An RStudio addin to assist with removing objects from the global environment. Features include removing objects according to name patterns and object type. During the course of an analysis, temporary objects are often created and this tool assists with removing them quickly. This can be useful when memory management within R is important.

Implement the alternating algorithm for supervised tensor decomposition with interactive side information. Details can be found in the publication Hu, Jiaxin, Chanwoo Lee, and Miaoyan Wang. "Generalized Tensor Decomposition with features on multiple modes." Journal of Computational and Graphical Statistics, Vol. 31, No. 1, 204-218, 2022 <doi:10.1080/10618600.2021.1978471>.

The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences.

QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It is based on the SummarizedExperiment class and contains functions for creating, merging, and subsetting objects. QTLExperiment also stores experiment metadata and has checks in place to ensure that transformations apply correctly.

The test-queue module is a parallel test runner, built using a centralized queue to ensure optimal distribution of tests between workers. It is specifically optimized for Continuous Integration (CI) environments: build statistics from each run are stored locally and used to sort the queue at the beginning of the next run.

This package provides an easy to use command. It takes an URL of the Research Organization Registry (ROR) as argument and creates a ROR symbol which links to the given URL---very similar to the orcidlink package from which it is derived. The symbol itself always fits with the chosen font size.

Add-on to the airGR package which provides the tools to assimilate observed discharges in daily GR hydrological models. The package consists in two functions allowing to perform the assimilation of observed discharges via the Ensemble Kalman filter or the Particle filter as described in Piazzi et al. (2021) <doi:10.1029/2020WR028390>.

If one treated group is matched to one control reservoir in two different ways to produce two sets of treated-control matched pairs, then the two control groups may be entwined, in the sense that some control individuals are in both control groups. The exterior match is used to compare the two control groups.

This package provides a collection of methods for the Bayesian estimation of Spatial Probit, Spatial Ordered Probit and Spatial Tobit Models. Original implementations from the works of LeSage and Pace (2009, ISBN: 1420064258) were ported and adjusted for R, as described in Wilhelm and de Matos (2013) <doi:10.32614/RJ-2013-013>.

The Scott-Knott Effect Size Difference (ESD) test is a mean comparison approach that leverages a hierarchical clustering to partition the set of treatment means (e.g., means of variable importance scores, means of model performance) into statistically distinct groups with non-negligible difference [Tantithamthavorn et al., (2018) <doi:10.1109/TSE.2018.2794977>].

Implement a shrinkage estimation for the univariate normal mean based on a preliminary test (pretest) estimator. This package also provides the confidence interval based on pivoting the cumulative density function. The methodologies are published in Taketomi et al.(2024) <doi:10.1007/s42081-023-00221-2> and Taketomi et al.(2024-)(under review).

Implement in an efficient approach to display the genomic data, relationship, information in an interactive circular genome(Circos) plot. interacCircos are inspired by circosJS', BioCircos.js and NG-Circos and we integrate the modules of circosJS', BioCircos.js and NG-Circos into this R package, based on htmlwidgets framework.

This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.

MetagenomeSeq is designed to determine features (be it OTU, species, etc.) that are differentially abundant between two or more groups of multiple samples. This package is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.

A memory-safer wrapper around system dynamic library loading primitives. The most important safety guarantee by this library is prevention of dangling-Symbols that may occur after a Library is unloaded. Using this library allows loading dynamic libraries (also known as shared libraries) as well as use functions and static variables these libraries contain.

This package provides functions to randomly select, return, and print quotes or entire scenes from the American version of the show the Office. Receive laughs from one of of the greatest sitcoms of all time on demand. Add these functions to your .Rprofile to get a good laugh everytime you start a new R session.

This package creates lowpass filters which are commonly used in ion channel recordings. It supports generation of random numbers that are filtered, i.e. follow a model for ion channel recordings, see <doi:10.1109/TNB.2018.2845126>. Furthermore, time continuous convolutions of piecewise constant signals with the kernel of lowpass filters can be computed.

This package provides functions are provided for calculating efficiency using multiplier DEA (Data Envelopment Analysis): Measuring the efficiency of decision making units (Charnes et al., 1978 <doi:10.1016/0377-2217(78)90138-8>) and cross efficiency using single and two-phase approach. In addition, it includes some datasets for calculating efficiency and cross efficiency.

Function multiroc() can be used for computing and visualizing Receiver Operating Characteristics (ROC) and Area Under the Curve (AUC) for multi-class classification problems. It supports both One-vs-One approach by M.Bishop, C. (2006, ISBN:978-0-387-31073-2) and One-vs-All approach by Murphy P., K. (2012, ISBN:9780262018029).

New wavelet methodology (vector wavelet coherence) (Oygur, T., Unal, G, 2020 <doi:10.1007/s40435-020-00706-y>) to handle dynamic co-movements of multivariate time series via extending multiple and quadruple wavelet coherence methodologies. This package can be used to perform multiple wavelet coherence, quadruple wavelet coherence, and n-dimensional vector wavelet coherence analyses.

a Shiny application containing a suite of graphical and statistical tools to support clinical assessment of low coverage regions.It displays three web pages each providing a different analysis module: Coverage analysis, calculate AF by allele frequency app and binomial distribution. uncoverAPP provides a statisticl summary of coverage given target file or genes name.

This package provides a collection of functions that perform operations on time-series accelerometer data, such as identify the non-wear time, flag minutes that are part of an activity bout, and find the maximum 10-minute average count value. The functions are generally very flexible, allowing for a variety of algorithms to be implemented.

This package can be used to conduct post hoc analyses of resampling results generated by models. For example, if two models are evaluated with the root mean squared error (RMSE) using 10-fold cross-validation, there are 10 paired statistics. These can be used to make comparisons between models without involving a test set.

These utilities facilitate the programmatic manipulations of formulas, expressions, calls, assignments and other R language objects. These objects all share the same structure: a left-hand side, operator and right-hand side. This package provides methods for accessing and modifying this structures as well as extracting and replacing names and symbols from these objects.