This package provides methods and functions for fitting maximum likelihood models in R. This package modifies and extends the mle classes in the stats4 package.

This is a package for constructing minimum-cost regular spanning subgraph as part of a non-parametric two-sample test for equality of distribution.

The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.

This package provides an implementation of Adaptive Base Error Model in Ultra-deep Sequencing data (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic single nucleotide variants (SNVs) in circulating cell free DNA (cfDNA).

This package provides a parallel backend for the %dopar% function using the snow package.

This package provides functions to perform k-prototypes partitioning clustering for mixed variable-type data according to Z.Huang (1998): Extensions to the k-Means Algorithm for Clustering Large Data Sets with Categorical Variables, Data Mining and Knowledge Discovery 2, 283-304.

This package provides methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers.

Tidyft is an extension of data.table. It uses modifification by reference whenever possible. This toolkit is designed for big data analysis in high-performance desktop or laptop computers. The syntax of the package is similar or identical to tidyverse.

This package provides a set of functions to generate high-resolution Venn and Euler plots. It includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.

This package provides functions for working with legends and axis lines of ggplot2, facets that repeat axis lines on all panels, and some knitr extensions.

This package provides fast machine learning algorithms including matrix factorization and divisive clustering for large sparse and dense matrices.

This package provides fast and accurate convolution-type smoothed quantile regression, implemented using Barzilai-Borwein gradient descent with a Huber regression warm start. Confidence intervals for regression coefficients are constructed using multiplier bootstrap.

This package provides alternative statistical methods for meta-analysis, including:

1. bivariate generalized linear mixed models for synthesizing odds ratios, relative risks, and risk differences

2. heterogeneity tests and measures that are robust to outliers;

3. measures, tests, and visualization tools for publication bias or small-study effects;

4. meta-analysis of diagnostic tests for synthesizing sensitivities, specificities, etc.;

5. meta-analysis methods for synthesizing proportions;

6. models for multivariate meta-analysis.

This package provides a collection of clean R Markdown HTML document templates using classless CSS styles. These documents use a minimal set of dependencies but still look great, making them suitable for use a package vignettes or for sharing results via email.

This is a subset of the original spatstat package, containing the user-level code from spatstat which performs geometrical operations, except for the geometry of linear networks.

This package contains genomic data for the plant pathogen Phytophthora infestans. It includes a variant file, a sequence file and an annotation file. This package is intended to be used as example data for packages that work with genomic data.

This package provides support for simple features, a standardized way to encode spatial vector data. It binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to PROJ for projection conversions and datum transformations.

With this package it is possible to define parameter spaces, constraints and dependencies for arbitrary algorithms, and to program on such spaces. It also includes statistical designs and random samplers. Objects are implemented as R6 classes.

This package enhances the R Optimization Infrastructure (ROI) package with a connection to the neos server. ROI optimization problems can directly be sent to the neos server and solution obtained in the typical ROI style.

This package holds the database for the extrafont package.

This package provides a set of tools to extract bibliographic content from the National Center for Biotechnology Information (NCBI) databases, including PubMed. The name RISmed is a portmanteau of RIS (for Research Information Systems, a common tag format for bibliographic data) and PubMed.

Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates tmap, the package for visualizing thematic maps.

This is a package for ratios of count data such as obtained from RNA-seq are modelled using Bayesian statistics to derive posteriors for effects sizes. This approach is described in Erhard & Zimmer (2015) <doi:10.1093/nar/gkv696> and Erhard (2018) <doi:10.1093/bioinformatics/bty471>.

This package provides a wrapper for the homologene database by the National Center for Biotechnology Information (NCBI). It allows searching for gene homologs across species. The package also includes an updated version of the homologene database where gene identifiers and symbols are replaced with their latest (at the time of submission) version and functions to fetch latest annotation data to keep updated.