The MetAlyzer S4 object provides methods to read and reformat metabolomics data for convenient data handling, statistics and downstream analysis. The resulting format corresponds to input data of the Shiny app MetaboExtract (<https://www.metaboextract.shiny.dkfz.de/MetaboExtract/>).

This package implements a procedure to automatically generate 2D masks for clusters on dimensional reduction plots from methods like t-SNE (t-distributed stochastic neighbor embedding) or UMAP (uniform manifold approximation and projection), with a focus on single-cell RNA-sequencing data.

Adapts the index-flood technique to extreme air temperature data. The package uses the additive approach proposed in Martins et al. (2022) <doi:10.1590/1678-4499.20220061> and adapt it to climate change conditions through the use of nonstationary parametric distributions.

Three-dimensional rendering for grid and ggplot2 graphics using cubes and cuboids drawn with an oblique projection. As a special case also supports primary view orthographic projections. Can be viewed as an extension to the isocubes package <https://github.com/coolbutuseless/isocubes>.

Calculates seat allocation using the D-Hondt method, Sainte-Lague method, and Modified Sainte-Lague method, all commonly used in proportional representation electoral systems. For more information on these methods, see Michael Gallagher (1991)<doi:10.1016/0261-3794(91)90004-C>.

Cluster analysis is one of the most fundamental problems in data science. We provide a variety of algorithms from clustering to the learning on the space of partitions. See Hennig, Meila, and Rocci (2016, ISBN:9781466551886) for general exposition to cluster analysis.

This package provides tools for estimating vaccine effectiveness and related metrics. The vaccineff_data class manages key features for preparing, visualizing, and organizing cohort data, as well as estimating vaccine effectiveness. The results and model performance are assessed using the vaccineff class.

This package provides a wrapper for the MediaWiki API, aimed particularly at the Wikimedia production wikis, such as Wikipedia. It can be used to retrieve page text, information about users or the history of pages, and elements of the category tree.

Implementation of corrected two-sample tests. A corrected version of the Pearson and Kendall correlation tests, the Mann-Whitney (Wilcoxon) rank sum test, the Wilcoxon signed rank test and a variance test are implemented. The package also proposes a test for the median and an independence test between two continuous variables of Kolmogorov-Smirnov's type. All these corrected tests are asymptotically calibrated in the sense that the probability of rejection under the null hypothesis is asymptotically equal to the level of the test. See <doi:10.48550/arXiv.2211.08784> for more details on the statistical tests.

Bindings to kernel methods for enforcing security restrictions. AppArmor can apply mandatory access control (MAC) policies on a given task (process) via security profiles with detailed ACL definitions. In addition this package implements bindings for setting process resource limits (rlimit), uid, gid, affinity and priority. The high level R function eval.secure builds on these methods to perform dynamic sandboxing: it evaluates a single R expression within a temporary fork which acts as a sandbox by enforcing fine grained restrictions without affecting the main R process. A portable version of this function is now available in the unix package.

This package generates a Miami plot with centered chromosome labels. The output is a ggplot2 object. Users can specify which data they want plotted on top vs. bottom, whether to display significance line(s), what colors to give chromosomes, and what points to label.

Create tree structures from hierarchical data, and traverse the tree in various orders. Aggregate, cumulate, print, plot, convert to and from data.frame and more. This is useful for decision trees, machine learning, finance, conversion from and to JSON, and many other applications.

This package provides tools for capturing logic in a Shiny app and exposing it as code that can be run outside of Shiny (e.g., from an R console). It also provides tools for bundling both the code and results to the end user.

This package provides three functions for dealing with dates: parse_iso_8601 recognizes and parses all valid ISO 8601 date and time formats, parse_date parses dates in unspecified formats, and format_iso_8601 formats a date in ISO 8601 format.

The R package decemedip is a novel computational paradigm developed for inferring the relative abundances of cell types and tissues measure by methylated DNA immunoprecipitation sequencing (MeDIP-Seq). This paradigm allows using reference data from other technologies such as microarray or WGBS.

Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.

KinSwingR integrates phosphosite data derived from mass-spectrometry data and kinase-substrate predictions to predict kinase activity. Several functions allow the user to build PWM models of kinase-subtrates, statistically infer PWM:substrate matches, and integrate these data to infer kinase activity.

This package provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

This package provides tools for reproducible, offline analysis of endurance-training data exported from Strava'. Provides data import, quality-control, cohort-reference, and visualization helpers for sports-science indicators including acute:chronic workload ratio, aerobic efficiency, cardiovascular decoupling, exposure, and personal-best profiles.

This package provides a lightweight modelling syntax for defining likelihoods and priors and for computing Bayes factors for simple one parameter models. It includes functionality for computing and plotting priors, likelihoods, and model predictions. Additional functionality is included for computing and plotting posteriors.

Model agnostic tool for decomposition of predictions from black boxes. Break Down Table shows contributions of every variable to a final prediction. Break Down Plot presents variable contributions in a concise graphical way. This package work for binary classifiers and general regression models.

Datasets related to the Comrades Marathon used in the book Antony Unwin (2024, ISBN:978-0367674007) "Getting (more out of) Graphics". The main dataset contains the times of every runner that finished in the time limit for each year the race was run.

Includes binning categorical variables into lesser number of categories based on t-test, converting categorical variables into continuous features using the mean of the response variable for the respective categories, understanding the relationship between the response variable and predictor variables using data transformations.