loci2path performs statistics-rigorous enrichment analysis of eQTLs in genomic regions of interest. Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB.

This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline.

OncoScore is a tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries.

Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC.

The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.

Wraps the Ace editor in a HTML widget. The Ace editor has support for many languages. It can be opened in the viewer pane of RStudio', and this provides a second source editor.

This package implements the distance measure for mixed-scale variables proposed by Buttler and Fickel (1995), based on normalized mean pairwise distances (Gini mean difference), and an R2 statistic to assess clustering quality.

Confirms if the number is Luhn compliant. Can check if credit card, IMEI number or any other Luhn based number is correct. For more info see: <https://en.wikipedia.org/wiki/Luhn_algorithm>.

This package provides functions to work with data frames to prepare data for further analysis. The functions for imputation, encoding, partitioning, and other manipulation can produce log files to keep track of process.

Make fake data that looks realistic, supporting addresses, person names, dates, times, colors, coordinates, currencies, digital object identifiers ('DOIs'), jobs, phone numbers, DNA sequences, doubles and integers from distributions and within a range.

Secant acceleration applied to derivative-free Spectral Residual Methods for solving large-scale nonlinear systems of equations. The main reference follows: E. G. Birgin and J. M. Martinez (2022) <doi:10.1137/20M1388024>.

Various diffusion models to forecast new product growth. Currently the package contains Bass, Gompertz, Gamma/Shifted Gompertz and Weibull curves. See Meade and Islam (2006) <doi:10.1016/j.ijforecast.2006.01.005>.

Allows the user to create a countdown in RMarkdown documents and shiny applications. The package is a wrapper of the JavaScript library flipdown.js'. See <https://pbutcher.uk/flipdown/> for more info.

Uses raw vectors to minimize memory consumption of categorical variables with fewer than 256 unique values. Useful for analysis of large datasets involving variables such as age, years, states, countries, or education levels.

An implementation of the methodologies described in Xi Liu, Afshin A. Divani, and Alexander Petersen (2022) <doi:10.1016/j.csda.2022.107421>, including truncated functional linear and truncated functional logistic regression models.

This package provides a collection of functions to perform Gaussian quadrature with different weight functions corresponding to the orthogonal polynomials in package orthopolynom. Examples verify the orthogonality and inner products of the polynomials.

Generates concise alternative text for data visualizations created with ggplot2'. Descriptions are produced by inspecting plot layers, labels, scales, and facets, with support for multiple languages and alternative text stored in plot metadata.

This package provides a collection of custom ggplot2'-based visualizations for data exploration and analysis. Each function handles data preprocessing and returns a object that can be further customized using standard ggplot2 syntax.

This package implements a geographically weighted non-negative principal components analysis, which consists of the fusion of geographically weighted and sparse non-negative principal components analyses <doi:10.17608/k6.auckland.9850826.v1>.

An excerpt of the data available at Gapminder.org. For each of 142 countries, the package provides values for life expectancy, GDP per capita, and population, every five years, from 1952 to 2007.

This package provides an interface to the GeoNode API, allowing to upload and publish metadata and data in GeoNode'. For more information about the GeoNode API, see <https://geonode.org/>.

This package provides functions for converting local HTML and XHTML files to PDF using an external backend. The package includes helper functions for backend setup, file conversion, and an optional Tk graphical interface.

This package implements the compartment model from Tokars (2018) <doi:10.1016/j.vaccine.2018.10.026>. This enables quantification of population-wide impact of vaccination against vaccine-preventable diseases such as influenza.

It provides a general framework to analyse dependence between point processes in time. It includes parametric and non-parametric tests to study independence, and functions for generating and analysing different types of dependence.