This package provides routines for parsing Affymetrix data files based upon file format information. The primary focus is on accessing the CEL and CDF file formats.

randfold computes the probability that, for a given sequence, the Minimum Free Energy (MFE) of the secondary structure is different from MFE computed with random sequences.

This package converts the output of the Sailfish and Salmon RNA-seq quantification tools so that it can be used with the Sleuth differential analysis package.

SCENIC (Single-cell regulatory network inference and clustering) is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

This package implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed data such as counts or binary matrices.

This package provides functions for viewing 2D and 3D data, including perspective plots, slice plots, surface plots, scatter plots, etc. It includes data sets from oceanography.

This package provides density, distribution, quantile and hazard functions of a stable variate, as well as generalized regression models for the parameters of a stable distribution.

This package implements targeted minimum loss-based estimators of counterfactual means and causal effects that are doubly-robust with respect both to consistency and asymptotic normality.

This package provides tools to automate the morphological delineation of riverside urban areas, based on a method introduced in Forgaci (2018) <doi:10.7480/abe.2018.31>. Delineation entails the identification of corridor boundaries, segmentation of the corridor, and delineation of the river space. The resulting delineation can be used to characterise spatial phenomena that can be related to the river as a central element.

This package provides a convenience wrapper that uses the rmarkdown package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites or email. reprex also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.

Perform mediation analysis via the fast-and-robust bootstrap test ROBMED (Alfons, Ates & Groenen, 2022a; <doi:10.1177/1094428121999096>), as well as various other methods. Details on the implementation and code examples can be found in Alfons, Ates, and Groenen (2022b) <doi:10.18637/jss.v103.i13>. Further discussion on robust mediation analysis can be found in Alfons & Schley (2024) <doi:10.31234/osf.io/2hqdy>.

Data on Asylum and Resettlement for the UK, provided by the Home Office <https://www.gov.uk/government/statistical-data-sets/immigration-system-statistics-data-tables>.

Simplifies aspects of linear regression analysis, particularly simultaneous inference. Additionally, supports "A Progressive Introduction to Linear Models" by Joshua French (<https://jfrench.github.io/LinearRegression/>).

This package provides methods for fitting identity-link GLMs and GAMs to discrete data, using EM-type algorithms with more stable convergence properties than standard methods.

The BAGofT assesses the goodness-of-fit of binary classifiers. Details can be found in Zhang, Ding and Yang (2021) <arXiv:1911.03063v2>.

Perform bulk and cell type-specific expression quantitative trail loci mapping with our novel method (Little et al. (2023) <doi:10.1038/s41467-023-38795-w>).

Helpful functions for the cleaning and manipulation of surveillance data, especially with regards to the creation and validation of panel data from individual level surveillance data.

This package provides functions for evaluating and visualizing ecological assessment procedures for surface waters containing physical, chemical and biological assessments in the form of value functions.

This package provides functions for financial analysis and financial modeling, including batch graphs generation, beta calculation, descriptive statistics, annuity calculation, bond pricing and financial data download.

Log-ratio Lasso regression for continuous, binary, and survival outcomes with (longitudinal) compositional features. See Fei and others (2024) <doi:10.1016/j.crmeth.2024.100899>.

Assists in generating binary clustered data, estimates of Intracluster Correlation coefficient (ICC) for binary response in 16 different methods, and 5 different types of confidence intervals.

This package provides methods for fitting log-link GLMs and GAMs to binomial data, including EM-type algorithms with more stable convergence properties than standard methods.

Find dark genes. These genes are often disregarded due to no detected mutation or differential expression, but are important in coordinating the functionality in cancer networks.

This package provides methods of selecting one from many numeric predictors for a regression model, to ensure that the additional predictor has the maximum effect size.