iSEEu (the iSEE universe) contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels, or modes allowing easy configuration of iSEE applications.

The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.

This is a package for multivariate data analysis and graphical display of microarray data. Functions are included for supervised dimension reduction (between group analysis) and joint dimension reduction of two datasets (coinertia analysis).

This package provides tools for estimating variance-mean dependence in count data from high-throughput genetic sequencing assays and for testing for differential expression based on a model using the negative binomial distribution.

This package provides a collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays.

This package provides tools to compute Gower's distance (or similarity) coefficient between records, and to compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP.

Compare complex R objects and reveal the key differences. This package was designed particularly for use in testing packages where being able to quickly isolate key differences makes understanding test failures much easier.

This package checks adherence to a given style, syntax errors and possible semantic issues. It supports on the fly checking of R code edited with RStudio IDE, Emacs and Vim.

This package provides a simple set of wrapper functions for data.table::fread() that allows subsetting or filtering rows and selecting columns of table-formatted files too large for the available RAM.

Many models contain tuning parameters (i.e. parameters that cannot be directly estimated from the data). These tools can be used to define objects for creating, simulating, or validating values for such parameters.

This package provides a build-time dependency for Cargo build scripts to assist in invoking the native C compiler to compile native C code into a static archive to be linked into Rustcode.

This package provides the asynchronous RPC client-server framework and message specification for Rigetti Quantum Cloud Services (QCS). It implements an efficient transport protocol by using ZeroMQ (ZMQ) sockets and MessagePack (msgpack) serialization.

Point and interval estimation of linear parameters with data obtained from complex surveys (including stratified and clustered samples) when randomization techniques are used. The randomized response technique was developed to obtain estimates that are more valid when studying sensitive topics. Estimators and variances for 14 randomized response methods for qualitative variables and 7 randomized response methods for quantitative variables are also implemented. In addition, some data sets from surveys with these randomization methods are included in the package.

Create, read and write GEXF (Graph Exchange XML Format) graph files (used in Gephi and others). It allows the user to easily build/read graph files including attributes, GEXF visual attributes (such as color, size, and position), network dynamics (for both edges and nodes) and edge weighting. Users can build/handle graphs element-by-element or massively through data-frames, visualize the graph on a web browser through gexf-js (a JavaScript library) and interact with the igraph package.

This package provides a build-time dependency for Cargo build scripts to assist in invoking the native C compiler to compile native C code into a static archive to be linked into Rust code.

This package provides a build-time dependency for Cargo build scripts to assist in invoking the native C compiler to compile native C code into a static archive to be linked into Rust code.

This package provides a build-time dependency for Cargo build scripts to assist in invoking the native C compiler to compile native C code into a static archive to be linked into Rust code.

Creating, rendering and writing BPMN diagrams <https://www.bpmn.org/>. Functionalities can be used to visualize and export BPMN diagrams created using the pm4py and bupaRminer packages. Part of the bupaR ecosystem.

This package performs the colocalisation tests described in Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>, Wallace (2020) <doi:10.1371/journal.pgen.1008720>, Wallace (2021) <doi:10.1371/journal.pgen.1009440>.

This package implements the convex clustering through majorization-minimization (CCMM) algorithm described in Touw, Groenen, and Terada (2022) <doi:10.48550/arXiv.2211.01877> to perform minimization of the convex clustering loss function.

The Discrete Transmuted Generalized Inverse Weibull (DTGIW) distribution is a new distribution for count data analysis. The DTGIW is discrete distribution based on Atchanut and Sirinapa (2021). <DOI: 10.14456/sjst-psu.2021.149>.

This package provides functions for (1) ranking, selecting, and prioritising genes, proteins, and metabolites from high dimensional biology experiments, (2) multivariate hit calling in high content screens, and (3) combining data from diverse sources.

Manipulates date ('Date'), date time ('POSIXct') and time ('hms') vectors. Date/times are considered discrete and are floored whenever encountered. Times are wrapped and time zones are maintained unless explicitly altered by the user.

Functional denoising and functional ANOVA through wavelet-domain Markov groves. Fore more details see: Ma L. and Soriano J. (2018) Efficient functional ANOVA through wavelet-domain Markov groves. <arXiv:1602.03990v2 [stat.ME]>.