning.
Changes in version 0.99.6 (2021-10-12)
Rename vignette.
Add session info and install section in vignette.
Use importFrom.
Changes in version 0.99.5 (2021-10-07)
Write description on multiple lines.
Put comment banners to indicate public and private sections in R6 class.
Changes in version 0.99.4 (2021-09-28)
Correct list index in vignette.
Changes in version 0.99.3 (2021-09-28)
Complete all chapters in README.
Remove ‘foo’ names in vignette.
Changes in version 0.99.2 (2021-09-23)
Define R_BUILD_TAR in makefile to build on UNIX.
Changes in version 0.99.1 (2021-09-23)
Upgrade maintenance files.
Ignore build folder.
Changes in version 0.99.0 (2021-09-16)
Submitted to Bioconductor
Changes in version 0.99.4 (2021-10-18)
When reading the zipped database, take the only XML file available, ignoring other files.
Changes in version 0.99.2 (2021-10-12)
Add ORCID, URL and BugReports.
Add session info and install sections in vignette.
Corrected indentations in vignette.
Changes in version 0.99.1 (2021-09-29)
Slight corrections for Bioconductor submission.
Changes in version 0.99.0 (2021-07-16)
Submitted to Bioconductor
Changes in version 0.99.4 (2021-10-13)
Merge both vignettes into a single one.
Remove messages from magick package.
Changes in version 0.99.3 (2021-10-12)
Add install section in vignette.
Use importFrom.
Add ORCID, URL and BugReports.
Changes in version 0.99.2 (2021-10-12)
Rename main vignette file.
Add reference.
Add session info in vignettes.
Changes in version 0.99.1 (2021-09-28)
Made some corrections for submitting to Bioconductor.
Changes in version 0.99.0 (2021-09-16)
Submitted to Bioconductor
Changes in version 0.99.3 (2021-10-18)
Remove deprecated slow frequency of request send.
Changes in version 0.99.2 (2021-10-12)
Add ORCID, URL and BugReports.
Add citation into vignette.
Add install and session info sections to vignette.
Changes in version 0.99.1 (2021-09-29)
Complete README.
Slight corrections for Bioconductor submission.
Add generated documentation files.
Changes in version 0.99.0 (2021-09-16)
Submitted to Bioconductor.
Changes in version 0.99.4 (2021-10-12)
Add session info and install section in vignette.
Rename vignette.
Use importFrom.
Add ORCID, URL and BugReports.
Changes in version 0.99.3 (2021-10-11)
Show progress when filtering results in geneSymbolToUniprotIds().
Changes in version 0.99.2 (2021-10-03)
Use biodb 1.1.10.
Changes in version 0.99.1 (2021-09-23)
Ignore build folder when building package.
Add documentation.
Changes in version 0.99.0 (2021-09-16)
Submitted to Bioconductor
Changes in version 2.50.0
MINOR CHANGES
BUG FIXES
Address issue where checking the list of Ensembl Archives would stop all queries from working if the main www.ensembl.org site was unavailable.
Fix bug introduced in getSequence() where asking for flanking sequences resulted in an invalid query.
The argument ‘host’ is no longer ignored in useEnsembl() (Thanks to forum user “A” - https://support.bioconductor.org/p/9139019/)
Changes in version 1.0.0
Changes in version 1.17.0
future
and doFuture
for simplification of
parallelization. All
control of parallel computation now done through BiocParallel
. Changes in version 0.99.0
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 0.99.18 (2020-06-01)
Importing “assay<-“ in the NAMESPACE
Changes in version 0.99.17 (2020-06-01)
Correcting the import of dependencies
Changes in version 0.99.16 (2020-06-01)
Avoiding the overlapping when loading dependencies
Changes in version 0.99.15 (2020-06-01)
Removing the redundant print and summary function
Changes in version 0.99.14 (2020-06-01)
Modifying the output of BUSseq_MCMC as a SingleCellExperiment object and allowing the input as that object as well
Changes in version 0.99.13 (2020-05-15)
Modifying the running example
Changes in version 0.99.12 (2020-05-15)
Revising the random number generator for MacOS
Changes in version 0.99.11 (2020-05-15)
Debugging for MacOS
Changes in version 0.99.10 (2020-05-15)
Continuing to debug for MacOS
Changes in version 0.99.9 (2020-05-15)
Modifying the warnings when building on MacOS
Changes in version 0.99.8 (2020-05-15)
Correcting the usage of OS macro
Changes in version 0.99.7 (2020-05-14)
Updating th source code for MacOS
Changes in version 0.99.6 (2020-05-13)
Downsizing the example dataset to avoid reaching the time limit of check
Changes in version 0.99.5 (2020-05-12)
Adding the macro for Mac in the source code
Shortening the vignettes
Adding Watched Tags BUSseq to my profile
Changes in version 0.99.4 (2020-05-12)
Correct R version dependency
Solve the warnings by missing parenthesees
Changes in version 0.99.3 (2020-05-08)
Set LazyData as TRUE for building vignette
Changes in version 0.99.2 (2020-05-08)
Correctly pushing by Git
Changes in version 0.99.1 (2020-05-07)
Revised the warnings by R CMD check, including adding parentheses in src and R dependency in DESCRIPTION
Changes in version 0.99.0 (2020-05-04)
Submitted to Bioconductor
Changes in version 0.99.0
NEW FEATURES
Changes in version 2.0.0
BACKWARDS-INCOMPATIBLE CHANGES
The CAGEset
class is removed.
Accessors using plain data.frame
formats are removed.
Modifier functions return the object instead of silently modifying it
in the global environment. Thus, you can use R pipes (|>
).
Removed export function that unconditionally wrote files to the
working directory, such as exportCTSStoBedGraph
. As a replacement
a
new converter is provided, exportToBrowserTrack
, that produces
UCSCData
objects that the user can then wite to files using the
rtracklayer package.
Removed the extractExpressionClass
function, as the information is
easily accessible from within the CTSS
or ConsensusClusters
objects.
NEW FEATURES
CTSSnormalizedTpmGR
and CTSStagCountGR
now accept "all"
as a
special
sample name to return them all in a GRangesList
object.
Plot interquantile width and expression clusters with ggplot2.
BUG FIXES
Corrected the getExpressionProfiles
function to accept CAGEexp
objects.
Updated the exampleCAGEexp
object to contain expression classes.
Restore paraclu support for CAGEexp objects.
Corrected a bug in aggregateTagClusters
that was causing
mislabelling
of tag clusters (PR#42).
Prevent plotReverseCumulatives
from crashing when values are not in
range. (PR#43).
Changes in version 2.11.3
BUG FIXES
Fix strange behavior from random number generation in R >= 4.1.1
Changes in version 2.11.2
BUG FIXES
Fix reference naming scheme for binning and alignment methods
Changes in version 2.11.1
BUG FIXES
Use as(x, ‘DFrame’) instead of as(x, ‘DataFrame’)
Fix logical length > 1 error in ‘segmentationTest()’
Changes in version 1.16.0 (2021-10-14)
New Features
Changes in version 2.6.0
New features
Changes in version 1.9.3 (2021-10-04)
Speed up final step in decontX when creating final decontaminated matrix
Changes in version 1.9.2 (2021-07-19)
Changes in version 0.0.1
Changes in version 1.5.4
Update CITATION
Changes in version 1.4.3
Fix netConditionsPlot function bug related to factors in data.frame
Changes in version 0.99.1
Documentation improvements.
Changes in version 0.99.0
Changes in version 3.27.7
Fix the error “!anyNA(m32) is not TRUE” in seqlevelsStyle is not handled.
Changes in version 3.27.6
Fix the error “pvalue” undefined columns selected in enrichmentPlot
Changes in version 3.27.5
update documentation of pipeline.rmd
Changes in version 3.27.4
use formatSeqnames function to handle the error from seqlevelsStyle: “cannot switch some of GRCm38’s seqlevels from NCBI to UCSC style”
Changes in version 3.27.3
use formatSeqnames function to handle the error from seqlevelsStyle: “!anyNA(m31) is not TRUE “
Changes in version 3.27.2
add keepExonsInGenesOnly for genomicElementDistribution
add upstream and downstream for assignChromosomeRegion function when define promoter and downstream regions.
Changes in version 3.27.1
Add the possibility of find overlaps by percentage covered of interval for function findOverlapsOfPeaks
Changes in version 1.29.2
extend functions for plotting peak profiles to support other types of bioregions (2021-10-15, Fri, @MingLi-292, #156, #160, #162, #163)
Changes in version 1.29.1
add example for seq2gene function (2021-05-21, Fri)
Changes in version 1.1.3
Overview:
New functionalities:
Fixed and improved input in CAPRIpop dataset format
Changes in version 1.1.1
Overview:
New functionalities:
Fixed bugs related with byrow options when reading CAPRI formatted datasets
Improved VisNetwork output to include information about samples inside nodes
Changes in version 2.14.0
Changes in version 0.99.0 (2021-01-22)
Changes in version 1.7.0
Changes in version 1.32.0
DEPRECATION NOTICE
Changes in version 4.1.4
import yulab.utils (2021-08-20, Fri)
Changes in version 4.1.3
Remove Human Gut Microbiome dataset as the functionalities are provided in https://github.com/YuLab-SMU/MicrobiomeProfiler (2021-08-15, Sun)
Changes in version 4.1.2
update kegg_species.rda and allow online download using KEGG api (2021-08-14, Sat)
Changes in version 4.1.1
Changes in version 1.5.2 (2021-10-04)
clustify_lists()
support for output of overlapping genes
(details_out = TRUE
)
Added truncated mean and trimean modes to average_clusters()
Changes in version 1.5.1 (2021-08-04)
clustify_lists()
support for uneven number of markers
Deprecated SeuratV2 support
Changes in version 1.7.4
MINOR
Minor fix: removed ` from Vignette
Changes in version 1.7.3
SIGNIFICANT USER-VISIBLE CHANGES
CNVfilteR specfically supports VCFs produced by Torrent Variant Caller
Changes in version 1.7.2
BUG FIXES
MINOR
Minor bug fixed: stop message was not completely shown on loadSNPsFromVCF()
Changes in version 1.7.1
MINOR
Changes in version 1.9.1
add uniquely_high_in_one_group
method in get_signatures()
.
add compare_partitions()
.
parallel computing is implemented with foreach + doParallel
Changes in version 1.9.0
use row/column* family functions in adjust_matrix()
to reduce the
memory
usage as well as improve the speed.
Changes in version 2.9.4
fixed a bug of missing right annotation legends for vertically concatenated heatmaps.
Legend()
: support border
to be set to asis
.
Rasterization: the default maximal size for temporary image is set to 30000 px (both for width and height).
add a new argument beside
in anno_barplot()
to position bars
beside each other.
add plot()
method for Heatmap
and HeatmapList
classes.
add anno_customize()
.
Changes in version 2.9.3
pheatmap()
/heatmap()
/heatmap.2()
: set default of run_draw to
FALSE.
throw error when the heatmaps (list) are already initialized by draw() when adding them.
set wrap = TRUE
in grid.grabExpr()
when capturing the legend
objects.
make_comb_mat()
: support GRangesList
object as input.
legends: fixed a bug of the grid heights were not correctedly calculated.
discrete annotations: neighbour grids are merged into one single grid if they have the same values.
anno_barplot()
: allows to add numbers on top of bars.
UpSet()
: axis labels are automatically formated for genomic
coordinates.
AnnotationFunction()
: add a new argument cell_fun
.
When the dendrogram height is zero, the corresponding viewport has scale (0, 1).
Changes in version 2.9.2
fixed a bug of bg_col
for transposed matrix in UpSet()
.
print warnings if names of annotations have different orders from the matrix row/column names.
Changes in version 2.9.1
fixed a bug of editing gTree object where the list element “just” has been changed to “justification” in recent R versions.
Changes in version 1.1.002 (2021-08-31)
Made the following significant changes
Added an internal function .retrieveClustersNumberK to suggest the clusters number to use in lusterCellsInternal().
Added suggestedClustersNumber slot in scRNAseq class to retrieve this suggested clusters number.
Added accessors getSuggestedClustersNumber and setSuggestedClustersNumber.
Updated all the objects used in examples and tests to have this slot.
Changes in version 1.5.7
CoreSets can now be made with treatment combination experiments via the TreatmentResponseExperiment class!
Changes in version 1.5.6
Fix bug in LongTable -> data.table coerce method that was causing rows of some assays to be dropped (closes issue #)
Changes in version 1.5.5
Overhauled LongTable coerce methods to use the LongTableDataMapper class instead of the deprecated ‘LongTable.config’ attribute
Changes in version 1.5.4
Fix bug in .sanitize input caused by length > 1 coercing to logical vector
Changes in version 1.5.3
Fix bug in connectivityScore caused by length > 1 coercing to logical vector; this should fix errors in RadioGx and PharmacoGx vignettes that were caused by failed R CMD build
Changes in version 1.5.2
Added a CoreSet-utils documentation section to document subset, intersect, combine and other set operations for a CoreSet object.
Changes in version 1.5.1
Fix bug in .rebuildProfiles where the function fails if replicate_id is assigned as a rowID column in the LongTable in @sensitivity
Changes in version 1.5.0
Changes in version 0.99.6
Calculation of column ranks now uses matrixStats::colRanks instead of an apply statement with base::rank.
Changes in version 0.99.0
Changes in version 1.12.0
Web server support (optimised to run in ShinyProxy)
Bug fixes and minor improvements
Changes in version 0.99.0
Changes in version 1.5.4 (2021-09-17)
It is not required anymore to specify exactly the right colours
Changes in version 1.5.3 (2021-09-16)
Added option to read in .h5 files
Changes in version 1.5.2 (2021-09-15)
Added description on how to handle images with couplet/patchwork
Changes in version 1.5.1 (2021-05-19)
Bugfix: erroneous dimension setting when legend=NULL
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 2.6.0
Major: We fixed a bug in DaMiR.ModelSelect. Now optimal models are correctly selected;
Major: Now users can plot specific graphs in DaMiR.Allplot and we added new plots;
Minor: We modified the color scale in corrplot
Changes in version 1.3.2
NEW FEATURES
Changes in version 1.5.1 (2021-09-01)
Changes in version 2.0.0
Changes
Some method’s names have been changed to make them easier to identify:
scira now is called Univariate Linear Model (ulm).
The column name for tf in the output tibbles has been changed to source.
Updated documentation for all methods.
Updated vignette and README.
decouple function now accepts order mismatch between the list of methods and the list of methods’s arguments.
New features
New methods added:
Multivariate Linear Model (mlm).
New decoupleR manuscript repository: https://github.com/saezlab/decoupleR_manuscript
New consensus score based on RobustRankAggreg::aggregateRanks() added when running decouple with multiple methods.
New statistic corr_wmean inside wmean.
Methods based on permutations or statistical tests now return also a p-value for the obtained score (fgsea, mlm, ora, ulm, viper, wmean and wsum).
New error added when network edges are duplicated.
New error added when the input matrix contains NAs or Infs.
Changes in version 1.1.0
New features
All new features allow for tidy selection. Making it easier to evaluate different types of data for the same method. For instance, you can specify the columns to use as strings, integer position, symbol or expression.
Methods
New decouple() integrates the various member functions of the decoupleR statistics for centralized evaluation.
New family decoupleR statists for shared documentation is made up of:
Converters
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 1.3.1
Changes in version 0.20.0
BUG FIXES
Changes in version 1.0.0
Changes in version 1.9.1 (2021-10-16)
Changes in version 1.1.2
Changes in version 2.1.4
Using non-linear fit to constrain similarity matrix.
Recalculate intensity for given peaks.
Direct alignment to root is added.
Multiple strategies for getting distance matrix and tree-agglomeration is added.
Remove peaks if not aligned.
Changes in version 2.1.0
Added support for IPF based Post-translation Modification alignment.
Added Minimum Spanning Tree based alignment for reference-free approach.
Reintegrate area under the peak for low-confidence peaks.
Supporting Savitzky-Golay smoothing while calculating area.
Added input to select peptides which to align.
Speed improvement in progressive alignment by storing new featues in lists instead of data frames.
Changes in version 3.3.4
Fix bFlip issues
Fix bug where mode not passed to summarizeOverlaps
Add $inter.feature config parameter
Changes in version 3.3.2
Re-compute FDR when fold change other than 0 is specified
Remove most gc() calls for performance
Roll in bugfixes
Changes in version 0.99.5
Data reformatting
Changes in version 0.99.4
Bug fix
Changes in version 0.99.3
Reduce size of tutorial data
Changes in version 0.99.1
Updated default number of cores to 2
Changes in version 0.99.0
Changes in version 1.4.1
fixed bug in log2_FC.R;
added rmarkdown as Suggests
in DESCRIPTION.
Changes in version 1.6
Bug Fixes:
Changes in version 3.19.4
upate error message of enricher_internal (2021-9-3, Fri)
Changes in version 3.19.3
upate DisGeNET and NCG data (2021-8-16, Mon)
Changes in version 3.19.2
bug fixed, change ‘is.na(path2name)’ to ‘all(is.na(path2name))’ (2021-06-21, Mon)
Changes in version 3.19.1
Changes in version 0.99.3 (2021-05-23)
Ensured that all global variables are well-defined in the namespace.
Changes in version 0.99.2 (2021-05-22)
Revised to address comments by the Bioconductor reviewer.
dStruct now uses the IRanges object from Bioconductor.
All function names follow camel case.
More descriptions of functions.
Added a test to check validity of code when running dStruct in the proximity_assisted mode.
Changes in version 0.99.1 (2021-04-11)
Fixed errors and warnings from checks by bioc-issue-bot.
Changes in version 0.99.0 (2021-04-07)
Submitted to Bioconductor
Changes in version 0.9.0
Changes in version 1.5.2
Changes in version 1.12
Changes in version 1.13.2
cnetplot now works with a named list (2021-08-23, Mon; clusterProfiler#362)
Changes in version 1.13.1
Changes in version 2.17.4
Fix issue with extracting 5’ or 3’ UTRs for transcript without UTRs.
Changes in version 2.17.3
Make parameter port
optional in the script to create EnsDb
databases.
Changes in version 2.17.2
Disable ideogram plotting in vignettes.
Changes in version 2.17.1
Fix error when importing uncompressed GTF files.
Changes in version 1.1.9 (2021-09-19)
min.baseq to reduce the effect of sequencing errors
very fast Fisher Exact from HTSlib
old code removed
Changes in version 1.1.0 (2021-05-21)
Changes in version 1.0.8
Minor bug fix in maxStepProb documentations
Changes in version 1.0.7
Exporting maxStepProb, which compute the MLE of initial and transition probabilities of a K-state HMM, as well as simulateMarkovChain, which simulates a Markov chain of length ‘n’ given a matrix of transition probabilities
Changes in version 1.0.6
Minor bug fix in controlEM documentation
Changes in version 1.0.5
Minor bug fix in callPatterns and info function (explict import of S4Vectors::mcols and utils::tail).
Exporting expStep function, which implements the E-step of EM algorithm (forward-backward & Viterbi algorithm) for a K-state HMM.
Changes in version 1.0.4
Adding function callPatterns to exp[ort] combinatorial patterns (or posterior probabilities) associated with a given set of genomic regions.
Adding function info to print summary statistics from epigraHMM output. This function will print the model’s BIC, log-likelihood, and combinatorial patterns associated with mixture model components.
Adding new example dataset helas3 with ENCODE ChIP-seq data from broad epigenomic marks H3K27me3, H3K36me3, and EZH2.
Adding option to prune combinatorial patterns associated with rare states. See vignette for details.
In differential peak calling, epigraHMM now exports combinatorial pattern table. See vignette for details.
Improvement of the vignette to clarify epigraHMM’s use of blacklisted regions and gap tracks.
Changes in version 1.0.3
Minor updates in the NEWS file as well as the README page.
Changes in version 1.0.2
epigraHMM now exports a function called segmentGenome that segments a given genome (e.g. ‘mm10’) into non-overlapping genomic windows while considering gap tracks and blacklisted regions.
Changes in version 1.0.1
Minor fix in the package DESCRIPTION file and version numbers
Changes in version 1.3.1
Aligning versions to the current bioconductor release
Added DietSeurat() call in vignette to prevent issues
Changes in version 1.19.1
default for typePlot: fix issue length > 1 in coercion to logical
fix for ggplot2 >= 3.3.4: replace guides(fill = FALSE) by guides(fill = ‘none’)
fix few notes check SummarizedExperiment + ggvis
Changes in version 2.1.0
MAJOR UPDATES
Changes in version 1.21.2
Allow writing of HaploPainter input files without a HaploPainter installation.
Changes in version 1.21.1
Add information on kinship-based relatedness to kinship sum test results.
Keep memory consumption constant. This allows arbitrary long simulation runs without running out of memory. Fixes issue #22. Due to the solution of that problem, histograms and densities reported by the simulation functions may slightly deviate from comparable former runs on the same data.
Changes in version 1.3.1 (2021-10-13)
Fix tests
Changes in version 1.3.0 (2020-11-27)
Rshiny modifications for figure in paper
Changes in version 1.19.7
Changes in version 1.19.4
plotGseaTable now accepts units vector for column widths
Changes in version 1.19.2
Fixed fora() failing to run on a single pathway
Fixed problems random gene set generation for large k (issue #94)
Changed default eps to 1e-50
Changes in version 0.99.13 (2021-08-11)
convert geom_density into geom_hist in plot_annoDistance function
Changes in version 0.99.11 (2021-07-16)
rename findIT_enrichInAll to findIT_enrichFisher
Changes in version 0.99.10 (2021-07-15)
move all shiny function in FindIT2 into InteractiveFindIT2
Changes in version 0.99.0 (2021-06-27)
Changes in version 2.0.0
New loadFry() function, written by Dongze He with contributions from Steve Lianoglou and Wes Wilson. loadFry() helps users to import and process alevin-fry quantification results. Can process spliced, unspliced and ambiguous counts separately and flexibly. Has specific output formats designed for downstream use with scVelo or velocity analysis. See ?loadFry for more details.
Adding correlation tests: Spearman or Pearson correlations of a numeric covariate with the log counts, or with the log fold changes across pairs. The Spearman correlation test with counts was already implemented in the original SAMseq method as response type = “Quantitative”. For new functionality see ‘cor’ argument in the ?swish man page.
Adding importAllelicCounts() to facilitate importing Salmon quantification data against a diploid transcriptome. Can import either as a ‘wide’ format or as ‘assays’. Leverages tximeta(). For gene-level summarization, importAllelicCounts() can create an appropriate tx2gene table with the necessary a1 and a2 suffices, and it will automatically set txOut=FALSE, see ?importAllelicCounts for more details.
Added a ‘q’ argument to plotInfReps to change the intervals when making point and line plots.
Switched the legend of plotInfReps so that reference levels will now be on the bottom, and non-reference (e.g. treatment) on top.
Changes in version 1.99.18
Added helper functionality to importAllelicCounts, so it will create an appropriate tx2gene table with the necessary a1 and a2 suffices, and it will automatically set txOut=FALSE.
Added a ‘q’ argument to plotInfReps to change the intervals when making point and line plots.
Switched the legend of plotInfReps so that reference levels will now be on the bottom, and non-reference (e.g. treatment) on top.
Added loadFry() to process alevin-fry quantification result. Can process spliced, unspliced and ambiguous counts separately and flexibly.
Changes in version 1.99.15
Adding correlation tests: Spearman or Pearson correlations of a numeric covariate with the log counts, or with the log fold changes across pairs. The Spearman correlation test with counts was already implemented in the original SAMseq method as response type = “Quantitative”. For new functionality see ‘cor’ argument in the ?swish man page.
Adding importAllelicCounts() to facilitate importing Salmon quantification data against a diploid transcriptome. Can import either as a ‘wide’ format or as ‘assays’. Leverages tximeta().
Changes in version 1.9.6
Specifying ties.method in matrixStats::rowRanks.
Changes in version 1.9.1
Added importAllelicCounts() with options for importing Salmon quantification on diploid transcriptomes.
Changes in version 0.99.0 (2021-04-15)
Changes in version 2.1.24
Added UpdateMetaclusters function, removed RelabelMetaclusters, ReassignMetaclusters and Reordermetaclusters functions.
Updated CheatSheet
Added code from UpdateDerivedValues for metaclustersMFIs to UpdateFlowSOM
Changes in version 2.1.23
Added checkNames = FALSE in MetaclusterMFIs
Changes in version 2.1.22
Reordered code in UpdateDerivedValues, RelabelMetaclusters, ReorderMetaclusters and ReassignMetaclusters.
Changes in version 2.1.21
Added ReorderMetaclusters, to reorder the metacluster levels.
Changes in version 2.1.20
Updated PlotManualBars, Plot2DScatters and FlowSOMmary so that it works with relabeled metaclusters.
Changes in version 2.1.19
AggregateFlowFrames accepts channels and markers
AggregateFlowFrames now gives a warning when files do not contain the same number of channels
AggregateFlowFrames now gives warnings when files do not contain the same markers
Bugfix in AggregateFlowFrames now works when one channel is given
Bugfix in PlotFileScatters now works when one channel is given
Added silent parameter in PlotFileScatters to stop messages
PlotFileScatters supports channels and markers now
Add info to FlowSOM object: date when flowSOM object is made, FlowSOM verion and arguments given to FlowSOM call
Fixed bug in PlotManualBars
Added silent parameter in NewData. GetFeatures’ silent parameter now also surpresses message from NewData (more concrete: ReadInput)
Changes in version 2.1.17
Added ReassignMetaclusters, to rename or split metaclusters
Fixed issue where a lot of warnings were printed in FlowSOMmary
PlotFilescatters now makes filenames unique if they are not and the function now works with output of AggregateFlowFrames
Changes in version 2.1.16
PlotManualBars allows input of NewData function
Changes in version 2.1.15
Fixed warnings with ggtexttable in FlowSOMmary
Changes in version 2.1.13
Added RelabelMetaclusters
PlotFileScatters now has a parameter to change the y-axis label to markers and/or channels (yLabel)
Now TRUE/FALSE vector is accepted as input in GetMarkers/GetChannels
Changes in version 2.1.11
Added example to AddAnnotation
Added example to NClusters, NMetaclusters
Changed examples that used fsom to flowSOM.res
Added textColor and textSize to AddLabels and PlotNumbers, PlotLabels
PlotNumbers can plot clusters and metaclusters with parameter “level”
In GetFeatures, the population parameter is changed to level
Added GetCounts and GetPercentages to get counts or percentages respectively per cluster or metacluster
FlowSOMmary doesn’t crash anymore with a column with the same values in heatmap
Included a print function for FlowSOM class
Fixed bug in PlotManualBars
PlotMarker also accept multiple markers now
Changes in version 2.1.8
Solved issue when matrix with no column was given to the SOM function
Changes in version 2.1.5
Scale parameter in FlowSOM function defaults to FALSE.
FlowSOM wrapper function now returns the FlowSOM object instead of a list containing the FlowSOM object and a metaclustering
The metaclustering is now found as an element in the flowSOM object. Also the number of metaclusters and the MFI values are stored and can be accessed by the NMetaclusters() and GetMetaclusterMFIs() functions.
If you want to reuse FlowSOM objects generated by previous versions, you can use the UpdateFlowSOM function.
FlowSOM now uses nClus = 10 as default instead of maxMeta = 10
FlowSOM now makes use of ggplot2 for plotting. PlotFlowSOM provides the main structure, and has parameters to adapt nodeSize, view (grid, MST or some own layout matrix), … PlotStars etc build on this by adding additional layers to the ggplot object. This also allows to easily incorporate multiple plots in all layout-tools such as ggarrange, cowplot, patchwork, …
GetChannels/GetMarkers can now also take a FlowSOM object as input instead of a flowFrame. New functions:
To easily generate a clear summary of the model with multiple plots, you can now use the FlowSOMmary function, which creates a pdf file.
GetFeatures allows to map new files (internally using the NewData function) and can return cluster counts, percentages and MFI values for each individual sample.
PlotFileScatters can be useful to get an overview of potential batch effects before running the FlowSOM algorithm
Changes in version 1.1.9
fobitools 1.0.0
Changes in version 2.0.0
MAJOR UPDATE Adding the Following Functionality:
Format, Library, and Testing Improvements
o Enable processing of libraries with 1:many reagent:target assignments
o Standardization and clarification of Annotation objects and symbol/identifier relationships
o Implementation of factored quantile normalization for timecourse screens
o Introduction of the simpleResult format and integration with associated functions
o Conditional testing framework for quantifying and visualizing signal agreement between contrasts
Transition to gene set enrichment testing via Sparrow
o Implement wrappers and provide recommendations fopr geneset enrichment testing in pooled screens
o Implementation of GREAT-style pathway mapping for libraries with heterogenous target:gene mappings
o Summarization tools for comparing enrichment signals across screens
New Visualization and Interpretation Tools
o Signal Summary Barchart (Single or Multiple Contrasts)
o Waterfall reagent/target/pathway visualization (Single Contrast)
o Contrast comparison plots:
Concordance at the Top (CAT)
Probability Space scatter plots
UpSet plots with conditional overlap framework
Changes in version 2.23.9
Subset covariance matrix to specified samples when sample.id argument is passed to fitNullModel when called with an AnnotatedDataFrame
Changes in version 2.23.8
Added option for recessive and dominant coding to assocTestSingle.
Changes in version 2.23.7
Implement MatrixGenotypeReader method for pcair by writing a temporary GDS file.
Changes in version 2.23.5
assocTestSingle, assocTestAggregate, admixMap, and pcrelate use the BiocParallel package for parallel execution on blocks of variants.
Changes in version 2.23.4
For assocTestAggregate, the total number of genotypes in a single iterator element (NxM where N=number of samples and M=number of variants) may be >2^31.
Changes in version 1.6.0
New features
Other notes
Changes in version 1.30.0
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
UCSC hg38 genome is now based on GRCh38.p13 instead of GRCh38.p12
UCSC mm10 genome is now based on GRCm38.p6 instead of GRCm38
seqlevelsStyle() setter now issues a warning when some seqlevels cannot be switched.
Changes in version 1.30.0
Changes in version 1.46.0
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.46.0
Changes in version 1.2.0
n
argument of annotatePC
was hard-coded. Now it can return
different number of enriched pathways.abs
argument of annotatePC
was fixed.plotAnnotatedPCA
function.drawWordcloud
has a new argument droplist
.plotAnnotatedPCA
is changed from PCs
to
PCnum
.studyTitle
for findStudiesInCluster
function. Changes in version 0.99.5
Revisions
fix platform build/check errors
Changes in version 0.99.4
Revisions
address reviewer’s comments
Changes in version 0.99.3
Revisions
remove seed
Changes in version 0.99.2
Revisions
change the maintainer
Changes in version 0.99.1
Revisions
modify the vignette for Bioc submission
Changes in version 0.99.0
NEW FEATURES
Changes in version 2021-09-22
0.99.5 make the consensus_views compatible ggtreeExtra and add package description. (2021-10-21, Thu)
Changes in version 0.0.10
update default color schemes in lower part of the SeqDiff plot (2021-08-20, Fri)
Changes in version 0.0.9
import R4RNA to fix R check (2021-08-03, Tue)
Changes in version 0.0.8
The migration of sequence recombination functionality from seqcombo package. (2021-07-20, Tue)
Changes in version 0.0.7
added ggSeqBundle() to plot Sequence Bundles for MSAs based ggolot2 (2021-03-18, Thu)
Changes in version 0.0.6
supports customize colors custom_color. (2020-12-28, Mon)
Changes in version 0.0.5
added new colors LETTER and CN6 provided by ShixiangWang.issues#8
Changes in version 0.0.4
added a Monospaced Font DroidSansMono (2020-3-23, Mon)
Changes in version 0.0.3
used a proportional scaling algorithm (2020-01-08, Wed)
Changes in version 0.0.2
tidy_msa for converting msa file/object to tidy data frame (2019-12-09, Mon)
Changes in version 0.0.1
Changes in version 0.99.0 (2021-08-08)
Changes in version 3.1.6
work with negative edge lengths (hclust may generate negative tree heights) (2021-09-29, Wed; @xiangpin, #441, #445)
Changes in version 3.1.5
bug fixed of nudge_x parameter in geom_segment2 (2021-09-03, Fri; @xiangpin, #433)
Changes in version 3.1.4
allow using options(layout.radial.linetype) to set linetype of radial layout (either ‘strainght’ or ‘curved’) (2021-08-13, Fri; @xiangpin, #427)
Changes in version 3.1.3
geom_tiplab supports fontface aesthetic (2021-07-06, Tue; @xiangpin)
Changes in version 3.1.2
geom_range supports aes mapping (2021-06-04, Fri)
Changes in version 3.1.1
Changes in version 1.3.6
fix the issue of gridlines when some data is removed. (2021-08-25, Wed)
Changes in version 1.3.5
update citation of ggtreeExtra (2021-08-25, Wed).
Changes in version 1.3.4
The ggplot2 (>=3.3.4) introduced computed_mapping.
Changes in version 1.3.3
c(TRUE, TRUE) && c(TRUE, TRUE) is not allowed in devel environment of bioconductor
Changes in version 1.3.1
https://github.com/YuLab-SMU/ggtreeExtra/issues/9
Changes in version 1.3.0
Changes in version 1.5
Choose a more reasonable scale for global overdispersion estimate
Make code more robust accidental internal NA’s
Add fallback mechanism in case the Fisher scoring fails to converge. Instead of returing NA, try again using the BFGS algorithm.
Better error message if the design contains NA’s
Changes in version 1.13.1
USER-LEVEL CHANGES
Changes in version 2.19.1
TCSS method (@qibaiqi, #35; 2021-08-02, Mon)
GOSemSim 2.18.0
Bioconductor 3.13 release
Changes in version 1.8.0
Improved parallelization implementation for a faster analysis performance.
resolved knitr error June 2021
Changes in version 1.56
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.50
BUG FIXES
Changes in version 1.22.0
Changes in version 1.27.1 (2021-07-28)
Updated CITATION FILE.
Added rmarkdown to Suggests.
Changes in version 1.1.3 (2021-07-06)
Modify the plotting functions.
Changes in version 1.1.2 (2021-06-14)
Add APIs for Seurat pipeline and igraph pipeline.
Changes in version 1.1.1 (2021-05-27)
Modify the package manual.
Changes in version 1.1.0 (2021-05-20)
The development version 1.1.0 is available in Bioconductor.
Changes in version 1.27.1
Changes in version 1.30.0
Changes in version 1.7.6 (2020-10-13)
Trigger bioc build
Changes in version 1.7.5 (2020-10-08)
Update R version dependency from 3.6 to 4.1
Changes in version 1.7.4 (2020-10-08)
Fix a typo
Add citation file
Changes in version 1.7.3 (2020-10-07)
Prepare for release
Changes in version 1.7.2 (2020-10-07)
Fix warnings in unit tests
Changes in version 1.7.1 (2020-10-07)
Update the man files
Changes in version 1.29.1
Changes in version 1.35
Changes in version 1.35.1
Changes in version 1.35.0
Changes in version 1.2.1
Caught an error where not having Not detected
column breaks the
function
Included ‘rmarkdown’ package in Suggests
Changes in version 0.99.17 (2021-09-16)
Changed the get_positivePPI() function
Changes in version 0.99.16 (2021-09-15)
Changes in version 1.9.1
msigdb_download() filters by distinct gene symbols within genesets (relevant to msigdb >=7.4.1)
Changes in version 1.9.0
Version bump for bioconductor
Changes in version 1.18.0
Bug fixes
Other notes
Changes in version 1.7.24 (2021-10-14)
Changes in version 0.99.9 (2021-10-22)
Removed certain unit tests for 64-bit windows
Changes in version 0.99.8 (2021-10-11)
Added patch detection method
Changes in version 0.99.7 (2021-10-10)
Added all unit tests
Fixed read_steinbock x/y axis defaults
Changes in version 0.99.0 (2021-09-14)
Bioconductor submission
Changes in version 0.3.12 (2021-09-01)
clean up for Bioconductor submission
Changes in version 0.3.11 (2021-08-19)
Added flip_x, flip_y argument for plotSpatial function
readSCEfromTXT does not require spot names anymore
knn graph construction can be pruned by distance
added
Changes in version 0.3.10 (2021-08-18)
Added countInteractions function
Added testInteractions function
Changes in version 0.3.9 (2021-07-29)
Added buildSpatialGraph function
Added plotSpatial function
Added aggregateNeighbors function
Changes in version 0.3.8 (2021-06-30)
Adjusted default parameters for read_steinbock function
Added updated test data
Changes in version 0.3.7 (2021-06-14)
added read_cpout function, docs and tests
Changes in version 0.3.6 (2021-06-04)
added read_steinbock function, docs and tests
Changes in version 0.3.5 (2021-05-20)
unit tests and docs for filterPixels
Changes in version 0.3.4 (2021-05-18)
added readImagefromTXT function and tests
Changes in version 0.3.3 (2021-05-17)
unit tests for binAcrossPixels
Changes in version 0.3.2 (2021-05-16)
adjusted plotSpotHeatmap function and unit test
Changes in version 0.3.1 (2021-05-15)
readSCEfromTXT accepts list and path
Changes in version 0.3.0 (2021-05-07)
Added helper functions for spillover correction
Removed redundant functions
Changes in version 0.2.0 (2019-11-28)
The functions calculateSummary, plotCellCounts, and plotDist have been added
Changes in version 0.1.0 (2019-09-17)
initial commit
Changes in version 1.25.2
bugfix immunoMeta contructor from single immunoClust-object
Changes in version 1.25.1
Changes in version 1.1.1 (2021-08-09)
Changes in version 1.8.1 (2020-08-16)
Fix name generation error for step 15.
Handle annotation names as strings even if they look like numbers.
Changes in version 1.1.4
For the three div blocks of heatmap widgets, now display:table-cell
is used so that
the positions of divs won’t change when changing the size of the
browser window.
Add a new vignette “Share interactive heatmaps to collaborators”.
Changes in version 1.1.3
fontawesome is directly from the fontawesome package.
also inherit row_names_gp and column_names_gp from the complete heatmap
content of js and css for specific heatmap is directly add to html instead of containing as files
Changes in version 1.1.2
Add save
argument in htShiny()
.
Changes in version 1.1.1
add new argument sub_heatmap_cell_fun
and sub_heatmap_layer_fun
to only set cell_fun
or layer_fun for sub-heatmaps.
Changes in version 2.0.0 (2021-10-20)
Changes in version 0.99
NEW FEATURES
Initial review.
Changes in version 0.99.0
Revise required files and format the code style.
Changes in version 2.28.0
SIGNIFICANT USER-VISIBLE CHANGES
DEPRECATED AND DEFUNCT
Changes in version 1.3.9 (2021-10-25)
FIXES
Fixed issues with function that make use of BiocParallel that sometimes failed on Windows platform
Changes in version 1.3.7 (2021-10-20)
NEW
FIXES
Fixed minor issues in data files refGenes_mm9 and function compute_near_integrations()
Changes in version 1.3.6 (2021-10-05)
NEW
FIXES
Fixed small issue in printing information in reports
Changes in version 1.3.5 (2021-09-21)
MAJOR CHANGES
NEW
New function for plotting sharing as venn/euler diagrams sharing_venn()
Changes in version 1.3.4
FIXES/MINOR UPDATES
Slightly modified included data set for better examples
Changes in version 1.3.3 (2021-07-30)
MAJOR CHANGES
MINOR CHANGES
NEW FUNCTIONALITY
FIXES
DEPRECATIONS
OTHER
Reworked documentation
Changes in version 1.3.2 (2021-06-28)
FIXES
Corrected issues in man pages
Changes in version 1.3.1 (2021-06-24)
NEW FUNCTIONALITY
MINOR UPDATES
Changes in version 2.5.3
Replace icons with fontawesome 5 versions
Changes in version 2.5.2
Bugfix for heatmap crashing if columns were ordered by a selection that was not shown
Changes in version 2.5.1
Changes in version 1.5.2
Fix bug in retrieving a feature set
Changes in version 1.5.1
Changes in version 1.15.02 (2021-09-14)
Update type: minor.
Various error message updates
Changes in version 1.15.01 (2021-09-01)
Update type: minor.
Version bump due to Bioconductor release.
preFilter() now applies the gene expression cutoff to both conditions instead of the overall average.
analyzePFAM() was updated to reflect recent updates to the tidyverse read_fwf function. It furhtermore now better distinguishes tap seperated and fixed with files.
Changes in version 1.21.1
FIX
rmarkdown dependcies
fix bug that will create difference with older versions (#19)
Changes in version 1.27.2
fix in evaluatePrediction() (avoid length>1 logical condition)
Changes in version 1.27.1
fix to avoid warnings arising from compiled code
fix in kebabsDemo() to avoid build warnings; executing this function now does not have any side effects anymore (previously, data objects were loaded into the global workspace)
Changes in version 1.27.0
new branch for Bioconductor 3.14 devel
Changes in version 3.50.0
Improve help pages for fry() and barcodeplot().
Revise Section 18.1.10 of User’s Guide so that coloring of X and Y genes is consistent between plots.
Fix bug in the MDS class method of plotMDS() (introduced in the
previous release) when new dim.plot
values are set.
Fix bug in read.idat() when annotation
contains NA values.
Changes in version 1.19.2
Eliminated some duplication resulting from relict “trimmed_databases” directory
Changes in version 1.18.1
Updated authors and maintainers
Formalized support for new lipid classes including bile salts, wax esters, quinones, etc.
Changes in version 1.10.1
NEW FEATURES
BUG FIXES
Changes in version 2.4.0
LRBase.XXX.eg.db-type annotation packages for organisms were deprecated.
The distribution of each SQLite file has been changed to the AnnotationHub-style.
By using LRBaseDbi, we can convert SQLite files acquired by the AnnotationHub’s query function into LRBase objects, which can then be used for analysis using LRBase.XXX.eg.db as before.
makeLRBasePackage function was deprecated.
.loadLRBaseDbiPkg was deprecated.
Changes in version 0.99.0 (2021-05-27)
Changes in version 1.7.1
Update tutorial data files
Update knitr dependency for bioconductor tests
Changes in version 3.14
NEW FUNCTIONS
BUG FIXES
ENHANCEMENTS
Changes in version 3.13
added feature-label output on May 10, 2021
Changes in version 3.12
added feature-label output on April 27, 2021
added cutoff value on March 06, 2021
Changes in version 1.5.4
Sync API with matrixStats v0.60.1.
Changes in version 1.5.2
Sync API with matrixStats v0.60.0.
Changes in version 1.5.1
Fix problem with function environment of fallback mechanism (<URL: https://github.com/Bioconductor/MatrixGenerics/issues/25> and <URL: https://github.com/Bioconductor/MatrixGenerics/pull/26>). Make sure that packages can use MatrixGenerics with the :: notation to call functions from sparseMatrixStats and DelayedMatrixStats.
Changes in version 1.1.2 (2021-09-06)
take sample IDs for shinyQC from colnames(se)
take feature IDs for shinyQC from rownames(se)
fix error in report.Rmd (change input for create_boxplot to se)
Changes in version 1.1.1 (2021-08-27)
fix bug in biocrates and maxQuant function
Changes in version 1.19.1 (2021-10-20)
BUG FIXES
Changes in version 1.3.3
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.1.3
fixed a bug in runTomTom where setting norc = TRUE failed on data import
Changes in version 1.1.1
runFimo now returns NULL and prints a message when text = FALSE and FIMO detects no matches instead of throwing a cryptic error message
Changes in version 1.30.0
MeSH-related packages (MeSH.XXX.eg.db, MeSH.db, MeSH.AOR.db, and MeSH.PCR.db) were deprecated.
The distribution of each SQLite file has been changed to the AnnotationHub-style.
By using MeSHDbi, we can convert SQLite files acquired by the AnnotationHub’s query function into MeSH objects, which can then be used for analysis using MeSH-related packages as before.
makeGeneMeSHPackage was deprecated.
.loadMeSHDbiPkg was deprecated.
Changes in version 1.19.3
cache mesh db and table (2021-09-01, Wed)
Changes in version 1.19.2
import yulab.utils (2021-8-19, Thu)
Changes in version 1.19.1
remove MeSH.db package and use AnnotationHub to get MeSHDb databases (2021-8-13, Fri)
Changes in version 2.0.0
Specification changed as “AnnotationHub-style”
Dependencies of MeSH.db, MeSH.AOR.db, MeSH.PCR.db, MeSH.Hsa.eg.db, MeSH.Aca.eg.db, MeSH.Bsu.168.eg.db, MeSH.Syn.eg.db were removed
Vignette changed for the specification change
All datasets removed
Changes in version 1.3.2
Changes to labelRows
new resolveConflicts + rtOrder argument added for automated resolution of conflicting feature pair alignment fows in combinedTable, with embedded C function (resolveRows.c)
new argument rtOrder paired with resolveConflicts determines if RT order consistency is expected when resolving alignment conflicts
duplicate column names for {labels, subgroup, alt} removed and no longer allowed in resulting combinedTable
Changes to metabCombiner
new check for metabCombiner object inputs: labelRows must be called before aligning a metabCombiner object with a new dataset
resolveConflicts method applied to metabCombiner object to eliminate conflicting alignments/ attain 1-1 matches for all features
new rtOrder argument controlling resolveConflicts similar to above
Changes in version 1.3.1
Changes to fit_gam()/ fit_loess
Changes to metabCombiner() & combinedTable / featdata slots
Changes to calcScores() / evaluateParams() / labelRows
Changes to write2file
Changes in version 1.1
MetaboCoreUtils 1.1.1
Changes in version 1.5.1 (2021-06-14)
NEW FEATURES
BUG FIXES
Fix in annotation backwards compatibility.
Fix bigGenePred gene annotation track generation.
Changes in version 0.99.27
Changes in version 1.11.5 (2021-10-12)
add assays in structural based on columns in transformations that are defined by the var argument in structural, adjacency matrices of type will be stored in the AdjacencyMatrix object defined in the columns of transformation
implement structural that it can also calculate mass differences of 0 for undirected networks
Changes in version 1.11.4 (2021-09-09)
shift calculation of as.data.frame(am) in mz_summary
several fixes of typos in the comments and vignette
fix rtCorrection function
Changes in version 1.11.3 (2021-08-30)
change calculation of mass differences, use the differences between (M_2+ppm)-(M_1-ppm) and (M_2-ppm)-(M_1+ppm) instead of (M_1-ppm)-(M_1) and (M_2+ppm)-(M_1) for querying against the list of transformations
Changes in version 1.11.2 (2021-08-30)
change error message in test_combine
Changes in version 1.1 (2021-06-04)
split transformCounts into transformSamples and transformFeatures
added log_modulo_skewness as a diversity index
added functions for summarizing dominant taxa information
added wrapper for adding dominant taxa information to colData
added specialized subsetting function for subsetting by prevalence (subsetByPrevalentTaxa/subsetByRareTaxa)
added mapTaxonomy
added estimateDivergence
bugfix: makePhyloseqFromTreeSummarizedExperiment checks now for rowTree be compatible
bugfix: meltAssay supports Matrix types
bugfix: meltAssay is able to include rowData also when there are duplicated rownames
added subsampleCounts for Subsampling/Rarefying data
Changes in version 0.99.0 (2021-09-29)
Three simulation models and three functions are added
Submitted to Bioconductor
Changes in version 1.1
Changes in version 2.1.2 (2020-07-01)
Core heatmap labeling improved
aggregate_top_taxa deprecated
bimodality and potential_analysis functions fixed
Changes in version 2.1.1 (2020-04-06)
Added overlap function
Changes in version 1.14.1 (2021-09-29)
Removed categorical method from associate function
Changes in version 0.99.0 (2021-09-01)
Changes in version 0.99.0
Changes in version 1.5.9
update mp_plot_ord to suppress the message of the third depend package. (2021-10-08, Fri)
Changes in version 1.5.8
add mp_aggregate function. (2021-09-26, Sun)
Changes in version 1.5.7
update the mp_plot_ord. (2021-09-13, Mon)
Changes in version 1.5.6
introduce include.lowest parameter in mp_filter_taxa. (2021-09-07, Tue)
Changes in version 1.5.5
fix the issue when the rowname or colnames of SummarizedExperiment is NULL for as.MPSE. (2021-08-26, Thu)
Changes in version 1.5.4
add mp_stat_taxa to count the number and total number taxa for each sample at different taxonomy levels (Kingdom, Phylum, Class, Order, Family, Genus, Species, OTU). (2021-08-03, Tue)
Changes in version 1.5.3
optimize the print for MPSE. (2021-07-22, Thu)
Changes in version 1.5.2
add mp_mantel and mp_mrpp for MPSE or tbl_mpse object. (2021-07-19, Mon)
add mp_envfit and update mp_cal_dist to support the distance calculation with continuous environment factors and rename mp_cal_adonis to mp_adonis, mp_cal_anosim to mp_anosim. (2021-07-17, Sat)
add mp_cal_rda, mp_cal_cca, mp_cal_adonis and mp_cal_anosim for MPSE or tbl_mpse object. (2021-07-16, Fri)
add mp_cal_dca, mp_cal_nmds and mp_extract_internal_attr. (2021-07-15, Thu)
add mp_cal_pca, mp_cal_pcoa and mp_extract_abundance. (2021-07-14, Wed)
add mp_cal_clust to perform the hierarchical cluster analysis of samples and mp_extract_dist to extract the dist object from MPSE object or tbl_mpse object. (2021-07-13, Thu)
add mp_cal_dist to calculate the distance between samples with MPSE or tbl_mpse object. (2021-07-12, Mon)
add mp_extract_sample, mp_extract_taxonomy, mp_extract_feature to extract the sample, taxonomy and feature (OTU) information and return tbl_df or data.frame. (2021-07-09, Fri)
add mp_cal_venn to build the input for venn plot (2021-07-09, Fri)
mp_cal_rarecurve add action argument to control whether the result will be added to MPSE and tbl_mpse or return directly. (2021-07-08, Thu)
add mp_cal_upset to get the input of ggupset. (2021-07-08, Thu)
add mp_extract_tree to extract the otutree or taxatree from MPSE or tbl_mpse object. (2021-07-07, Wed)
add pull and slice to support the MPSE object. (2021-07-06, Tue)
add mp_cal_rarecurve to calculate the rarecurve of each sample with MPSE or tbl_mpse. (2021-07-06, Tue)
add mp_cal_abundance to calculate the relative abundance of each taxonomy class with MPSE or tbl_mpse. (2021-07-05, Mon)
add mp_decostand provided several standardization methods for MPSE, tbl_mpse and grouped_df_mpse. (2021-07-04, Sun)
add mp_import_qiime to parse the output of qiime old version. (2021-07-03, Sat)
add taxatree slot to MPSE. (2021-06-30, Wed)
add mp_cal_alpha function for MPSE or mpse object. (2021-07-01, Thu)
add rownames<- to support renaming the names of feature. (2021-07-01, Thu)
add mp_import_qiime2 and mp_import_dada2 to parse the output of dada2 or qiime2 and return MPSE object. (2021-07-02, Fri)
update print information for MPSE, tbl_mpse and grouped_df_mpse. (2021-06-29, Tue)
add [ to the accessors of MPSE. (2021-06-29, Tue)
use MPSE object. (2021-06-28, Mon)
Formatted output.
update as.MPSE and as.treedata for grouped_df_mpse object.
(2021-06-29, Tue) - This feature is useful to explore the
microbiome data in taxa tree. This feature has been replaced by
the taxatree slot
Changes in version 1.5.1
Changes in version 1.1.0
Bioconductor release!
Changes in version 1.0.13
adds new HLA-KIR interaction A03_A11_KIR3DL2 defined as (A03 | A11) & KIR3DL2.
Changes in version 1.0.12
fixes bug causing MiDAS subsetting to break omnibus testing.
Changes in version 1.0.11
runMiDAS inheritance_model argument is no longer by defaut ‘additive’. Now it is required to specify desired inheritance model, when appplicable.
Changes in version 1.0.10
fix bug causing Bw6 groups to be counted twice in hla_NK_lingads experiment.
Changes in version 1.0.9
fix bug causing runMiDAS errors when statistical model evaluated with a warrning.
Changes in version 1.0.8
fixed bug causing filterByVariables and filterByFrequency to strip omnibus groups from target experiment.
Changes in version 1.0.7
fixed bug causing HWETest filtration to strip omnibus groups from target experiment
Changes in version 1.0.6
removed unused expression dictionaries
Changes in version 1.0.4
In frequency calculations the “NA”s were counted as non-carriers, this has been changed such that “NA” samples are now omitted.
Changes in version 1.0.3
warnings and errors occuring upon model evaluation are now summarized into more readable form
Changes in version 1.0.2
fixed problem vignettes index entry values, preventing vignettes from being build
Changes in version 1.0.1
Changes in version 1.1.0 (2021-10-12)
Changes in version 1.39
v1.39.1 Initial support for the Allergy and Asthma array.
v1.39.2 More support for the Allergy and Asthma array.
v1.39.3 Bug fix that prevented R CMD build from working.
Changes in version 1.1.5 (2021-08-24)
Updated citation
Changes in version 1.1.3 (2021-05-27)
Added new option for model_type, one_dimensional
Added new filtering parameters, keep_all_below_boundary and enforce_left_cutoff
Added demonstrations of new models and parameters to vignette
Changes in version 1.1.3 (2021-08-22)
Changes made in the vignette
Changes in version 1.1.2 (2021-08-22)
Link example data on zenodo in vignette
Changes in version 1.1.1 (2021-06-03)
Addition to miRanda Files
Changes in version 1.2.0
Release version for Bioconductor 3.14. See changes for 1.1.x.
Changes in version 1.1
IMPORTANT: R2 is now reported in percentages for intra, multi and gain. Collecting results from running mistyR < 1.1.11 will lead to miscalcuation of gain.R2. Update the performance.txt files by multiplying the values in columns intra.R2 and multi.R2 by 100.
Changes in version 1.0.3
Vignette output switched from BiocStyle to rmarkdown for pdfs due to BiocStyle issue.
Changes in version 1.0.2
Avoid calls to os-dependent file.info in tests.
Changes in version 1.0.1
Changes in version 6.18.0
new features / enhancements / changes
bug fixes
Changes in version 0.99.5
Updated R/monaLisa-package.R file
Changes in version 0.99.4
Suppressed warnings from matchPWM (due to presence of Ns) in regression vignette
Changes in version 0.99.3
Updated README.md file
Changes in version 0.99.2
Addressed failing test in calcBinnedKmerEnr
Changes in version 0.99.1
Added legend position and size arguments to plotSelectionProb()
Changes in version 0.99.0
Preparation for Bioconductor submission
Changes in version 0.2.0
Changes in version 1.0.0
Major changes
Changes in version 1.37.5
Change the style of motifPile.
Fix the bug of the ylab grid.
Changes in version 1.37.4
Fix the bug that the rownames were not checked for alignment.
Changes in version 1.37.3
Fix the bug method argument of matAlign is ignored.
Changes in version 1.37.2
Improve importMatrix to read the tags from file.
Changes in version 1.37.1
handle the error “failed to load cairo DLL”
Changes in version 1.1.8
Fixed test that was resulting in error duet to version 1.1.6 updated way to read the files.
Changes in version 1.1.7
Removed parentheses from the news that was causing issues in Bioconductor.
Changes in version 1.1.6
Bug fixed: If a table was missing, the report was not generated.
Changes in version 1.1.5
The plot generated by PlotPTM() will now indicate (in the legend title) whether the Post-Translational modifications have been aggregated or not as a result of the parameter aggregate_PTMs.
The function PlotPeptidesIdentified() and PlotProteinsIdentified() now return a plot containing Missing Values, Frequency of Identified by Match Between Runs and Frequency of identified by MS/MS. With this, the funciton PlotIdentificationType() becomes obsolete.
The function PlotProteinCoverage() now can take as input multiple UniprotID in a vector format.
The function PlotPTMAcrossSamples() now can take as input multiple PTM_of_Interest in a vector format.
Change in the function make_MQCombined() to read faster the tables and reducing the overall time required to generate a report.
Changes in version 1.1.4
The function PlotProteinCoverage() now reports the coverage individually in each plot rather than the total protein coverage.
MQmetrics now is adapted to MaxQuant v.2.x, since the column names are different than in MaxQuant v.1.x. MQmetrics will detect the MaxQuant version used and read the columns accordingly.
Enhanced error message in PlotiRT() and PlotiRTScore() when irt peptides are note found. Enhanced error message for PlotProteinCoverage() when the UniprotID is not found.
Changes in version 1.1.3
In the function PlotPTM() a parameter combine_same_residue_ptms has been added. It combines multiple PTMs happening in the same residue such as: Dimethyl (KR), Trimethyl (KR).
Changes in version 1.1.2
Improved aesthethics in the plots from PlotCombinedDynamicRange() and PlotAllDynamicRange().
Changes in version 1.1.1
Changes in version 1.25.3
further changes to get rid of compiler warnings
Changes in version 1.25.2
removed build/ directory from repo to avoid installation problems
Changes in version 1.25.1
update of gc
minor changes to get rid of compiler warnings
Changes in version 1.25.0
new branch for Bioconductor 3.14 devel
Changes in version 1.1
Changes in 1.1.4
Changes in 1.1.3
Changes in 1.1.2
Changes in 1.1.1
Changes in version 1.1
Changes in 1.1.3
Changes in 1.1.2
Changes in 1.1.1
Changes in version 1.0.0
Changes in version 1.3.0
Users can now specify the rank of the model to fit by msImpute
Added mspip for identification transfer between runs using Maxquant results (Beta phase only)
Added evidenceToMatrix which creates limma compatible objects from MaxQuant evidence table
Changes in version 2.19
Changes in 2.19.2
Changes in 2.19.1
Changes in version 1.19.2
XCMS 3 compatability update (M-R-JONES) https://github.com/computational-metabolomics/msPurity/pull/91
Changes in version 1.19.1
Bug fix for flagRemove (full width was not calculated as expected)
Changes in version 1.1.1
Changes in version 1.2.1
Changes in version 2.2.3 (2021-10-06)
Minor change: fix the bug when df.prior is infinite
Changes in version 2.2.2 (2021-09-21)
Major change: extend groupComparisonTMT() function to cover repeated measures design
Allow flexible order of condition in dataProcessPlotsTMT.
Fix bug in Condition label in dataProcessPlotsTMT.
Improve MSstatsTestSingleProteinTMT() by directly reading lmerTest output. This may make statistics slightly different due to different numeric accuracy
fix bug when condition name contains ‘group’
change the x-axis order in profile plot
Changes in version 2.0.1 (2021-06-14)
update comments of PD converter function
fix bug in proteinSummarization() function when MBimpute = F
Changes in version 1.20.0
Bug fixes and minor improvements
Changes in version 2.0.0 (2020-11-23)
Update selection of significant results in the ‘topDirs’ function. Major change, results will be more strict compared to pre-2.0.0 version
Removed ‘BLMA’ and ‘metap’ dependency, added ‘aggregation’ dependency
P-values are aggregated using ‘max’ by default. I.e., for a region differentially interacting with multiple regions, a maximum p-value will be selected. Fisher, Lancaster, and Sidak methods are also available
Harmonize counting of significant regions using ‘p.adj_cutoff’ only (‘alpha’ cutoff removed)
The ‘manhattan’ function is harmonized with ‘topDirs’
The ‘perm_test’ function is harmonized with ‘topDirs’
Update vignettes to match functions
Changes in version 1.1.27
Bug fixes
New Features
read_header and read_sumstats now both work with .bgz files.
Changes in version 1.1.26
New Features
Extra mappings for FRQ column, see data(“sumstatsColHeaders”) for details
Changes in version 1.1.23
New Features
format_sumstats(frq_is_maf) check added to infer if FRQ column values are minor/effect allele frequencies or not. frq_is_maf allows users to rename the FRQ column as MAJOR_ALLELE_FRQ if some values appear to be major allele frequencies
Changes in version 1.1.19
New Features
format_sumstats(convert_ref_genome) now implemented which can perform liftover to GRCh38 from GRCh37 and vice-versa enabling better cohesion between different study’s summary statistics.
Changes in version 1.1.11
Bug fixes
New Features
Input summary statistics with A0/A1 corresponding to ref/alt can now be handled by the mappign file as well as A1/A2 corresponding to ref/alt.
Changes in version 1.1.2
New Features
Bug fixes
check_n_num now accounts for situations where N is a character vector and converts to numeric.
Changes in version 1.1.1
Bug fixes
Changes in version 1.7.2
Changes in version 1.3.1 (2021-10-10)
Updated version number to match Bioconductor
Changes in version 1.2.1 (2021-08-08)
Changes in version 2.27.1
Add missing atomic_count_sync.hpp BH file (see PR #248 by vjcitn)
Changes in version 2.27.0
New Bioc devel version
Changes in version 2.0.0
Changes in version 1.1.2 (2020-09-28)
Update license
Changes in version 1.1.1 (2020-08-13)
Documentation updates
Handle new parameters from ggiraph update
Changes in version 1.1.0 (2020-05-19)
Initial Bioconductor devel 3.14 version
Changes in version 0.99.0
Changes in version 1.3.3
Changes
update description to accommodate changes in knitr/rmarkdown packages
update dummy data files to new format so vignette can run
Changes in version 1.3.1
Changes
include ability to iteratively acquire and visualize Bkg std error
new arguments to choose whether to calculate Bkg std error
accomodate StereoGene version 2.22, esp. seeding of analysis
better run analysis on track files outside local directory
Changes in version 1.5.3
Moved RCy3, scater, clusterExperiment and netSmooth to “Suggests” to reduce dependency burden
Sped up vignettes by limiting all to binary classification and limiting number of layers
Removed TL;DR from vignettes as usefulness in question but maintainance high. Developers notes:
Added Dockerfile and Github Actions for automated testing
GHA auto-generates a Docker image with netDx which gets pushed to shraddhapai/netdx_devenv
Changes in version 1.5.2
Added wrapper functions for ease-of-use. Includes:
getResults() to plot results of running the predictor
getPSN() for creating and visualizing integrated PSN
confusionMatrix() to visualize confusion matrix
tSNEPlotter() to visualize tSNE of integrated PSN (doesn’t require Cytoscape)
Added CITATION file with citations to netDx methods and software paper
Changes in version 1.5.1
Adding support for Java 16.
Disabling CNV-based vignette to allow other three vignettes to run without causing build timeout on devel system
Changes in version 1.53.2 (2021-07-28)
Changes in version 1.9.3
Bug fixes for importing macs2 logs
Changes in version 1.9.2
Bug fixes for later versions of ggplot2
Changes in version 1.8.1
Bug fix in .makeSidebar
Changes in version 1.18.2
Changed deprecated ‘GenomeInfoDb::fetchExtendedChromInfoFromUCSC’ to ‘GenomeInfoDb::getChromInfoFromUCSC’ in R/methods.R
Changes in version 1.18.1
Fixing R 4.1.0 _R_CHECK_LENGTH_1_LOGIC2 error in tests/testthat/utils.R:applyMap by using inherits() instead of class() to account for hadleyverse
Changes in version 1.0.0
Changes in version 0.99.12 (2021-10-26)
Fixed bug in MakeSE() and CoordToGR()
Changes in version 0.99.10 (2021-10-20)
Accounts for when NxtIRFdata cannot fetch data from ExperimentHub
Changes in version 0.99.9 (2021-10-20)
Added GetCoverageBins()
Add warning in IRFinder if coordinate sorted BAM file takes too long to run.
Fixed missing coverage data at both ends of plot track.
Changes in version 0.99.8 (2021-10-13)
Fixed memory leak when writing COV files
Changes in version 0.99.6 (2021-10-12)
Added GetCoverageRegions() which calculates the mean coverage of each region in a given GRanges object
Added BAM2COV() which calculates and creates COV files from BAM files
Changes in version 0.99.2 (2021-10-07)
Fixed bug in Find_FASTQ
Changes in version 0.99.0 (2021-09-29)
Bioconductor Release
Changes in version 0.99.0
NEW FEATURES
Changes in version 3.2.0
Changes in version 3.1.2 (2021-10-06)
Better test of poset transformation
Changes in version 3.1.1 (2021-10-06)
XOR, AND, OR dependencies: plots of DAGs honor all possible values.
Few miscell minor changes.
Changes in version 3.11
Enhancements
Bug Fixes
Added a fix to the density estimate used by gate_tautstring
Changes in version 3.10
API Changes
Simple renaming
Classes and methods no longer exported
Bug Fixes
Changes in version 2.11.1
Changes in version 1.13.7
SIGNIFICANT USER-VISIBLE CHANGES
Massive improvement in speed of coveragePerTiling
Improved p-shifting analysis (also added verbose output)
Added possible optimization for annotation
Rewritten vignettes
Changes in version 0.99.9
New Features
Fixes
Adjusted vignette yamls to make resulting htmls smaller.
Changes in version 0.99.8
New Features
create_background now uses all_genes when all 3 species are the same.
Changes in version 0.99.7
New Features
Fixes
report_orthologs no longer throws error due to not finding tar_genes.
Changes in version 0.99.6
Fixes
Allow all messages to be suppressed in report_orthologs.
Changes in version 0.99.3
New Features
New method “babelgene” added to convert_orthologs.
Changes in version 0.99.2
Fixes
GenomeInfoDbData now required.
Changes in version 0.1.0
New Features
Changes in version 1.3 (2021-10-14)
Changes in version 0.99.0 (2021-09-21)
Changes in version 2.20.0
Other notes
Changes in version 2.6.0
Changes in version 1.7.1 (2021-06-21)
Error due to change in behavior for default axis label in ggplot2 histogram
GGplot2 ‘guide’ depreciation warning
Changes in version 0.1.0
Changes in version 2.5.3
The original constructor and all accessors remain in the package for full backwards compatibility
Changes in version 2.5.2
Fix: remove ‘fdr’ item from geneDrugSensitivity return vector
Changes in version 2.5.1
Fix: reverted GDSCsmall.rda and CCLEsmall.rda to original data format; they were accidentally pushed with MultiAssayExperiments in @molecularProfiles
Changes in version 2.5.0
Changes in version 1.19.1
USER-VISIBLE CHANGES
Added support for TreeSummarizedExperiment class
Added support for phyloseq class
Updated vignette
Changed main argument name from df to x
INTERNAL
Changes in version 1.1.1 (2021-08-05)
Changes in version 1.2.1
Changes in version 1.7.8
only mainInput is required in config file
Changes in version 1.7.7
use config file for input files, refspec selection and othes settings
Changes in version 1.6.6
turn off auto sizing for large number of taxa or genes (>= 10.000)
Changes in version 1.6.5
fixed filter for “species relation”
added midpoint colors
Changes in version 1.6.2
increase default font size for profile and domain plot
make links to DBs: ncbi taxonomy, ncbi protein, uniprot, pfam, smart
Changes in version 1.6.1
modified taxonomy ranks (ropensci#875)
improved rank indexing function (ropensci#874)
improved x-axis label (#116)
Changes in version 1.19.50 (2021-10-14)
New functions
Neda added the identify.modules(), make.filter(), and apply.filter() functions, but not exported them yet.
Changes in version 1.19.30 (2021-09-08)
Bug Fixes
The averaged.network() function does not have the nodes argument in bnlearn Version >=4.7, and thus this argument was removed.
Changes in version 1.19.24 (2021-08-06)
New functions
Bug Fixes
A bug fix in the gene.mapping() function that used to occur when we had multiple output databases.
Changes in version 1.19.10 (2021-06-25)
Changes in existing functions
The message.if() function can now write the message in a text file.
Changes in version 1.19.8 (2021-05-25)
Bug Fixes
Changes in version 1.65.1
new feature:
–allow parameter Prefix' in
run.plgem’ to be passed down to
plgem.fit' when
writeFiles=TRUE’
bug fix:
–only check existence of fittingEvalFileName' when both
fittingEval’ and
plot.file' are TRUE in
plgem.fit’
new feature:
–added parameter Prefix' to
run.plgem’ to be passed down to
plgem.write.summary' when
writeFiles=TRUE’
bug fix:
–fixed error occurring when running run.plgem' with
plotFile=TRUE’
Changes in version 0.99.11
BUG FIXES
o :
added back to readHic for strawr
region parsing.
o plotHicSquare
subsetting fixed for off diagonal regions.
NEW FEATURES
o All Hi-C functions now allow input of remote Hi-C files.
Changes in version 0.99.9
This package was previously called BentoBox.
Changes in version 0.99.0
NEW FEATURES
o Version bump to 0.99.0 for Bioconductor package submission.
o bb_mapColors
function for users to map a vector to a palette
of colors.
o linecolor
parameter in bb_plotPairs
, bb_plotPairsArches
,
and bb_plotRanges
now accepts a single value, a vector of colors,
a colorby
object, or the value “fill”.
Changes in version 0.0.0.14
BUG FIXES
o R version requirement changed to (R >= 4.1.0) for proper plot placement.
NEW FEATURES
o colorby
object now has a scalePerRegion
parameter to scale
numerical
colorby
data to the range of data in a plotted genomic region.
Changes in version 0.0.0.13
SIGNIFICANT USER-VISIBLE CHANGES
o bb_plotManhattan
fill
paramete now accepts a single value,
a vector of colors, or a colorby
object.
Changes in version 0.0.0.12
SIGNIFICANT USER-VISIBLE CHANGES
o colorby
constructor now includes optional palette specification.
o bb_plotPairs
, bb_plotPairsArches
, and bb_plotRanges
fill
parameter
now accepts a single value, a vector of colors, or a colorby
object.
BUG FIXES
o GInteractions
assembly match checking moved before dataframe
conversion.
Changes in version 0.0.0.11
SIGNIFICANT USER-VISIBLE CHANGES
o Data moved to plotgardenerData
package.
o Default genome assembly updated to “hg38”.
BUG FIXES
o Streamlined parameter parsing and data reading logic.
Changes in version 0.0.0.10
NEW FEATURES
o Added unit tests with testthat
.
o bb_annoDomains
function addition.
o bb_plotSignal
vertical orientation.
Changes in version 0.0.0.9
NEW FEATURES
o Added a NEWS
file to track changes to the package.
BUG FIXES
o Updated viewport parsing for package grid
version 4.1.0.
Changes in version 1.1.1 (2021-06-09)
Changes in version 1.25.1
adjusted NAMESPACE to account for changes in BiocGenerics package
Changes in version 1.25.0
new branch for Bioconductor 3.14 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 1.3.3 (2021-09-28)
The default for MinPts DBSCAN parameter has been changed to 100
Changes in version 1.3.2 (2021-09-21)
Vignette edits
Changes in version 1.3.1 (2021-07-19)
Change y of x.y.z version number to comply with the release
Add MD as a maintainer
Changes in version 1.3.3
plotPromoters is deprecated
Implemented three new functions
Changes in version 2.21.1
Changes in version 2020-10-14 (2020-10-14)
Model matrices are not accessed in the local and not in the global enviroment
Changes in version 2020-09-01 (2020-09-01)
Fixed issue with rownames when using Progeny with Permutations function
Changes in version 2020-06-09 (2020-06-09)
Website: Google Analytics
Changes in version 2020-04-27 (2020-04-27)
PROGENy website development
Major update with the following main points:
Added the mouse model matrix containing 14 pathways
The human model matrix extended to 14 pathways
Added the following functions: progenyPerm, progenyScatter, progenySavePlots, getModel
Added tests and test data
Added the vignette for usage the PROGENy on single-cell RNA-seq data
Added functionality to work with Seurat objects
Changes in version 1.33
Changes in version 1.0
Changes in version 1.25.1
add bin, compareChromatograms and compareSpectra
Changes in version 1.25.0
Bioc devel (3.14) version bump
Changes in version 1.20.0
Improve species and genome selection
Changes in version 1.18.6
ShinyProxy support
Bug fixes
Orange region (the reference exon) is now on top of blue region
Changes in version 1.18.5
Fix loading twice when selecting a new event (visual interface)
Changes in version 1.18.4
Remove warning related with TCGA data when MD5 checks fail
Changes in version 1.18.3
Fix Bioconductor build report’s timeout when creating vignettes on Windows
Changes in version 1.18.2
Fix issues with unit tests in Bioconductor
Changes in version 1.18.1
Changes in version 1.1.4 (2021-09-23)
removal of the loaded prtset data to avoid any local path problems
Changes in version 1.1.1 (2021-09-13)
Added graphical interface
Changes in version 2.0.0
NEW FEATURES
Report median absolute pairwise difference (MAPD) of tumor vs normal log2 ratios in runAbsoluteCN
Improved mapping bias estimates: variants with insufficient information for position-specific fits (default 3-6 heterozygous variants) are clustered and assigned to the most similar fit
Make Cosmic.CNT INFO field name customizable
SIGNIFICANT USER-VISIBLE CHANGES
Cleanup of naming of command line arguments (will throw lots of deprecated warnings, but was long overdue)
More robust alignment of on- and off-target tumor vs normal log2 ratios. Ratios are shifted so that median difference of neighboring on/off-target pairs is 0. This should fix spurious segments consisting of only on- or off-target regions in high quality samples where those minor off-sets sometimes exceeded the noise.
Added min.variants argument to runAbsoluteCN
Added PureCN version to runAbsoluteCN results object (ret$version)
Added pairwise sample distances to normalDB output object helpful for finding noisy samples or batches in normal databases
Do not error out readCurationFile when CSV is missing and directory is not writable when re-generating it (#196)
Add segmentation parameters as attributes to segmentation data.frame
Added min.betafit.rho and max.betafit.rho to calculateMappingBias*
Made –normal_panel in PureCN.R defunct
BUGFIXES
Fix for crash when –normal_panel in NormalDB.R contained no variants (#180).
Fix for crash when rtracklayer failed to parse –infile in FilterCallableLoci.R (#182)
More robust parsing of VCF with missing GT field (#184)
Fix for bug and crash when mapping bias RDS file contains variants with multiple alt alleles (#184)
Added missing dependency ‘markdown’
Fix for crash when only a small number of off-target intervals pass filters (#190)
Fix for crash when PSCBS segmentation was selected without VCF file (#190)
Fix for crash when Hclust segmentation was selected without segmentation file (#190)
Fix for crashes when not many variant pass filters (#192, #195)
Fix for crash when provided segmentation does not have chromosomes in common with VCF (#192) or does not provide all chromosomes present in the coverage file (#192)
Changes in version 1.31
qcmetrics 1.31.1
Changes in version 1.29.6 (2021-10-23)
BUG FIXES
segmentBins() would report the sample names as “NA” in output messages if the sample name contained hyphens, or other symbols automatically replaced by data.frame(…, check.names = TRUE). This was a harmless bug.
Changes in version 1.29.5 (2021-10-20)
PERFORMANCE
MISCELLANEOUS
Moved ‘future’ from Imports to Suggests.
Changes in version 1.29.4 (2021-10-16)
DOCUMENTATION
DEPRECATION AND DEFUNCT
Argument ‘seeds’ of segmentBins() is defunct. It has been deprecated and ignored since QDNAseq 1.21.3 (September 2019).
Changes in version 1.29.3 (2021-10-04)
NEW FEATURES
Now argument ‘logTransform’ of exportBins() is ignored if ‘type’ = “calls”.
Now exportBins() returns the pathname to the files written.
SOFTWARE QUALITY
Test code coverage was increased from 42% to 52%.
Add package test for exportBins().
BUG FIXES
exportBins(fit, format = “seg”, …) and format = “vcf” would merge segments with equal copy-number calls if they were interweaved with copy-neutral segments.
exportBins(fit, format = “seg”, …) and format = “vcf” produced an obscure error with messages “Error in dimnames(x) <- dn : length of ‘dimnames’ 2 not equal to array extent” for samples with no copy-number abberations.
exportBins(fit, format = “seg”, file = …) and format = “vcf” did not respect argument ‘file’ but instead wrote files of its own names to the current working directory.
exportBins() would corrupt option ‘scipen’. Now it is left unchanged.
KNOWN ISSUES
callBins() produces warnings on “Recycling array of length 1 in vector- array arithmetic is deprecated. Use c() or as.vector() instead.” in R (>= 3.4.0). This is a problem in the package ‘CGHcall’ dependency and is something that needs to be fixed there. For further details, please see https://github.com/tgac-vumc/CGHcall/issues/2.
Changes in version 1.29.2 (2021-09-22)
SOFTWARE QUALITY
Test code coverage was increased from 32% to 39%.
Added package tests for binReadCounts().
BUG FIXES
binReadCounts() would fail when specifying argument ‘chunkSize’. The fix was to require ‘future’ package version 1.22.1 or newer.
Changes in version 1.29.1 (2021-08-26)
SOFTWARE QUALITY
Changes in version 1.3.0
QFeatures 1.3.6
QFeatures 1.3.5
QFeatures 1.3.4
QFeatures 1.3.3
QFeatures 1.3.2
QFeatures 1.3.1
QFeatures 1.3.0
Changes in version 1.9.2 (2021-09-01)
Added Hmisc to Imports
Changes in version 1.9.1 (2021-06-24)
Added qsmoothGC function (Contributed from Koen Van den Berge)
Changes in version 1.34.0
USER-VISIBLE CHANGES
removed automatic downloading and installation of BSgenome references
added option to parallelize qExportWig
Changes in version 1.18.0
New features
Bug fixes and minor improvements
Changes in version 1.1.2 (2021-05-28)
reviewers’ suggestions were implemented, docs updated, typos fixed
new methods for simulation of AMR and test data sets
NULL as a default for data.samples (to use all)
doRNG is used to ensure reproducibility during parallel computing
a couple of new defaults for previously required parameters for easy usage
Changes in version 1.1.0 (2021-05-21)
released at bioconductor
Changes in version 1.1 (2021-05-31)
Improved error handling of system2 call in .rawrrSystem2Source by logging stdout and stderr and make them available from the R console.
Added helper function .checkReaderFunctions.
Use pipe | > in vignette. |
Changes in version 2.14.0
Cleaned up dependencies, dramatically reducing RCy3 package installation time
Changes in version 1.7.5 (2021-09-28)
Fixed documentation of “plot_heatmap”
Changes in version 1.7.4 (2021-09-24)
Added new plotting function “plot_heatmap”
Changes in version 1.7.3 (2021-09-14)
Updated vignette to introduce the “open_reactome” command
Changes in version 1.7.2 (2021-09-09)
Fixed timeout issue during large requests in perform_reactome_analysis
Changes in version 1.7.1 (2021-06-09)
Fixed bug in scRNA-seq vignette.
Changes in version 1.19.2
BUG FIXES
Changes in version 1.3.9
BUG FIXES
Resolved https://github.com/LieberInstitute/recount3/issues/7.
Changes in version 1.3.7
NEW FEATURES
Added the create_hub() function for creating UCSC track hub configuration files for using the UCSC Genome Browser to explore the recount3 BigWig base-pair coverage files.
Changes in version 1.3.2
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
Changes in version 1.3.1
Changes in version 1.5.3 (2021-08-04)
Changes in version 1.12.2
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
DEPRECATED AND DEFUNCT
BUG FIXES
changed implementation show_all_metadata() for better preformance
Changes in version 1.12.1
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
removed is_GMQL from read_gmql function The entire dataset must have the right folder structure in order to works correctly <dataset_name> —> <files>
Swap order of arguments ‘dir_out’ and ‘name’ of the collect() function so now the latter comes before the former.
DEPRECATED AND DEFUNCT
BUG FIXES
Changes in version 2.38.0
NEW FEATURES
Added support for reading attributes where the datatype is either a 64-bit or unsigned 32-bit integer.
Added many functions for working with file creation property lists. (Thanks to @ilia-kats for the contribution, https://github.com/grimbough/rhdf5/pull/95)
Added support for variable length and UTF-8 encoded string datasets. (Thanks to Aaron Lun @LTLA for the contribution, https://github.com/grimbough/rhdf5/pull/88)
CHANGES
BUG FIXES
Changes in version 1.16
Bug fixes
AR and RANLIB programs used to compile R are now also used to compile the HDF5 library. This resolves issue when the default versions found on a system are incompatible with options used to build R. (thanks to @miesav, https://github.com/grimbough/Rhdf5lib/pull/41)
Fixed issue in Windows installation introduced by upstream changes to libcurl distributed by rwinlibs. (https://github.com/grimbough/Rhdf5lib/pull/42)
Changes in version 0.99.11
Package
Status
Pre-release. This version is prior to the first official release (v1.0.0), anticipated in Oct. 2021.
Changes in version 0.99.0
Changes in version 1.7.1 (2021-07-27)
Changes in version 2.21
CHANGES IN VERSION 2.21.1
CHANGES IN VERSION 2.21.0
Changes in version 1.99.01
Changes in version 1.49.1 (2021-07-28)
Changes in version 2.1
rpx 2.1.12
rpx 2.1.11
rpx 2.1.10
rpx 2.1.9
rpx 2.1.8
New PXDataset2 class with richer interface and more stable data downloading functions. PXDataset and PXDataset2 work transparently and PXDataset2 is now default.
Add deprecation notice in PXDataset() constructor.
rpx 2.1.7
rpx 2.1.6
rpx 2.1.5
Improve documentation.
Check for cached PXDataset object validity.
rpx 2.1.4
Fix bug in PXDdataset internal data storage.
New pxCachedProjects() function that return the cached projects.
Fixes and improvements in the documentation.
rpx 2.1.3
PXDatasets are also cached upon creation and retrieved from cache next time they are generated.
cache is now returned by rpxCache().
rpx 2.1.2
rpx 2.1.1
Changes in version 1.5.4
scatterPlot()
doesn’t warn anymore that we’re using a deprecated
parm to remove the guide
Changes in version 1.5.1
calculateSimMatrix()
now allows using arbitrary keys from Orgdb
packages. Credit: illumination-k. Thanks!
Changes in version 2.10
DEPRECATED AND DEFUNCT
Changes in version 2.24.0
Bug fixes and minor improvements
Changes in version 1.14.0
Changes in version 0.32.0
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 0.99.25 (2021-06-25)
Changes in version 1.22.0
Rename colour_columns_by in plotHeatmap to color_columns_by to match other arguments.
Add color_rows_by and row_annotation_colors arguments to plotHeatmap, similar to analogous column arguments.
Change text_by annotations in plotReducedDim to use geom_text_repel from ggrepel.
Changes in version 1.7.3 (2021-07-26)
scDblFinder now includes both cluster-based and random modes for artificial doublet generation
thresholding has been streamlined
default parameters have been optimized using benchmark datasets
added the directDblClassification
method
Changes in version 1.17.1 (2021-07-21)
Improved PsiNorm vignette.
Fix bug that prevented PSINORM_FN() to be exported.
Changes in version 1.5.2
remove loading warnings
Changes in version 1.5.1
update vignette
Changes in version 1.3.3
docs: created a vignette about advanced usage of scp
Changes in version 1.3.2
docs: created a QFeatures recap vignette
Changes in version 1.3.1
refactor: deprecated rowDataToDF. This function is now replaced by QFeatures::rbindRowData.
Changes in version 1.3
Changes in version 1.3.0
Changes in version 1.7.3 (2021-10-07)
Removing more tests attempting to verify that parallelized outputs perfectly match their serial counterparts.
Changes in version 1.7.2 (2021-09-15)
Removing tests checking that sequential and parallel calls to scPCA() produce identical outputs when BiocParallel’s SerialParam() is used. This due to new handing of random number generation in BiocParallel version 1.28.
Changes in version 0.99.8
Included citation for the package
Changes in version 0.99.7
Removed global assignment in multiAdaSampling.
Changes in version 0.99.6
Revised further to address comments/feedbacks
Changes in version 0.99.5
Fixed NEWS to match the version bump
Changes in version 0.99.4
Minor change to example in matPC function
Changes in version 0.99.3
Cleaned the GSE87795 subset data to a SingleCellExperiment object
Changes in version 0.99.2
version bump with submission to Bioconductor
Changes in version 0.99.1
Cleaning repository to pass BiocCheck
Changes in version 0.99.0
Code formats/documentations have been revised to meet Bioconductor requirements
Changes in version 0.1.1
Changes in version 0.1.0
Changes in version 2.4.0
Regularizer parameter (L2_A/L1_A) was added in cellCellDecomp() (“ntd”, “ntd2”).
Multilinear CX Decompotision was added in cellCellDecomp() (“cx”).
convertNCBIGeneID is removed.
The vignettes were modified.
Support of LRBase.XXX.eg.db-type packages is completely deprecated
Changes in version 0.99.00
Changes in version 1.5.1
Prepare for release
Changes in version 1.4.1
Prepare for release
Changes in version 1.15.1
Changes in version 1.11.2
New functionality
Changes in version 1.7.3 (2021-08-24)
Improved get_targets function by supporting different output format.
Changes in version 1.7.2 (2021-06-14)
Supported automatic downloads of ExperimentHub cached files.
Changes in version 1.19.1
Changes in version 2.3.2 (2021-10-24)
Other refactors and bug fixes
Changes in version 2.3.1 (2021-10-15)
Several bug fixes
Changes in version 2.2.2 (2021-10-10)
Changes in version 1.9.4
Fix: special case when tree root has more than one lineage path
Changes in version 1.9.3
Fix: invalid parallel mutations at divergent node.
Update DESCRIPTION, README and vignettes.
Changes in version 1.9.2
Allow partially plot ‘lineagePath’.
Improved ‘plotMutSites’ function for ‘lineagePath’.
Changes in version 1.9.1
Add ‘useSites’ argument to ‘setSiteNumbering’ function.
First ‘stable’ path as default ‘lineagePath’.
Enable plot functions for ‘parallelSites’.
Changes in version 1.4.0 (2021-09-09)
Changes in version 1.0
Enhancements
Breaking Changes from Pre-release
Changes in version 1.3.0 (2021-09-28)
added S4 wrappers for Seurat and GeoMxSet objects
added custom profile matrix generation from single cell data
added ~75 profile matrices avaliable to download for human and mouse
Changes in version 1.3.2 (2021-07-27)
spatialData moved from colData to int_colData
restructuring of vignette and added imgData section
Changes in version 1.99.0 (2021-10-14)
Implemented overlaying feature: overlay template images in raster format with SHMs, where charcoal and transparency options are provided.
Implemented Spatial Single Cell functionality: co-visualize single cells and bulk tissues by placing single-cell embedding plots (PCA, tSNE, UMAP) and SHMs side by side, cell cluster assignments are defined in the app or provided by users, in dimensionality plots shapes are not restricted to 6, etc.
Spatial enrichment was synced to R command line.
Implemented Sigle and Multiple search mode for gene IDs.
Changes in version 0.99.7
added direct support for GenomicInteractions objects
improved vignettes
removed biomaRt requests
added support for R 4.1
added ‘Transcription’ Bioconductor Views annotation
Changes in version 0.99.0
initial pre-release
Changes in version 1.3
Changes in 1.3.11
Changes in 1.3.10
Changes in 1.3.9
Changes in 1.3.8
Changes in 1.3.7
Changes in 1.3.6
Changes in 1.3.5
Changes in 1.3.4
Changes in 1.3.3
Changes in 1.3.2
Changes in 1.3.1
Changes in version 0.1.0
Changes in version 1.18.0 (2021-10-27)
• Added functionality to simulate directly from empirical values
• Added eqtl.coreg parameter to splatPop
• Fixed a bug where too many cells were simulated in splatPop with multiple batches
• Fixed duplicate cell names in splatPopSimulate
Improved checks for group.prob in SplatParams
Automatically rescale group.prob during setting if it doesn’t sum to 1
Changes in version 1.0.3
Other minor changes.
Changes in version 1.0.2
Bug fix for single sample analysis.
Changes in version 1.0.1
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 1.5.3
fix variable_meta assignment
Changes in version 1.5.2
use ontology slots instead of STATO
Changes in version 1.5.7
improve NA handling in fold_change computations
Changes in version 1.5.5
change t-test outputs to data.frame
fix NA bug in feature_boxplot chart
use new ontology system in place of stato
Changes in version 1.5.2
add outputs to auto-generated documentation
fix fold change threshold using median (#56)
add fold change using means (#57)
HSD param “unbalanced” is no longer ignored
Changes in version 1.5.1
fixed broken paired tests
Changes in version 1.4.2
fix fold change threshold using median (#56)
HSD param “unbalanced” is no longer ignored
Changes in version 1.4.1
fixed broken paired tests
Changes in version 1.24.0
NEW FEATURES
Add ‘checkDimnames’ argument to SummarizedExperiment() constructor function
Add showAsCell() method for SummarizedExperiment objects.
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 0.99.6 (2021-10-25)
Fixed text for consistency in package name
Changes in version 0.99.5 (2021-10-21)
Fixed text for consistency in package name
Changes in version 0.99.4 (2021-10-12)
Changes in version 0.99.3 (2021-10-11)
Fixed .gitignore file to fix build error
Changes in version 0.99.2 (2021-09-14)
Fixed bug in script
Changes in version 0.99.0 (2021-08-24)
Submitted to Bioconductor
Changes in version 0.99.0 (2021-04-28)
Changes in version 0.99.0 (2021-04-28)
Changes in version 2021-07-02 (2021-07-02)
Changes:
Changes in version 2.17
Changes in version 2.17.3
Changes in version 2.17.2
Changes in version 2.17.1
Changes in version 1.5.4
Added the function EstimageGenomeRearrangements that generates rearrangement scenarios of large scale genomic events using the double cut and join model.
Changes in version 1.5.3
Added the function SequenceSimilarity and made improvements to runtime in DisjointSet.
Changes in version 1.4.1
Changes in version 1.3.15
New Feature
Minor Change
Bump version requirements of spsComps, systemPipeR, systemPipeRdata
In global.R, now use spsOption with the .list argument to set up options instead of the base options function.
Replace includeMardown() by markdown(readLines()) so we don’t need additional {markdown} package as dependency.
Bug Fix
Fix links and image urls that were not working or changed.
Changes in version 1.3.10
New Feature
Add code display buttons to most plots that will show code to reproduce the plot.
Add two args buttonType and placeholder to dynamicFile, now users can specify what bootstrap color the button is and use placeholder to specify initial text on the upload bar.
Enhanced the original shiny fileInput, now users can also specify icon and button bootstrap colors for “server” mode in dynamicFile.
Major Change
Redesign of a few steps in Workflow module. The new version of {systemPipeR} fundamentally changed how the workflow will be run. To sync to this new version, WF module has to been redesigned. Major change happens on workflow step selection. This requires users to install systemPipeR > 1.27.10
New methods to initiate the WF project
New workflow plot
New step selection mechanism
New step editing functionalities
Minor Change
Bug Fix
#85 fix dynamicFile icon not working
Also add some icon validation code
Fix the admin server tabs get loaded twice. Added a flag to prevent this from happening.
Changes in version 1.3.0
Update version number to 1.3.0 per Bioconductor regulation.
Changes in version 0.99
NEW FEATURES
Changes in version 1.5.1 (2021-08-27)
Fixed a bug in createPrimerTrack()
Added citation
Changes in version 1.50.0
NEW FEATURES
FindAllPeaks: Allow for asymmetric RT deviations. Formerly, the window search parameter was plus o minus a tolerance; now it can be different on either side of the expected RT.
ncdf4_convert_from_path: New flag to convert CDF files recursively.
checkRimLim: show multiple samples at the same time, as opposed to a single sample in previous versions.
BUG FIXES
Make sure that the assertion that checks for NULL or NA is operating in a scalar. For vectors use another assertion.
Code clean-up. Remove unneeded files.
Changes in version 1.5.0
Bug Fixes
Major Changes
Minor Changes
Changes in version 2.21.1
Function GDCPrepare for TARGET-ALL-P3 fixed
Function getMC3MAF fixed
Changes in version 1.14.0
Minor changes and bug fixes
Changes in version 1.6.1
Changes in version 1.15
Changes in version 1.15.1
Changes in version 1.3.4
Fix bug in tests when run on Windows due to uninherited namespace imports for testthat::context and testthat::expect_equal inside a bplapply call
Changes in version 1.3.3
Debugging BioC build ERROR caused by updates to CoreGx
Changes in version 1.3.2
For now just deleting protocolData from the metadata of the SummarizedExperiment, but will eventually need to be fixed upstream in ORCESTRA
Changes in version 1.3.1
Molecular profile data is now subset in test to keep package size down
Changes in version 1.3.0
Changes in version 1.29.8
Fix the a typo in read hic data.
Changes in version 1.29.7
Fix the bug ‘breaks’ are not unique
Changes in version 1.29.6
Add smooth curve to the tracks.
Changes in version 1.29.5
Improve gene track plots.
Changes in version 1.29.4
Fix the issue for auto-rescale lolliplot by emphasizing exon region when there are continues exons.
Changes in version 1.29.3
Add the possibility to lolliplot to emphasize exon or intron region.
Changes in version 1.29.2
Fix the yaxis when user supplied yaxis is greater than max scores.
Changes in version 1.29.1
Update documentation lolliplot for rescale parameter.
Changes in version 0.1
Change default of overdispersion_shrinkage to TRUE if overdispersion = TRUE for acosh_transform() and shifted_log_transform()
Changes in version 0.1.0
Changes in version 1.2.2
BUG FIX
Improved tab delimiter processing, argument processing for RCy3::getEdgeInfo()
Changes in version 1.2.1
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.5.1
Object transformation functions condensed into the
treeAndLeaf
function, to be made automatically [2020-08-24].
TreeAndLeaf function became more automated.
The igraph object manipulation was upgraded, through the use of RedeR functions.
Changes in version 1.17.2
introduce force.ultrametric parameter in read.mcmctree
Changes in version 1.17.1
Changes in version 0.1.0 (2021-07-03)
Changes in version 0.99.0 (2021-08-15)
Changes in version 1.19.1 (2021-08-30)
Bug fix
Substitute | by | . |
Changes in version 0.99.0
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
None.
Changes in version 0.3.2
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
None.
Changes in version 0.3.1
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
None.
Changes in version 0.3.0
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
None.
Changes in version 0.2.2
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
The BPPARAM was not being passed through to internal bplapply calls.
Changes in version 0.2.1
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
None.
Changes in version 0.2.0
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
Changes in version 1.12.0
NEW FEATURES
New function, sequence_complexity(): Using either the Wootton-Federhen, Trifonov, or DUST algorithms, calculate sequence complexity in sliding windows. A version for small arbitrary strings is also provided: calc_complexity().
New function, mask_ranges(): Similarly to mask_seqs(), mask specific positions in a XStringSet object by replacing the letters with a specific filler character.
New function, motif_range(): Get the min/max range of possible logodds scores for a motif.
New function, calc_windows(): Utility function for calculating coordinates for sliding windows.
New function, window_string(): Utility function for retrieving sliding windows in a string.
New function, slide_fun(): Utility function which wraps window_string() and vapply() together.
motif_pvalue(method): P-values and scores can now be calculated dynamically instead of exhaustively, substantially increasing both speed and accuracy for bigger jobs. The previous exhaustive method can still be used however, as the dynamic method does not allow non-finite values and thus must be pseudocount-adjusted.
scan_sequences(calc.pvals, calc.qvals, motif_pvalue.method, calc.qvals.method): The calc.pvals argument defaults to TRUE. The P-value calculation method now defaults to dynamic P-values (the previous method was an exhaustive calculation), though this can be changed via motif_pvalue.method. Additionally, adjusted P-values can be calculated as either BH, FDR or a Bonferroni-adjusted P-value. More details can be found in the Sequence Searches vignette.
write_homer(threshold, threshold.type): Finer control over the final motif logodds threshold included with the written motif is now available, using the style of argument parsing from scan_sequences(). The previous logodds_threshold argument is now deprecated and set to NULL, but if set (e.g. an older script is being re-run) then the old behaviour of write_homer() will be used.
MINOR CHANGES
New global option, options(pseudocount.warning): Disable the message printed when a motif is pseudocount-adjusted.
Slight performance gains in get_bkg() window code.
motif_pvalue(): Clarify that, indeed, background probabilities are taken into account when calculating P-values from score inputs. The background adjustment takes place during the initial conversion to PWM.
motif_pvalue(): When bkg.probs are provided, use those when converting to a PWM.
scan_sequences(): The default threshold is now 0.0001 (using threshold.type = “pvalue”).
The axis text in view_motifs() is now black instead of grey.
create_motif(): When a named background vector is provided, it is sorted according to the alphabet characters.
scan_sequences(): Check that the sequences aren’t shorter than the motifs.
print.universalmotif_df: Changed warning message when subsetting to an incomplete universalmotif_df object. Also added a way to turn off informative messages/warnings via the boolean universalmotif_df.warning global option.
Miscellaneous changes and additions to the vignettes and various function manual pages.
Changes in version 1.10.2
BUG FIXES
read_homer() now correct parses enrichment P-value and logodds score.
Changes in version 1.10.1
BUG FIXES
Restore temporarily disabled ggtree(layout=”daylight”) example in the MotifComparisonAndPvalues.Rmd vignette, as tidytree is now patched.
Fixed some awkwardness in view_motifs() panel spacing and title justification.
Changes in version 0.99.0 (2021-06-07)
Changes in version 1.3.1
Changes in version 0.0.0.9000
Changes in version 1.7
Changes in version 1.2.0
Changes in version 1.5.1
Changes in version 1.1.3 (2021-10-05)
Changes in version 3.15.5
Disable testing on windows i386, providing some speedup
Disable parallel processing on Windows, causing an issue in testthat on BioC build check
Changes in version 3.15.4
Fix in plot
with type = "XIC"
to plot an empty plot if no data is
present.
Skip re-indexing of peaks to features if not necessary. This results in performance improvements for MS1 only data.
Changes in version 3.15.3
Add manualFeatures
allowing to manually define and add features to
an
XCMSnExp
object.
Add plotChromatogramsOverlay
function to support plotting of
multiple EICs
from the same sample into the same plot (eventually stacked).
Add feature grouping by EIC similarity: EicSimilarityParam
.
Import compareChromatograms
from MSnbase
.
Add feature grouping by similar retention time: `SimilarRtimeParams.
Add feature grouping by similarity of feature abundances across
samples:
AbundanceSimilarityParam
.
Add feature grouping methodology based on MsFeatures
.
Changes in version 3.15.2
Fix LC-MS/MS vignette.
Changes in version 3.15.1
Compatibility fix for nls() in R >= 4.1, contributed by Rick Helmus.
Changes in version 1.4.0
Add arguments to control how slots are converted in AnnData2SCE() and SCE2AnnData(). Each slot can now be fully converted, skipped entirely or only selected items converted.
Add support for converting the raw slot to an altExp in AnnData2SCE()
Add recursive conversion of lists in AnnData2SCE()
Add progress messages to various functions. These can be controlled by function arguments or a global variable.
Add long tests for various public datasets. This should help to make the package more robust
Fix bug in converting dgRMatrix sparse matrices
Correctly handle DataFrame objects stored in adata.obsm
Changes in version 1.7.1 (2021-06-18)
rmarkdown
to Suggests in DESCRIPTION to resolve changes in
knitr
Changes in version 1.0.2
NEW FEATURES
Updated the vignettes.
Changes in version 1.0.1
NEW FEATURES
Changes in version 1.9.1 (2021-06-18)
rmarkdown
to Suggests in DESCRIPTION to resolve changes in
knitr
Changes in version 3.2.0
The curatedMetagenomicData() function now has a rownames argument:
“long”, the default character string derived from MetaPhlAn3
“short”, the NCBI Taxonomy species name from the CHOCOPhlAn database
“short” row names are validated against NCBI Taxonomy with taxize
“NCBI”, the NCBI Taxonomy ID from the CHOCOPhlAn database
“NCBI” row names are validated against NCBI Taxonomy with taxize
rowData becomes NCBI Taxonomy ID numbers instead of taxa names
The sparse matrix data structure was switched from dgTMatrix to dgCMatrix
A few studies were reprocessed because of a minor error related to MetaPhlAn3
Changes inside the package were made to address bugs discovered by users
The combined_metadata object has been removed
Changes in version 0.99.4 (2021-10-18)
Update vignette output
Edit DESCRIPTION file
Changes in version 0.99.3 (2021-10-07)
Remove analysis/graphical functions from the master branch
Accepted by Bioconductor
Changes in version 0.99.2 (2021-09-24)
Remove cached files from git history
Modify packages based on reviewer’s comment
Changes in version 0.99.0 (2021-09-16)
The curatedTBData package collects 49 transcriptomic studies
Package vignette is updated to Rmd syntax and uses BiocStyle
All data is reprocessed in R (v4.1)
Move all data to ExperimentHub
Added a NEWS.md file to track changes to the package
Submitted to Bioconductor
Changes in version 1.7.1
21Q3 data added for crispr, copyNumber, TPM, mutationCalls and metadata datasets. Newer versions for the other datasets were not released.
CERES CRISPR data has been deprecated and has been replaced with Chronos CRISPR dependency in 21Q3 and all future releases. For more information, see: https://cancerdatascience.org/blog/posts/ceres-chronos/
Changes in version 1.5.2 (2021-10-13)
Daniel Dimitrov is assigned as the new maintainer
Changes in version 1.4.2 (2021-10-08)
Fixed lazy data warning
Improved test coverage
Changes in version 1.4.1 (2021-05-25)
Rebuild all regulons
Fixed ambiguously mode of regulation in mouse regulons
Changes in version 0.99.0
All set for the Bioconductor submission!
Changes in version 0.9.0
Getting ready for the submission to Bioconductor
Added a NEWS.md file to track changes to the package.
Changes in version 1.1.1 (2021-05-25)
Changes in version 3.13
Add MSigDB datasets
Add note in vignettes
Changes in version 1.1.5 (2021-09-08)
GrieneisenTS data added
HintikkaXO data added
Minor fixes
Changes in version 1.2.0
added MSigDB v7.4
removed gene-sets from the “archived” category from all collections
removed direct object referencing functions (e.g. msigdb.v7.2.hs.SYM()). Objects should be retrieved using the getMsigdb() function only or by querying the ExperimentHub
added IMEx PPI data
Changes in version 1.23.4
temporarily disable all vignettes until CAMERA issue is fixed
Changes in version 1.23.2
switch to mzML files in the ISA-Tab metadata
temporarily disable the vignette for the old xcms interface causing a build failure
Changes in version 1.23.1
add mzML versions of mzData files converted by OpenMS FileConverter
Changes in version 0.99.3 (2021-09-27)
Now uses BiocFileCache to store a copy of ExperimentHub resources. Allows for faster subsequent recalls
Changes in version 0.99.0 (2021-09-17)
Submitted to Bioconductor
Changes in version 1.1.1 (2021-03-05)
Changes in version 1.31.1
Fix mztab file name (required for new rpx)
Changes in version 1.31.0
New version for Bioc 3.14 (devel)
Changes in version 0.99.6
Changes in version 2.1.1
Temporarily rolled Ensemble version back to 75 to eliminate numerous non-coding transcripts
Methylation array information based on the latest manifest file
Changes in version 2.1.0
Release May 2021
Added annotation for the Mouse Methylation Bead Chip (thanks to Maxi Schoenung for his great contribution!).
Updated SNP information to GRCm38.p4, the last version available through NCBI.
Changes in version 0.99.3
removed usage of paste() function in error handling functions
Changes in version 0.99.2
Added NEWS.md file to track changes to the package.
Formatted functions to shorten lines
Removed usage of T/F in test cases
Removed usage of ‘paste’ in condition signals
Changes in version 0.99.1
added tests for queryATAC function
added new error checking to queryATAC and fetchATAC functions
Changes in version 1.1.1
Changes in version 1.6.0
New features
Bug fixes and minor improvements
Updates to seqFISH vignette and documentation.
Updated to changes in SummarizedExperiment where assayDimnames are checked.
scNMT defaults to version ‘1.0.0’s QC filtered cells. For unfiltered cells see version section in ?scNMT.
Changes in version 0.99.9
Changes in version 0.99.1
Add infoOnly argument to get details about download size
Changes in version 0.99.0
Add documentation
Prepare for Bioconductor submission
Changes in version 0.1.0
Add a NEWS.md file to track changes to the package.
Changes in version 1.2.1
Changes in version 1.0.0
Changes in version 0.99.4
Updated workflow image
Changes in version 0.99.3
Adjusted QC plotting histogram function to remove user-defined limits
Changes in version 0.99.2
Version update for bioconductor build review
Changes in version 0.99.1
NEW FEATURES
No new NEWS to report
Forty seven software packages were removed from this release (after being deprecated in Bioc 3.13): AffyExpress, affyQCReport, AnnotationFuncs, ArrayTools, bigmemoryExtras, BiocCaseStudies, CancerMutationAnalysis, ChIPSeqSpike, CompGO, CoRegFlux, CrossICC, cytofast, DBChIP, dexus, EasyqpcR, EDDA, eisa, ELBOW, ExpressionView, FlowRepositoryR, genoset, HCABrowser, HCAExplorer, HCAMatrixBrowser, Imetagene, mdgsa, metagenomeFeatures, methyAnalysis, MSEADbi, OutlierD, pcot2, PCpheno, Polyfit, POST, RchyOptimyx, RDAVIDWebService, RNAither, RNAprobR, rnaSeqMap, SAGx, samExploreR, seqplots, simulatorZ, SSPA, ToPASeq, XBSeq, yaqcaffy
Please note: CexoR and IntramiRExploreR, previously announced as deprecated in 3.13, fixed their packages and remained in Bioconductor.
Twenty three software packages are deprecated in this release and will be removed in Bioc 3.15: affyPara, ALPS, alsace, BrainStars, destiny, dualKS, ENCODExplorer, ENVISIONQuery, FindMyFriends, GeneAnswers, gramm4R, KEGGprofile, MouseFM, MSGFgui, MSGFplus, MSstatsTMTPTM, PanVizGenerator, predictionet, RGalaxy, scClassifR, slinky, SRGnet, SwimR
Eleven experimental data packages were removed this release (after being deprecated in BioC 3.13): ceu1kg, ceu1kgv, ceuhm3, cgdv17, dsQTL, facsDorit, gskb, hmyriB36, JctSeqData, MAQCsubsetAFX, yri1kgv
Five experimental data packages are deprecated in this release and will be removed in Bioc 3.15: ABAData, brainImageRdata, PCHiCdata, RITANdata, tcgaWGBSData.hg19
Ninety annotation packages were removed from this release (after being deprecated in Bioc 3.13): 12 LRBase.XXX.eg.db packages (replaced with AHLRBaseDbs), MafDb.gnomAD.r3.0.GRCh38, MafH5.gnomAD.r3.0.GRCh38, 73 MeSH.XXX.eg.db packages (replaced with AHMeSHDbs), greengenes13.5MgDb, ribosomaldatabaseproject11.5MgDb, silva128.1MgDb
One annotation package was deprecated in this release and will be removed in Bioc 3.15: org.Pf.plasmo.db
One workflow package was removed from this release (after being deprecated in Bioc 3.13): eQTL
No workflow packages were deprecated in this release.