Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at https://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.

This package implements an efficient O(n) algorithm based on bucket-sorting for fast computation of standard clustering comparison measures. Available measures include adjusted Rand index (ARI), normalized information distance (NID), normalized mutual information (NMI), adjusted mutual information (AMI), normalized variation information (NVI) and entropy.

This package provides a platform-independent API to access the operating system's credential store. It currently supports Keychain on macOS, Credential Store on Windows, the Secret Service API on GNU/Linux, and a simple, platform independent store implemented with environment variables. Additional storage back-ends can be added easily.

Libretro is a simple but powerful development interface that allows for the easy creation of emulators, games and multimedia applications that can plug straight into any libretro-compatible frontend. RetroArch is the official reference frontend for the libretro API, currently used by most as a modular multi-system game/emulator system.

This package provides functionality for processing and statistical analysis of multiplexed assays of variant effect (MAVE) and similar data. The package contains functions covering the full workflow from raw FASTQ files to publication-ready visualizations. A broad range of library designs can be processed with a single, unified interface.

The goal of amp.sim is to transform NONMEM models into R syntax so they can be used for simulations using the deSolve', nlmixr2 or mrgsolve package. Additionally, functionality is included to aid simulations performed directly in NONMEM and to automatically create shiny apps for simulation models.

Allows for multiple group item response theory alignment a la Mplus to be applied to lists of single-group models estimated in lavaan or mirt'. Allows item sets that are overlapping but not identical, facilitating alignment in secondary data analysis where not all items may be shared across assessments.

Combines the magick and imager packages to streamline image analysis, focusing on feature extraction and quantification from biological images, especially microparticles. By providing high throughput pipelines and clustering capabilities, biopixR facilitates efficient insight generation for researchers (Schneider J. et al. (2019) <doi:10.21037/jlpm.2019.04.05>).

Prevents and detects information leakage in biomedical machine learning. Provides leakage-resistant split policies (subject-grouped, batch-blocked, study leave-out, time-ordered), guarded preprocessing (train-only imputation, normalization, filtering, feature selection), cross-validated fitting with common learners, permutation-gap auditing, batch and fold association tests, and duplicate detection.

This package provides a computational tool to describe patterns in black and white images from natural structures. bwimage implemented functions for exceptionally broad subject. For instance, bwimage provide examples that range from calculation of canopy openness, description of patterns in vertical vegetation structure, to patterns in bird nest structure.

Parameters of a user-specified probability distribution are modelled by a multi-layer perceptron artificial neural network. This framework can be used to implement probabilistic nonlinear models including mixture density networks, heteroscedastic regression models, zero-inflated models, etc. following Cannon (2012) <doi:10.1016/j.cageo.2011.08.023>.

The primary motivation of this package is to take the things that are great about the R packages flextable <https://davidgohel.github.io/flextable/> and officer <https://davidgohel.github.io/officer/>, take the standard and complex pieces of formatting clinical tables for regulatory use, and simplify the tedious pieces.

Functionalities for analyzing high-dimensional and longitudinal biomarker data to facilitate precision medicine, using a joint model of Bayesian sparse factor analysis and dependent Gaussian processes. This paper illustrates the method in detail: J Cai, RJB Goudie, C Starr, BDM Tom (2023) <doi:10.48550/arXiv.2307.02781>.

Gives access to data visualisation methods that are relevant from the statistician's point of view. Using D3''s existing data visualisation tools to empower R language and environment. The throw chart method is a line chart used to illustrate paired data sets (such as before-after, male-female).

Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community ecological data. The original package description is in Goslee and Urban (2007) <doi:10.18637/jss.v022.i07>, with further statistical detail in Goslee (2010) <doi:10.1007/s11258-009-9641-0>.

This package provides functions to produce ggplot2'-based plots of objects produced by functions in the vegan package. Provides fortify()', autoplot()', and tidy() methods for many of vegan''s functions. The aim of ggvegan is to make it easier to work within the tidyverse with vegan'.

This package provides a unified algorithm, blockwise-majorization-descent (BMD), for efficiently computing the solution paths of the group-lasso penalized least squares, logistic regression, Huberized SVM and squared SVM. The package is an implementation of Yang, Y. and Zou, H. (2015) <doi:10.1007/s11222-014-9498-5>.

Read all commit messages of your local git repository and sort them according to tags or specific text pattern into chapters of a HTML book using bookdown'. The git history book presentation helps organisms required to testify for every changes in their source code, in relation to features requests.

Regression models for interval censored data. Currently supports Cox-PH, proportional odds, and accelerated failure time models. Allows for semi and fully parametric models (parametric only for accelerated failure time models) and Bayesian parametric models. Includes functions for easy visual diagnostics of model fits and imputation of censored data.

For a single variable, the IVY Plot stacks tied values in the form of leaflets. Five leaflets join to form a leaf. Leaves are stacked vertically. At most twenty leaves are shown; For high frequency, each leaflet may represent more than one observation with multiplicity declared in the subtitle.

The Lorentz transform in special relativity; also the gyrogroup structure of three-velocities. Performs active and passive transforms and has the ability to use units in which the speed of light is not unity. Includes some experimental functionality for celerity and rapidity. For general relativity, see the schwarzschild package.

Create custom labels, badges, certificates and other documents. Automate the production of potentially large numbers of herbarium and collection labels, accreditation badges, attendance and participation certificates, etc, and deliver them automatically. Documents are generated in PDF format, which requires a working installation of LaTeX', such as TinyTeX'.

Computing metabolite set enrichment analysis (MSEA) (Yamamoto, H. et al. (2014) <doi:10.1186/1471-2105-15-51>), single sample enrichment analysis (SSEA) (Yamamoto, H. (2023) <doi:10.51094/jxiv.262>) and over-representation analysis (ORA) that accounts for undetected metabolites (Yamamoto, H. (2024) <doi:10.51094/jxiv.954>).

Estimation of models with dependent variable left-censored at zero. Null values may be caused by a selection process Cragg (1971) <doi:10.2307/1909582>, insufficient resources Tobin (1958) <doi:10.2307/1907382>, or infrequency of purchase Deaton and Irish (1984) <doi:10.1016/0047-2727(84)90067-7>.