This is a collection of publically available spatial omics datasets. Where possible we have curated these datasets as either SpatialExperiments, MoleculeExperiments or CytoImageLists and included annotations of the sample characteristics.

This program is derived from comint-mode and provides the following features:

• TAB completion same as Node.js REPL

• file name completion in string

• incremental history search

This library lets elisp authors easily define an idiomatic command to reformat the current buffer using a command-line program, together with an optional minor mode which can apply this command automatically on save.

This package provides a class for typesetting scripts containing both lyrics and prose, in the style used by the student revues (revy) at the Faculties of Science at the University of Copenhagen (uchp).

RegioneReloaded is a package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and the creation of ready-to-publish graphs. It takes over and expands on all the features of its predecessor regioneR. It also incorporates a strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. RegioneReloaded builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs.

This package provides functions for microbiome data analysis that take into account its compositional nature. Performs variable selection through penalized regression for both, cross-sectional and longitudinal studies, and for binary and continuous outcomes.

Find functions in an unstructured directory and explore their dependencies. Sourcing of R source files is performed without side-effects: from R scripts that have executable code and function definitions only functions are sourced.

Computes spatial position models: the potential model as defined by Stewart (1941) <doi:10.1126/science.93.2404.89> and catchment areas as defined by Reilly (1931) or Huff (1964) <doi:10.2307/1249154>.

Plots protein properties and visualizes position of peptide immunogens within protein sequence. Allows evaluation of immunogens based on structural and functional annotations to infer suitability for antibody-based methods aiming to detect native proteins.

Query, extract, and plot genealogical data from The Mathematics Genealogy Project <https://mathgenealogy.org/>. Data is gathered from the WebSocket server run by the geneagrapher-core project <https://github.com/davidalber/geneagrapher-core>.

This package takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.

This package provides a method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. ActiveDriverWGS detects coding and noncoding driver elements using whole genome sequencing data.

Defines the classes used for "class comparison" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class comparison includes tests for differential expression; see Simon's book for details on typical problem types.

Allows manual creation of themes and logos to be used in applications created using the shinydashboard package. Removes the need to change the underlying css code by wrapping it into a set of convenient R functions.

Summarise patient-level drug utilisation cohorts using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. New users and prevalent users cohorts can be generated and their characteristics, indication and drug use summarised.

This grants the functionality of the Maxar Geospatial Platform (MGP) Streaming API. It can search for images using the WFS method. It can Download images using WMS WMTS. It can also Download a full resolution image.

This is a comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. It provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.

This package provides a set of predicates and assertions for checking the types of variables. This is mainly for use by other package developers who want to include run-time testing features in their own packages.

rotate-text allows you rotate to commonly interchanged text with a single keystroke. For example, you can toggle between "frame-width" and "frame-height", between "public", "protected" and "private" and between "variable1", "variable2" through "variableN".

EventMachine implements a single-threaded engine for arbitrary network communications. EventMachine wraps all interactions with sockets, allowing programs to concentrate on the implementation of network protocols. It can be used to create both network servers and clients.

Spectroscope is a Behavior-Driven Development (BDD) framework built on RubyTest, designed to emulate RSpec in most respects. It is assertion framework independent so any number of assertion systems can be used, such as Assay or AE.

This package provides functionality for random generation of spatial data in the spatstat family of packages. It generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes (simple sequential inhibition, Matern inhibition models, Matern cluster process, Neyman-Scott cluster processes, log-Gaussian Cox processes, product shot noise cluster processes) and simulation of Gibbs point processes (Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler).

Retail shopping transactions for 2,469 households over one year. Originates from the 84.51° Complete Journey 2.0 source files <https://www.8451.com/area51> which also includes useful metadata on products, coupons, campaigns, and promotions.

This package provides a test bench for the comparison of missing data imputation methods in uni-variate time series. Imputation methods are compared using different error metrics. Proposed imputation methods and alternative error metrics can be used.