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.

Alpha Vantage has free historical financial information. All you need to do is get a free API key at <https://www.alphavantage.co>. Then you can use the R interface to retrieve free equity information. Refer to the Alpha Vantage website for more information.

An implementation of Extreme Bounds Analysis (EBA), a global sensitivity analysis that examines the robustness of determinants in regression models. The package supports both Leamer's and Sala-i-Martin's versions of EBA, and allows users to customize all aspects of the analysis.

Bindings for hierarchical regression models for use with the parsnip package. Models include longitudinal generalized linear models (Liang and Zeger, 1986) <doi:10.1093/biomet/73.1.13>, and mixed-effect models (Pinheiro and Bates) <doi:10.1007/978-1-4419-0318-1_1>.

mlr3pipelines enriches mlr3 with a diverse set of pipelining operators (PipeOps) that can be composed into graphs. Operations exist for data preprocessing, model fitting, and ensemble learning. Graphs can themselves be treated as mlr3 Learners and can therefore be resampled, benchmarked, and tuned.

This package implements various 3D rotation parameterizations and defines conversions between them. At their heart, each rotation parameterization is a 3×3 unitary (orthogonal) matrix (based on the StaticArrays.jl package), and acts to rotate a 3-vector about the origin through matrix-vector multiplication.

The mime-types library provides a library and registry for information about Multipurpose Internet Mail Extensions (MIME) content type definitions. It can be used to determine defined filename extensions for MIME types, or to use filename extensions to look up the likely MIME type definitions.

git filter-repo is a versatile tool for rewriting history, which roughly falls into the same space of tool like git filter-branch but with more capabilities. git filter-repo is now recommended by the Git project instead of git filter-branch.

This package provides tools for managing SingleCellExperiment objects as projects. Includes functions for analysis and visualization of single-cell data. Also included is a shiny app for visualization of pre-processed scRNA data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

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

Approximate false positive rate control in selection frequency for random forest using the methods described by Ender Konukoglu and Melanie Ganz (2014) <arXiv:1410.2838>. Methods for calculating the selection frequency threshold at false positive rates and selection frequency false positive rate feature selection.

This package provides tools to support research on vowel covariation. Methods are provided to support Principal Component Analysis workflows (as in Brand et al. (2021) <doi:10.1016/j.wocn.2021.101096> and Wilson Black et al. (2023) <doi:10.1515/lingvan-2022-0086>).

Detect the number and locations of change points. The locations can be either exact or in terms of ranges, depending on the available computational resource. The method is based on Jie Ding, Yu Xiang, Lu Shen, Vahid Tarokh (2017) <doi:10.1109/TSP.2017.2711558>.

S4 class wrappers for the ODBC and Pool DBI connection, also provides some utilities to paste small datasets to clipboard, rename columns. It is used by the package stacomiR for connections to the database. Development versions of stacomiR are available in R-forge.

The Cancer Genome Atlas (TCGA) is a program aimed at improving our understanding of Cancer Biology. Several TCGA Datasets are available online. TCGAretriever helps accessing and downloading TCGA data hosted on cBioPortal via its Web Interface (see <https://www.cbioportal.org/> for more information).

Obtain historical and near real time data related to stocks, index and currencies from the Yahoo Finance API. This package is community maintained and is not officially supported by Yahoo'. The accuracy of data is only as correct as provided on <https://finance.yahoo.com/>.

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

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.

Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.

Leverage the existing open access TCGA data on Terra with well-established Bioconductor infrastructure. Make use of the Terra data model without learning its complexities. With a few functions, you can copy / download and generate a MultiAssayExperiment from the TCGA example workspaces provided by Terra.

This package provides a GUI with which the user can construct and interact with Bootstrap methods on Classical Biplots and with Clustering and/or Disjoint Biplot. This GUI is also aimed for estimate any numerical data matrix using the Clustering and Disjoint Principal component (CDPCA) methodology.

Copernicus Digital Elevation Model datasets (DEM) of 90 and 30 meters resolution using the awscli command line tool. The Copernicus (DEM) is included in the Registry of Open Data on AWS (Amazon Web Services) and represents the surface of the Earth including buildings, infrastructure and vegetation.

Simulate one or many frequentist confidence clinical trials based on a specified set of parameters. From a two-arm, single-stage trial to a perpetually run Adaptive Platform Trial, this package offers vast flexibility to customize your trial and observe operational characterisitics over thousands of instances.

The separate p-values of SNPs, RNA expressions and DNA methylations are calculated by KM regression. The correlation between different omics data are taken into account. This method can be applied to either samples with all three types of omics data or samples with two types.