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.

This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures.

R functions for criterion profile analysis, Davison and Davenport (2002) <doi:10.1037/1082-989X.7.4.468> and meta-analytic criterion profile analysis, Wiernik, Wilmot, Davison, and Ones (2020) <doi:10.1037/met0000305>. Sensitivity analyses to aid in interpreting criterion profile analysis results are also included.

This package provides a pair of functions for renaming and encoding data frames using external crosswalk files. It is especially useful when constructing master data sets from multiple smaller data sets that do not name or encode variables consistently across files. Based on similar commands in Stata'.

This package provides a simple way to manage application settings by loading configuration values from .env or .ini files. It supports default values, type casting, and environment variable overrides, enabling a clean separation of configuration from code. Ideal for managing credentials, API keys, and deployment-specific settings.

This package provides a structured profile likelihood algorithm for the logistic fixed effects model and an approximate expectation maximization (EM) algorithm for the logistic mixed effects model. Based on He, K., Kalbfleisch, J.D., Li, Y. and Li, Y. (2013) <doi:10.1007/s10985-013-9264-6>.

Published meta-analyses routinely present one of the measures of heterogeneity introduced in Higgins and Thompson (2002) <doi:10.1002/sim.1186>. For critiquing articles it is often better to convert to another of those measures. Some conversions are provided here and confidence intervals are also available.

Create a kite-square plot for contingency tables using ggplot2', to display their relevant quantities in a single figure (marginal, conditional, expected, observed, chi-squared). The plot resembles a flying kite inside a square if the variables are independent, and deviates from this the more dependence exists.

This package provides an extension to the lolog package by introducing the minTriadicClosure() statistic to capture higher-order interactions among triplets of nodes. This function facilitates improved modelling of group formations and triadic closure in networks. A smoothing parameter has been incorporated to avoid numerical errors.

This package provides flexible dictionary-based cleaning that allows users to specify implicit and explicit missing data, regular expressions for both data and columns, and global matches, while respecting ordering of factors. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

This package provides functions to facilitate model-based clustering of nodes in a network in a mixture of experts setting, which incorporates covariate information on the nodes in the modelling process. Isobel Claire Gormley and Thomas Brendan Murphy (2010) <doi:10.1016/j.stamet.2010.01.002>.

Given a network (e.g. a food web), estimates several network indices. These include: Ascendency network indices, Direct and indirect dependencies, Effective measures, Environ network indices, General network indices, Pathway analysis, Network uncertainty indices and constraint efficiencies and the trophic level and omnivory indices of food webs.

Control Philips Hue smart lighting. Use this package to connect to a Hue bridge on your local network (remote authentication not yet supported) and control your smart lights through the Philips Hue API. All API V1 endpoints are supported. See API documentation at <https://developers.meethue.com/>.

This package provides path_chain class and functions, which facilitates loading and saving directory structure in YAML configuration files via config package. The file structure you created during exploration can be transformed into legible section in the config file, and then easily loaded for further usage.

Data obtained from surveys contains information not only about the survey responses, but also the survey metadata, e.g. the original survey questions and the answer options. The surveydata package makes it easy to keep track of this metadata, and to easily extract columns with specific questions.

This package provides a set of spatial accessibility measures from a set of locations (demand) to another set of locations (supply). It aims, among others, to support research on spatial accessibility to health care facilities. Includes the locations and some characteristics of major public hospitals in Greece.

This package provides a diverse collection of U.S. datasets encompassing various fields such as crime, economics, education, finance, energy, healthcare, and more. It serves as a valuable resource for researchers and analysts seeking to perform in-depth analyses and derive insights from U.S.-specific data.

Wavelet decomposition method is very useful for modelling noisy time series data. Wavelet decomposition using haar algorithm has been implemented to developed hybrid Wavelet GBM (Gradient Boosting Method) model for time series forecasting using algorithm by Anjoy and Paul (2017) <DOI:10.1007/s00521-017-3289-9>.

Rossby wave ray paths are traced from a determined source, specified wavenumber, and direction of propagation. "raytracing" also works with a set of experiments changing these parameters, making possible the identification of Rossby wave sources automatically. The theory used here is based on classical studies, such as Hoskins and Karoly (1981) <doi:10.1175/1520-0469(1981)038%3C1179:TSLROA%3E2.0.CO;2>, Karoly (1983) <doi:10.1016/0377-0265(83)90013-1>, Hoskins and Ambrizzi (1993) <doi:10.1175/1520-0469(1993)050%3C1661:RWPOAR%3E2.0.CO;2>, and Yang and Hoskins (1996) <doi:10.1175/1520-0469(1996)053%3C2365:PORWON%3E2.0.CO;2>.

The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motifs and amino acid sequence motifs. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.

This package provides an R interface to the Tabler HTML template. tablerDash is a light Bootstrap 4 dashboard template. There are different layouts available such as a one page dashboard or a multi-page template, where the navigation menu is contained in the navigation bar.

dandelionR is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation. It provides the necessary functions to interface with scRepertoire and a custom implementation of an absorbing Markov chain for pseudotime inference, inspired by the Palantir Python package.

Convenience functions for aggregating a data frame or data table. Currently mean, sum and variance are supported. For Date variables, the recency and duration are supported. There is also support for dummy variables in predictive contexts. Code has been completely re-written in data.table for computational speed.

This package provides simple assertions with sensible defaults and customisable error messages. It offers convenient assertion call wrappers and a general assert function that can handle any condition. Default error messages are user friendly and easily customized with inline code evaluation and styling powered by the cli package.