The zlog package offers functions to transform laboratory measurements into standardised z or z(log)-values. Therefore the lower and upper reference limits are needed. If these are not known they could be estimated from a given sample.

This package provides access to phyloinformatic data in NeXML format. The package should add new functionality to R such as the possibility to manipulate NeXML objects in more various and refined way and compatibility with ape objects.

This package provides a dependency manager for R projects that allows you to manage the R packages your project depends on in an isolated, portable, and reproducible way.

This package guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.

This package provides functions to re-arrange, extract, and work with distances.

This package provides functionality to define and train neural networks similar to PyTorch but written entirely in R using the libtorch library. It also supports low-level tensor operations and GPU acceleration.

This package is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. It easily enables widely-used analytical techniques, including the identification of highly variable genes, dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.

This package provides a collection of Lua filters that extend the functionality of R Markdown templates (e.g., count words or post-process citations).

This package provides an interface to the NetCDF file formats designed by Unidata for efficient storage of array-oriented scientific data and descriptions. Most capabilities of NetCDF version 4 are supported. Optional conversions of time units are enabled by UDUNITS version 2, also from Unidata.

Cyclomatic complexity is a software metric, used to indicate the complexity of a program. It is a quantitative measure of the number of linearly independent paths through a program's source code. This package provides tools to compute this metric.

This package provides a series of additional Tcl commands and Tk widgets with style and various functions to supplement the tcltk package

This package provides header library and R functions to solve minimum cost bipartite matching problem using Huhn-Munkres algorithm (Hungarian algorithm; <https://en.wikipedia.org/wiki/Hungarian_algorithm>; Kuhn (1955) <doi:10.1002/nav.3800020109>).

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

This package provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.

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.

This package provides functions for importing, exporting, plotting and other manipulations of bitmapped images.

This package provides a normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction.

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 a functional gradient descent algorithm (boosting) for optimizing general risk functions utilizing component-wise (penalised) least squares estimates or regression trees as base-learners for fitting generalized linear, additive and interaction models to potentially high-dimensional data.

This package provides simple utility functions to read from and write to the system clipboards.

This package provides functionality to compute various node centrality measures on networks. Included are functions to compute betweenness centrality (by utilizing Madduri and Bader's SNAP library), implementations of Burt's constraint and effective network size (ENS) metrics, Borgatti's algorithm to identify key players, and Valente's bridging metric. The betweenness, Key Players, and bridging implementations are parallelized with OpenMP.

This package provides a computationally stable approach of fitting a Gaussian Process (GP) model to a deterministic simulator.

This package provides an R interface to the NCBI's EUtils API, allowing users to search databases like GenBank PubMed, process the results of those searches and pull data into their R sessions.

This package provides useful tools for structural equation modeling.