This package provides functions to securely retrieve secrets from a Bitwarden Secrets Manager vault using the Bitwarden CLI', enabling secret and configuration management within R packages and workflows. For more information visit <https://bitwarden.com/products/secrets-manager/>.

Applies affine and similarity transformations on vector spatial data (sp objects). Transformations can be defined from control points or directly from parameters. If redundant control points are provided Least Squares is applied allowing to obtain residuals and RMSE.

An algorithm which can be used to determine an objective threshold for signal-noise separation in large random matrices (correlation matrices, mutual information matrices, network adjacency matrices) is provided. The package makes use of the results of Random Matrix Theory (RMT). The algorithm increments a suppositional threshold monotonically, thereby recording the eigenvalue spacing distribution of the matrix. According to RMT, that distribution undergoes a characteristic change when the threshold properly separates signal from noise. By using the algorithm, the modular structure of a matrix - or of the corresponding network - can be unraveled.

Traditional noise filtering methods aim at removing noisy samples from a classification dataset. This package adapts classic and recent filtering techniques for use in regression problems, and it also incorporates methods specifically designed for regression data. In order to do this, it uses approaches proposed in the specialized literature, such as Martin et al. (2021) [<doi:10.1109/ACCESS.2021.3123151>] and Arnaiz-Gonzalez et al. (2016) [<doi:10.1016/j.eswa.2015.12.046>]. Thus, the goal of the implemented noise filters is to eliminate samples with noise in regression datasets.

R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains qs files with MAE data processed by gDR.

Subsampled Hi-C in HEK cells expressing the NHA9 fusion with an F to S mutated IDR ("FS") or without any mutations to the IDR ("Wildtype" or "WT"). These files are used for testing mariner functions and some examples.

This package contains companion data to the scanMiR package. It contains `KdModel` (miRNA 12-mer binding affinity models) collections corresponding to all human, mouse and rat mirbase miRNAs. See the scanMiR package for details.

Inspect interactively the spatially-resolved transcriptomics data from the 10x Genomics Visium platform as well as data from the Maynard, Collado-Torres et al, Nature Neuroscience, 2021 project analyzed by Lieber Institute for Brain Development (LIBD) researchers and collaborators.

Import, manipulate and explore results generated by Antares', a powerful open source software developed by RTE (Réseau de Transport dâ à lectricité) to simulate and study electric power systems (more information about Antares here : <https://antares-simulator.org/>).

This package implements the adaptive sampling procedure, a framework for both positive unlabeled learning and learning with class label noise. Yang, P., Ormerod, J., Liu, W., Ma, C., Zomaya, A., Yang, J. (2018) <doi:10.1109/TCYB.2018.2816984>.

This package provides functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format. Note that the latest version of XQuartz seems to be necessary under MacOS.

An R client for the currencyapi.com currency conversion API. The API requires registration of an API key. Basic features are free, some require a paid subscription. You can find the full API documentation at <https://currencyapi.com/docs> .

Read, construct and write CDISC (Clinical Data Interchange Standards Consortium) Dataset JSON (JavaScript Object Notation) files, while validating per the Dataset JSON schema file, as described in CDISC (2023) <https://www.cdisc.org/standards/data-exchange/dataset-json>.

This package creates ensemble taxonomic assignments of amplicon sequencing data in R using outputs of multiple taxonomic assignment algorithms and/or reference databases. Includes flexible algorithms for mapping taxonomic nomenclatures onto one another and for computing ensemble taxonomic assignments.

Reads annual and quarterly financial reports from companies traded at B3, the Brazilian exchange <https://www.b3.com.br/>. All data is downloaded and imported from CVM's public ftp site <https://dados.cvm.gov.br/dados/CIA_ABERTA/>.

An R client for the iplookupapi.com IP Lookup API. The API requires registration of an API key. Basic features are free, some require a paid subscription. You can find the full API documentation at <https://iplookupapi.com/docs> .

Adaptive estimation of the first-order intensity function of a spatio-temporal point process using kernels and variable bandwidths. The methodology used for estimation is presented in González and Moraga (2022). <doi:10.48550/arXiv.2208.12026>.

This package provides methods and models for analysing multigraphs as introduced by Shafie (2015) <doi:10.21307/joss-2019-011>, including methods to study local and global properties <doi:10.1080/0022250X.2016.1219732> and goodness of fit tests.

This package contains functions for data preparation, prediction of transition probabilities, estimating semi-parametric regression models and for implementing nonparametric estimators for other quantities. See Meira-Machado and Roca-Pardiñas (2011) <doi:10.18637/jss.v038.i03>.

Bayesian toolbox for quantitative proteomics. In particular, this package provides functions to generate synthetic datasets, execute Bayesian differential analysis methods, and display results as, described in the associated article Marie Chion and Arthur Leroy (2023) <arXiv:2307.08975>.

Disk-based implementation of Functional Pruning Optimal Partitioning with up-down constraints <doi:10.18637/jss.v101.i10> for single-sample peak calling (independently for each sample and genomic problem), can handle huge data sets (10^7 or more).

Singular spectrum analysis (SSA) decomposes a time series into interpretable components like trends, oscillations, and noise without strict distributional and structural assumptions. For method details see Golyandina N, Zhigljavsky A (2013). <doi:10.1007/978-3-642-34913-3>.

This package provides a simple authentification mechanism for single shiny applications. Authentification and password change functionality are performed calling user provided functions that typically access some database backend. Source code of main applications is protected until authentication is successful.

Extract trends from monthly and quarterly economic time series. Provides two main functions: augment_trends() for pipe-friendly tibble workflows and extract_trends() for direct time series analysis. Includes key econometric filters and modern parameter experimentation tools.