Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.

This package provides full screen and partial loading screens for Shiny with spinners, progress bars, and notifications.

Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation.

This package provides two convenience functions assert() and test_pkg() to facilitate testing R packages.

This package provides a collection of templates to author preregistration documents for scientific studies in PDF format.

This package provides a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution.

Use finite state transducers to compactly represent sets or maps of many strings (> 1 billion is possible).

This package provides a library for working with graphs in the GFA format.

This library provides methods to read Adobe Font Metrics (afm) files and use the data therein.

This package provides a job queue that uses PostgreSQL for storing jobs and locking between worker processes.

This pure ruby library provides spawn() which is almost perfectly compatible with ruby 1.9's.

Command-line tool and C library for reading files from popular stats packages like SAS, Stata and SPSS.

This package provides simple utility functions that are shared across several packages maintained by the Tanay lab.

This package provides functions to conduct hypothesis tests and derive confidence intervals for quantiles, linear combinations of quantiles, ratios of dependent linear combinations and differences and ratios of all of the above for comparisons between independent samples. Additionally, quantile-based measures of inequality are also considered.

Reference-based multiple imputation of ordinal and binary responses under Bayesian framework, as described in Wang and Liu (2022) <arXiv:2203.02771>. Methods for missing-not-at-random include Jump-to-Reference (J2R), Copy Reference (CR), and Delta Adjustment which can generate tipping point analysis.

This package provides utilities to re-use content across chapters of a Bioconductor book. This is mostly based on functionality developed while writing the OSCA book, but generalized for potential use in other large books with heavy compute. Also contains some functions to assist book deployment.

This package provides a library for rolling windows operations. The package enables full control over the window length, window lag, and time indices. With a runner one can apply any R function on rolling windows. The package eases work with equally and unequally spaced time series.

This package provides the random ferns classifier by Ozuysal, Calonder, Lepetit and Fua (2009) <doi:10.1109/TPAMI.2009.23>, modified for generic and multi-label classification and featuring OOB error approximation and importance measure as introduced in Kursa (2014) <doi:10.18637/jss.v061.i10>.

Mediation analysis for multiple mediators by penalized structural equation models with different types of penalties depending on whether there are multiple mediators and only one exposure and one outcome variable (using sparse group lasso) or multiple exposures, multiple mediators, and multiple outcome variables (using lasso, L1, penalties).

This package provides struct RGB/RGBA/etc. for sharing pixels between crates + convenience methods for color manipulation. It allows no-copy high-level interoperability. It also adds common convenience methods and implements standard Rust traits to make `RGB`/`RGBA` pixels and slices first-class Rust objects.

Parse a BibTeX file to a data.frame to make it accessible for further analysis and visualization.

Discrete factor analysis for dependent Poisson and negative binomial models with truncation, zero inflation, and zero inflated truncation.

This package provides methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.

Integrated toolbox supporting common file formats used for intracranial Electroencephalography (iEEG) and deep-brain stimulation (DBS) study.