The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for detecting significant expression dynamics often fail when the expression dynamics show a large heterogeneity. Moreover, these methods often cannot cope with irregular and sparse measurements. The method proposed here is specifically designed for the analysis of perturbation responses. It combines different scores to capture fast and transient dynamics as well as slow expression changes, and performs well in the presence of low replicate numbers and irregular sampling times. The results are given in the form of tables including links to figures showing the expression dynamics of the respective transcript. These allow to quickly recognise the relevance of detection, to identify possible false positives and to discriminate early and late changes in gene expression. An extension of the method allows the analysis of the expression dynamics of functional groups of genes, providing a quick overview of the cellular response. The performance of this package was tested on microarray data derived from lung cancer cells stimulated with epidermal growth factor (EGF). Paper: Albrecht, Marco, et al. (2017)<DOI:10.1186/s12859-016-1440-8>.

This package provides functions to retrieve headers, titles, and footnotes from structured metadata sources (e.g., Excel or CSV files) for annotating tables, listings, and figures in clinical study reports (CSRs) or other formal deliverables. It supports separation of metadata from analysis code in clinical reporting workflows.

This package provides a tbl_ts class (the tsibble') for temporal data in an data- and model-oriented format. The tsibble provides tools to easily manipulate and analyse temporal data, such as filling in time gaps and aggregating over calendar periods.

This package provides a convenient R interface to the National Health Service NHS Technology Reference Update Distribution (TRUD) API', allowing users to list available releases for their subscribed items, retrieve metadata, and download release files. For more information on the API, see <https://isd.digital.nhs.uk/trud/users/guest/filters/0/api>.

The tmap package provides two plotting modes for static and interactive thematic maps. This package extends tmap with two additional modes based on Mapbox GL JS and MapLibre GL JS'. These modes feature interactive vector tiles, globe views, and other modern web-mapping capabilities, while maintaining a consistent tmap interface across all plotting modes.

This package provides a dataset of predefined color palettes based on the Star Trek science fiction series, associated color palette functions, and additional functions for generating customized palettes that are on theme. The package also offers functions for applying the palettes to plots made using the ggplot2 package.

Measuring angles between points in a landscape is much easier than measuring distances. When the location of three points is known the position of the observer can be determined based solely on the angles between these points as seen by the observer. This task (known as triangulation) however requires onerous calculations - these calculations are automated by this package.

Streamline the processing of Telraam data, sourced from open data mobility sensors. These tools range from data retrieval (without the need for API knowledge) to data visualization, including data preprocessing.

This package provides functions to access historical and real-time national hydrometric data from Water Survey of Canada data sources and then applies tidy data principles.

Include the Twitter status widgets in HTML pages created using R markdown. The package uses the Twitter javascript APIs to embed in your document Twitter cards associated to specific statuses. The main targets are regular HTML pages or dashboards.

Simple utilities to generate a Dockerfile from a directory or project, build the corresponding Docker image, push the image to DockerHub, and publicly share the project via Binder.

An open-access tool/framework that constitutes the core functions to analyze terrestrial water cycle data across various spatio-temporal scales.

Time series prediction is a critical task in data analysis, requiring not only the selection of appropriate models, but also suitable data preprocessing and tuning strategies. TSPredIT (Time Series Prediction with Integrated Tuning) is a framework that provides a seamless integration of data preprocessing, decomposition, model training, hyperparameter optimization, and evaluation. Unlike other frameworks, TSPredIT emphasizes the co-optimization of both preprocessing and modeling steps, improving predictive performance. It supports a variety of statistical and machine learning models, filtering techniques, outlier detection, data augmentation, and ensemble strategies. More information is available in Salles et al. <doi:10.1007/978-3-662-68014-8_2>.

This package provides a collection of tools for trade practitioners, including the ability to calibrate different consumer demand systems and simulate the effects of tariffs and quotas under different competitive regimes. These tools are derived from Anderson et al. (2001) <doi:10.1016/S0047-2727(00)00085-2> and Froeb et al. (2003) <doi:10.1016/S0304-4076(02)00166-5>.

Core parts of the C API of R are wrapped in a C++ namespace via a set of inline functions giving a tidier representation of the underlying data structures and functionality using a header-only implementation without additional dependencies.

Creates, manipulates, queries and repairs vectors of parameter terms. Parameter terms are the labels used to reference values in vectors, matrices and arrays. They represent the names in coefficient tables and the column names in mcmc and mcmc.list objects.

This package provides functions to compute and plot tracheidograms, as in De Soto et al. (2011) <doi:10.1139/x11-045>.

There are some experimental scenarios where each experimental unit receives a sequence of treatments across multiple periods, and treatment effects persist beyond the period of application. It focuses on the construction and calculation of the parametric value of the residual effect designs balanced for carryover effects, also referred to as crossover designs, change-over designs, or repeated measurements designs (Aggarwal and Jha, 2010<doi:10.1080/15598608.2010.10412013>). The primary objective of the package is to generate a new class of Balanced Ternary Residual Effect Designs (BTREDs), balanced for carryover effects tailored explicitly for situations where the number of periods is less than or equal to the number of treatments. In addition, the package provides four new classes of Partially Balanced Ternary Residual Effect Designs (PBTREDs), constructed using incomplete block designs, initial sequences, and rectangular association scheme. In addition, one extra function is included to help study the parametric properties of a given residual effect design.

Combine a list of taxa with a phylogeny to generate a starting tree for use in total evidence dating analyses.

This package provides functions for the retrieval, manipulation, and visualization of geospatial data, with an aim towards producing 3D landscape visualizations in the Unity 3D rendering engine. Functions are also provided for retrieving elevation data and base map tiles from the USGS National Map <https://apps.nationalmap.gov/services/>.

This package implements the TWO-Component Single Cell Model-Based Association Method (TWO-SIGMA) for gene-level differential expression (DE) analysis and DE-based gene set testing of single-cell RNA-sequencing datasets. See Van Buren et al. (2020) <doi:10.1002/gepi.22361> and Van Buren et al. (2021) <doi:10.1101/2021.01.24.427979>.

This package performs the detection of linear trend changes for univariate time series by implementing the bottom-up unbalanced wavelet transformation proposed by H. Maeng and P. Fryzlewicz (2023). The estimated number and locations of the change-points are returned with the piecewise-linear estimator for signal.

This package provides functions for defining and conducting a time series prediction process including pre(post)processing, decomposition, modelling, prediction and accuracy assessment. The generated models and its yielded prediction errors can be used for benchmarking other time series prediction methods and for creating a demand for the refinement of such methods. For this purpose, benchmark data from prediction competitions may be used.

Efficient sampling of truncated multivariate (scale) mixtures of normals under linear inequality constraints is nontrivial due to the analytically intractable normalizing constant. Meanwhile, traditional methods may subject to numerical issues, especially when the dimension is high and dependence is strong. Algorithms proposed by Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> are adopted for overcoming difficulties in simulating truncated distributions. Efficient rejection sampling for simulating truncated univariate normal distribution is included in the package, which shows superiority in terms of acceptance rate and numerical stability compared to existing methods and R packages. An efficient function for sampling from truncated multivariate normal distribution subject to convex polytope restriction regions based on Gibbs sampler for conditional truncated univariate distribution is provided. By extending the sampling method, a function for sampling truncated multivariate Student's t distribution is also developed. Moreover, the proposed method and computation remain valid for high dimensional and strong dependence scenarios. Empirical results in Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> illustrated the superior performance in terms of various criteria (e.g. mixing and integrated auto-correlation time).