This package enables regression and classification on high-dimensional data with different relative strengths of penalization for different feature groups, such as different assays or omic types. The optimal relative strengths are chosen adaptively. Optimisation is performed using a variational Bayes approach.

This package provides functions to analyze methylation data can be found here. Some functions are relevant for single cell methylation data but most other functions can be used for any methylation data. Highlight of this workflow is the comprehensive quality control report.

simPIC is a package for simulating single-cell ATAC-seq count data. It provides a user-friendly, well documented interface for data simulation. Functions are provided for parameter estimation, realistic scATAC-seq data simulation, and comparing real and simulated datasets.

High-throughput single-cell measurements of DNA methylation allows studying inter-cellular epigenetic heterogeneity, but this task faces the challenges of sparsity and noise. We present vmrseq, a statistical method that overcomes these challenges and identifies variably methylated regions accurately and robustly.

This package contains the resample and windowfilter command line utilities. The resample command allows changing the sampling rate of a sound file, while the windowfilter command allows designing Finite Impulse Response (FIR) filters using the so-called window method.

This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.

This package provides bindings to libsodium: a library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a Diffie-Hellman function by Daniel Bernstein, which has become very popular after it was discovered that the NSA had backdoored Dual EC DRBG.

This package provides miscellaneous functions for SciViews or general use, including tools to manage a temporary environment attached to the search path for temporary variables you do not want to save() or load(); test the current platform; showing progress bars, etc.

This package provides a set of Shiny apps for effective communication and understanding in statistics. The current version includes properties of normal distribution, properties of sampling distribution, one-sample z and t tests, two samples independent (unpaired) t test and analysis of variance.

This package implements the Python leidenalg module to be called in R. It enables clustering using the Leiden algorithm for partitioning a graph into communities. See also Traag et al (2018) "From Louvain to Leiden: guaranteeing well-connected communities." <arXiv:1810.08473>.

Quality Ensured Demonstrations (QED) is a test framework for Test Driven Development (TDD) and Behaviour Driven Development (BDD) utilizing Literate Programming techniques. QED sits somewhere between lower-level testing tools like Test::Unit and requirement specifications systems like Cucumber.

Multivariate optimal allocation for different domains in one and two stages stratified sample design. R2BEAT extends the Neyman (1934) â Tschuprow (1923) allocation method to the case of several variables, adopting a generalization of the Bethelâ s proposal (1989). R2BEAT develops this methodology but, moreover, it allows to determine the sample allocation in the multivariate and multi-domains case of estimates for two-stage stratified samples. It also allows to perform both Primary Stage Units and Secondary Stage Units selection. This package requires the availability of ReGenesees', that can be installed from <https://github.com/DiegoZardetto/ReGenesees>.

An implementation of the radviz projection in R. It enables the visualization of multidimensional data while maintaining the relation to the original dimensions. This package provides functions to create and plot radviz projections, and a number of summary plots that enable comparison and analysis. For reference see Hoffman *et al.* (1999) (<doi:10.1145/331770.331775>) for original implementation, see Di Caro *et al* (2012) (<doi:10.1007/978-3-642-13672-6_13>), for the original method for dimensional anchor arrangements, see Demsar *et al.* (2007) (<doi:10.1016/j.jbi.2007.03.010>) for the original Freeviz implementation.

This package provides a convenient R wrapper to the Comet API, which is a cloud platform allowing you to track, compare, explain and optimize machine learning experiments and models. Experiments can be viewed on the Comet online dashboard at <https://www.comet.com>.

Implementation of estimators for inferring the mean of censored cost data. Including the estimators BT from Bang and Tsiatis (2000) <doi:10.1093/biomet/87.2.329> and ZT from Zhao and Tian (2001) <doi:10.1111/j.0006-341X.2001.01002.x>.

DNA copy number data evaluation using both their initial form (copy number as a noisy function of genomic position) and their approximation by a piecewise-constant function (segmentation), for the purpose of identifying genomic regions where the copy number differs from the norm.

Easy access to species distribution data for 6 regions in the world, for a total of 226 anonymised species. These data are described and made available by Elith et al (2020) <doi:10.17161/bi.v15i2.13384> to compare species distribution modelling methods.

Several tests for differential methylation in methylation array data, including one-sided differential mean and variance test. Methods used in the package refer to Dai, J, Wang, X, Chen, H and others (2021) "Incorporating increased variability in discovering cancer methylation markers", Biostatistics, submitted.

This package provides a wrapper for the DeepL API <https://developers.deepl.com/docs>, a web service for translating texts between different languages. A DeepL API developer account is required to use the service (see <https://www.deepl.com/pro#developer>).

Matrix algebra using the Eigen C++ library: determinant, rank, inverse, pseudo-inverse, kernel and image, QR decomposition, Cholesky decomposition, Schur decomposition, Hessenberg decomposition, linear least-squares problems. Also provides matrix functions such as exponential, logarithm, power, sine and cosine. Complex matrices are supported.

Package provides a set of tools for robust estimation and inference for probit model with endogenous covariates. The current version contains a robust two-step estimator. For technical details, see Naghi, Varadi and Zhelonkin (2022), <doi:10.1016/j.ecosta.2022.05.001>.

This package provides an interface for image recognition using the Google Vision API <https://cloud.google.com/vision/> . Converts API data for features such as object detection and optical character recognition to data frames. The package also includes functions for analyzing image annotations.

Clustering algorithm developed for use with plot inventories of species. It groups plots by subsets of diagnostic species rather than overall species composition. There is an unsupervised and a supervised mode, the latter accepting suggestions for species with greater weight and cluster medoids.

An easy-to-use workflow that provides tools to create, update and fill literature matrices commonly used in research, specifically epidemiology and health sciences research. The project is born out of need as an easyâ toâ use tool for my research methods classes.