It contains pre-compiled Gene Ontology gene sets for all organisms available on the Ensembl database. It also includes GO gene sets for organisms on Ensembl Plants, Ensembl Metazoa, Ensembl Fungi and Ensembl Protists. The data was collected with the biomaRt package.

Use the high-precision arithmetic provided by the R package Rmpfr to compute a custom-made Gauss quadrature nodes and weights, with up to 33 nodes, using a moment-based method via moment determinants. Paul Kabaila (2022) <arXiv:2211.04729>.

Statistical methodology for sparse multivariate extreme value models. Methods are provided for exact simulation and statistical inference for multivariate Pareto distributions on graphical structures as described in the paper Graphical Models for Extremes by Engelke and Hitz (2020) <doi:10.1111/rssb.12355>.

This package provides a combined slider and numeric input for usage in a Shiny app. The slider and the numeric input are linked together: each one is updated when the other one changes. Many styling properties are customizable (e.g. colors and size).

This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The epivizrServer package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by Bioconductor packages.

Real life data is muddy, fuzzy and unpredictable. This makes data manipulations tedious and bringing the data to right shape alone is a major chunk of work. Functions in this package help us get an understanding of dataframes to dramatically reduces data coding time.

This package provides a developer-facing interface to Arrow Database Connectivity (ADBC) for the purposes of driver development, driver testing, and building high-level database interfaces for users. ADBC is an API standard for database access libraries that uses Arrow for result sets and query parameters.

Third parties often change the page numbers without rerunning makeindex. One would like to make the page numbers in the index entries more robust. This bundle provides robustindex.sty and robustglossary.sty, which use the \pageref mechanism to maintain correct page numbers.

parinfer-rust-emacs is an Emacs-centric fork of parinfer-rust, itself an implementation of Shaun Lebron’s Parinfer. This builds a shared library intended to be loaded by the emacs-parinfer-rust-mode Emacs plugin, though a standalone binary is built also.

Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance.

Computing the Mann-Whitney effect based on copula models. Estimation of the association parameter in survival copula models. A description of the underlying methods is described in Nakazono et al. (2024) <doi:10.3390/math12101453> and Nakazono et al. (accepted for publication in Statistical Papers).

Provides functions which facilitate writing multi-file Emacs packages and running from the source tree without having to "install" code or fiddle with load-path.

The main function, load-relative, loads an Emacs Lisp file relative to another (presumably currently running) Emacs Lisp file.

repl-utilities is a set of utilities which ease life at the REPL. It includes three sorts of features: introspective procedures, miscellaneous utility functions, and, pulling them together, methods to conveniently keep these symbols and optionally additional symbols available in whichever package you switch to.

Computation and visualization of matrix correlation coefficients. The main method is the Similarity of Matrices Index, while various related measures like r1, r2, r3, r4, Yanai's GCD, RV, RV2, adjusted RV, Rozeboom's linear correlation and Coxhead's coefficient are included for comparison and flexibility.

This package provides a tm Source to create corpora from a corpus prepared in the format used by the Alceste application (i.e. a single text file with inline meta-data). It is able to import both text contents and meta-data (starred) variables.

runewidth provides functions to get fixed width of the character or string. It is a fork of https://github.com/mattn/go-runewidth, updated to the newest Unicode and having various helper functions removed, so all that remains is just the runewidth.RuneWidth() function.

The Read activity allows the laptop to act as a book reader. It has a simple interface, and will view many kinds of text and image-based book-like materials. It will have particular strengths in handheld mode, with extremely low power consumption and simple navigation controls.

Interface and documentation for the Experiment Hub records needed by the CENTRE Bioconductor software package. The Experiment Hub records contains the precomputed fisher combined p-values, CRUP correlations. Additionally, the records hold ChIP-seq and RNA-seq data used for the example of the software package.

The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012).

Plots calibration curves and computes statistics for assessing calibration performance. See Lasai et al. (2025) <doi:10.48550/arXiv.2503.08389>, De Cock Campo (2023) <doi:10.48550/arXiv.2309.08559> and Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>.

This package provides classes and methods that allow the user to manage life table, actuarial tables (also multiple decrements tables). Moreover, functions to easily perform demographic, financial and actuarial mathematics on life contingencies insurances calculations are contained therein. See Spedicato (2013) <doi:10.18637/jss.v055.i10>.

This package provides functions for reading (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and writing (tab, csv, mMass MSD, mzML, imzML) different file formats of mass spectrometry data into/from MALDIquant objects.

This package provides two multiplex imaging datasets collected on Vectra instruments at the University of Colorado Anschutz Medical Campus. Data are provided as a Spatial Experiment objects. Data is provided in tabular form and has been segmented and phenotyped using Inform software. Raw .tiff files are not included.

Bio-commandeer provides an opinionated method of running shell commands from within Ruby. The advantage of bio-commandeer over other methods of running external commands is that when something goes wrong, messages printed to the STDOUT and STDERR streams are reported, giving extra detail to ease debugging.