Simulation of random vectors from truncated multivariate normal and t distributions based on the algorithms proposed by Yifang Li and Sujit K. Ghosh (2015) <doi:10.1080/15598608.2014.996690>.

Evaluation of alternatives based on multiple criteria using weighted technique for Order preference by similarity to an ideal solution method. Reference: Hwang CL. (1981, ISBN:978-3-540-10558-9).

iSEEtree is an extension of iSEE for the TreeSummarizedExperiment data container. It provides interactive panel designs to explore hierarchical datasets, such as the microbiome and cell lines.

This package provides functions for preprocessing, automated gating and meta-analysis of cytometry data. It also provides functions that facilitate the collection of cytometry data from the ImmPort database.

maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.

This package provides a model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from the literature or experts.

The package r-alevinqc generates quality control reports summarizing the output from an alevin run. The reports can be generated as HTML or PDF files, or as Shiny applications.

This package provides an R interface to the QuickJS portable JavaScript engine. The engine is bundled entirely within the package, requiring no external system dependencies beyond a C compiler.

This package provides some low-level utilities to use for R package development. It currently provides managers for multiple package specific options and registries, vignette, unit test and bibtex related utilities.

This package provides a smooth mapping of multidimensional points into low-dimensional space defined by a self-organizing map. It is designed to work with FlowSOM and flow-cytometry use-cases.

ReadyMedia (formerly known as MiniDLNA) is a simple media server, which serves multimedia content to compatible clients on the network. It aims to be fully compliant with DLNA and UPnP-AV standards.

SaTScan'(TM) <https://www.satscan.org> is software for finding regions in Time, Space, or Time-Space that have excess risk, based on scan statistics, and uses Monte Carlo hypothesis testing to generate P-values for these regions. The rsatscan package provides functions for writing R data frames in SaTScan'-readable formats, for setting SaTScan parameters, for running SaTScan in the OS, and for reading the files that SaTScan creates.

By using RAINBOWR (Reliable Association INference By Optimizing Weights with R), users can test multiple SNPs (Single Nucleotide Polymorphisms) simultaneously by kernel-based (SNP-set) methods. This package can also be applied to haplotype-based GWAS (Genome-Wide Association Study). Users can test not only additive effects but also dominance and epistatic effects. In detail, please check our paper on PLOS Computational Biology: Kosuke Hamazaki and Hiroyoshi Iwata (2020) <doi:10.1371/journal.pcbi.1007663>.

Analyze multi-level one-way experimental designs where there are unequal sample sizes and population variance homogeneity can not be assumed. To conduct the Gabriel test <doi:10.2307/2286265>, create two vectors: one for your observations and one for the factor level of each observation. The function, rgabriel, conduct the test and save the output as a vector to input into the gabriel.plot function, which produces a confidence interval plot for Multiple Comparison.

The cnpy library written by Carl Rogers provides read and write facilities for files created with (or for) the NumPy extension for Python'. Vectors and matrices of numeric types can be read or written to and from files as well as compressed files. Support for integer files is available if the package has been built with as C++11 which should be the default on all platforms since the release of R 3.3.0.

This package provides a toolbox created by members of the International Union for Conservation of Nature (IUCN) Red List of Ecosystems Committee for Scientific Standards. Primarily, it is a set of tools suitable for calculating the metrics required for making assessments of species and ecosystems against the IUCN Red List of Threatened Species and the IUCN Red List of Ecosystems categories and criteria. See the IUCN website for detailed guidelines, the criteria, publications and other information.

Clustering method to cluster both effects curves, through quantile regression coefficient modeling, and curves in functional data analysis. Sottile G. and Adelfio G. (2019) <doi:10.1007/s00180-018-0817-8>.

This tool is for parsing public drug databases such as DrugBank XML database <https://go.drugbank.com/>. The parsed data are then returned in a proper R object called dvobject'.

Client for programmatic access to the South Florida Water Management District's DBHYDRO database at <https://www.sfwmd.gov/science-data/dbhydro>, with functions for accessing hydrologic and water quality data.

This package performs the exact test on whether there is a difference between two survival curves. Exact confidence interval for the hazard ratio can also be generated for the Cox model.

This package provides a collection of functions to manage, to investigate and to analyze bivariate financial returns by Copulae. Included are the families of Archemedean, Elliptical, Extreme Value, and Empirical Copulae.

Streamline the creation of common charts by taking care of a lot of data preprocessing and plot customization for the user. Provides a high-level interface to create plots using ggplot2'.

Fits gastric emptying time series from MRI or scintigraphic measurements using nonlinear mixed-model population fits with nlme and Bayesian methods with Stan; computes derived parameters such as t50 and AUC.

This package provides geographical faceting functionality for ggplot2'. Geographical faceting arranges a sequence of plots of data for different geographical entities into a grid that preserves some of the geographical orientation.