An interactive document on the topic of one-way and two-way analysis of variance using rmarkdown and shiny packages. Runtime examples are provided in the package function as well as at <https://kartikeyab.shinyapps.io/ANOVAShiny/>.

Utility functions to check data, variables and conditions for functions used in admiral and admiral extension packages. Additional utility helper functions to assist developers with maintaining documentation, testing and general upkeep of admiral and admiral extension packages.

Routines for the graphical representation of correlation matrices by means of correlograms, MDS maps and biplots obtained by PCA, PFA or WALS (weighted alternating least squares); See Graffelman & De Leeuw (2023) <doi: 10.1080/00031305.2023.2186952>.

Generates skeletons of closed 2D polygons using Voronoi diagrams. It provides methods for sf', terra', and geos objects to compute polygon centerlines based on the generated skeletons. Voronoi, G. (1908) <doi:10.1515/crll.1908.134.198>.

Create shareable data sets from raw data files that contain protected elements. Relying on master crosswalk files that list restricted variables, package functions warn users about possible violations of data usage agreement and prevent writing protected elements.

Make inference in a mixture of discrete Laplace distributions using the EM algorithm. This can e.g. be used for modelling the distribution of Y chromosomal haplotypes as described in [1, 2] (refer to the URL section).

The tools herein calculate, print, summarize and plot pairwise differences that result from generalized linear models, general linear hypothesis tests and multinomial logistic regression models. For more information, see Armstrong (2013) <doi:10.32614/RJ-2013-021>.

This package provides functions for sequencing studies allowing for multiple functional annotation scores. Score type tests and an efficient perturbation method are used for individual gene/large gene-set/genome wide analysis. Only summary statistics are needed.

Useful functions to standardize software outputs from ProteomeDiscoverer, Spectronaut, DIA-NN and MaxQuant on precursor, modified peptide and proteingroup level and to trace software differences for identifications such as varying proteingroup denotations for common precursor.

Facilitates hierarchical clustering analysis with functions to read data in txt', xlsx', and xls formats, apply normalization techniques to the dataset, perform hierarchical clustering and construct scatter plot from principal component analysis to evaluate the groups obtained.

This package provides functions to fits simple linear regression models with log normal errors and identity link, i.e. taking the responses on the original scale. See Muggeo (2018) <doi:10.13140/RG.2.2.18118.16965>.

This package provides an implementation of piecewise normalisation techniques useful when dealing with the communication of skewed and highly skewed data. It also provides utilities that recommends a normalisation technique based on the distribution of the data.

Collection of functions to get files in parquet format. Parquet is a columnar storage file format <https://parquet.apache.org/>. The files to convert can be of several formats ("csv", "RData", "rds", "RSQLite", "json", "ndjson", "SAS", "SPSS"...).

This package provides data about the Star Wars movie franchise in a set of relational tables or as a complete DuckDB database. All data was collected from the open source Star Wars API <https://swapi.dev/>.

This package provides an integrated user interface and workflow for the analysis of running, cycling and swimming data from GPS-enabled tracking devices through the trackeR <https://CRAN.R-project.org/package=trackeR> R package.

This package provides a shiny app that generates plots and summary tables from repeat-dose toxicology study results to facilitate holistic evaluation of the drug safety of active pharmaceutical ingredients (API) prior to initiation of clinical trials.

An interface to twitter-text', a JavaScript library which is responsible for determining the length/validity of a tweet and identifying/linking any URLs or special tags (e.g. mentions or hashtags) which may be present.

An adaptation for estuaries (tidal waters) of weighted regression on time, discharge, and season to evaluate trends in water quality time series. Please see Beck and Hagy (2015) <doi:10.1007/s10666-015-9452-8> for details.

This package infers cell type-specific expression based on co-expression similarity with known cell type marker genes. Can make accurate predictions using publicly available expression data, even when a cell type has not been isolated before.

By leveraging statistical properties (log-rank test for survival) of patient cohorts defined by binary thresholds, poor-prognosis patients are identified by the sigsquared package via optimization over a cost function reducing type I and II error.

This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate.

This package provides a collection of functions to support matrix calculations for probability, econometric and numerical analysis. There are additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics.

This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.

This package provides wrapper types and traits for secret management which help ensure they aren't accidentally copied, logged, or otherwise exposed (as much as possible), and also ensure secrets are securely wiped from memory when dropped.