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).

This package provides Bayesian inference methods for infectious disease transmission models in healthcare settings. Implements Markov Chain Monte Carlo (MCMC) algorithms for estimating transmission parameters from patient-level data including admission, discharge, and testing events as described in Thomas et al. (2015) <doi:10.1093/imammb/dqt021>.

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.

The necessary external data to run the flowWorkspace and openCyto vignette is found in this package. This data package contains two flowJo, one diva xml workspace and the associated fcs files as well as three GatingSets for testing the flowWorkspace, openCyto and CytoML packages.

Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Simple, fast, and automatic encodings for category data using a data.table backend. Most of the methods are an implementation of "Sufficient Representation for Categorical Variables" by Johannemann, Hadad, Athey, Wager (2019) <arXiv:1908.09874>, particularly their mean, sparse principal component analysis, low rank representation, and multinomial logit encodings.

This is a package providing tools to quantify and interpret multiple sources of biological and technical variation in gene expression experiments. It uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. The package includes dream differential expression analysis for repeated measures.

This package provides utilities for dealing with distributions. Functionality includes sample skewness and kurtosis, log-histogram, tail plots, moments by integration, changing the point about which a moment is calculated, functions for testing distributions using inversion tests and the Massart inequality. Also included is an implementation of the incomplete Bessel K function.

Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets.

Tests for Kaiser-Meyer-Olkin (KMO) and communalities in a dataset. It provides a final sample by removing variables in a iterable manner while keeping account of the variables that were removed in each step. It follows the best practices and assumptions according to Hair, Black, Babin & Anderson (2018, ISBN:9781473756540).

Implementation of functions to assign corresponding common job prestige scores (SIOPS, ISEI), the official job or group title and the ISCO-88 code to given ISCO-08 codes. ISCO-08 is the latest version of the International Standard Classification of Occupations which is used to organise information on labour and jobs.

This package performs a sentiment analysis of textual contents in R. This implementation utilizes various existing dictionaries, such as Harvard IV, or finance-specific dictionaries. Furthermore, it can also create customized dictionaries. The latter uses LASSO regularization as a statistical approach to select relevant terms based on an exogenous response variable.

This package defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.

This package provides methods and tools for performing multistep-ahead time series forecasting using conformal prediction methods including classical conformal prediction, adaptive conformal prediction, conformal PID (Proportional-Integral-Derivative) control, and autocorrelated multistep-ahead conformal prediction. The methods were described by Wang and Hyndman (2024) <doi:10.48550/arXiv.2410.13115>.

This package provides a suite of functions to use with regression models, including summaries, residual plots, and factor comparisons. Used as part of the Model Fitting module of iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions.

Multi-precision library that allows to store and operate with arbitrarily big integers without loss of precision. It includes a large list of tools to work with them, like: - Arithmetic and logic operators - Modular-arithmetic operators - Computer Number Theory utilities - Probabilistic primality tests - Factorization algorithms - Random generators of diferent types of integers.

This library converts a Float to a String with ultimate control how many digits after the decimal point are shown and how the remaining digits are rounded. It rounds, floors and ceils the common way (i.e. half up) or the commerical way (ie. half away from zero).

RocBandwidthTest is designed to capture the performance characteristics of buffer copying and kernel read/write operations. The help screen of the benchmark shows various options one can use in initiating cop/read/writer operations. In addition one can also query the topology of the system in terms of memory pools and their agents.