This package provides functions for performing graphical difference testing. Differences are generated between raster images. Comparisons can be performed between different package versions and between different R versions.

This package creates plots of peptides from shotgun proteomics analysis of secretome and lysate samples. These plots contain associated protein features and scores for potential secretion and truncation.

Automated analysis and modeling of longitudinal omics data (e.g. breath metabolomics') using generalized spline mixed effect models. Including automated filtering of noise parameters and determination of breakpoints.

Implementation of methods for minimizing ill-conditioned problems. Currently only includes regularized (quasi-)newton optimization (Kanzow and Steck et al. (2023), <doi:10.1007/s12532-023-00238-4>).

This package provides one function, which is a wrapper around purrr::map() with some extras on top, including parallel computation, progress bars, error handling, and result caching.

R's implementation of the JavaScript library path-to-regexp', it aims to provide R web frameworks features such as parameter handling among other URL path utilities.

This package performs hybrid multi-stage factor analytic procedure for controlling acquiescence in restricted solutions (Ferrando & Lorenzo-Seva, 2000 <https://www.uv.es/revispsi/articulos3.00/ferran7.pdf>).

This package provides routines to check identifiability of linear structural equation models and factor analysis models. The routines are based on the graphical representation of structural equation models.

This package contains methods for simulation and for evaluating the pdf, cdf, and quantile functions for symmetric stable, symmetric classical tempered stable, and symmetric power tempered stable distributions.

Import, process, summarize and visualize raw data from metabolic carts. See Robergs, Dwyer, and Astorino (2010) <doi:10.2165/11319670-000000000-00000> for more details on data processing.

Uses thresholded partial least squares algorithm to create a regression or classification model. For more information, see Lee, Bradlow, and Kable <doi:10.1016/j.crmeth.2022.100227>.

Flexible simulation of time series using time series components, including seasonal, calendar and outlier effects. Main algorithm described in Ollech, D. (2021) <doi:10.1515/jtse-2020-0028>.

This package provides easy access to a curated selection of pre-processed data sets relevant to the COVID-19 outbreak in the UK for teaching and demonstration purposes.

This package provides a continuous version of the receiver operating characteristics (ROC) curve to assess both classification and continuity performances of biomarkers, diagnostic tests, or risk prediction models.

This package provides a tool for calculating and drawing "variable trees". Variable trees display information about nested subsets of a data frame. <doi:10.18637/jss.v114.i04>.

Another implementation of general regression neural network in R based on Specht (1991) <DOI:10.1109/72.97934>. It is applicable to the functional approximation or the classification.

mpv is a general-purpose audio and video player. It is a fork of mplayer2 and MPlayer. It shares some features with the former projects while introducing many more.

RolDE detects longitudinal differential expression between two conditions in noisy high-troughput data. Suitable even for data with a moderate amount of missing values.RolDE is a composite method, consisting of three independent modules with different approaches to detecting longitudinal differential expression. The combination of these diverse modules allows RolDE to robustly detect varying differences in longitudinal trends and expression levels in diverse data types and experimental settings.

The Stuttgart Neural Network Simulator (SNNS) is a library containing many standard implementations of neural networks. This package wraps the SNNS functionality to make it available from within R. Using the RSNNS low-level interface, all of the algorithmic functionality and flexibility of SNNS can be accessed. Furthermore, the package contains a convenient high-level interface, so that the most common neural network topologies and learning algorithms integrate seamlessly into R.

Replication Rate (RR) is the probability of replicating a statistically significant association in genome-wide association studies. This R-package provide the estimation method for replication rate which makes use of the summary statistics from the primary study. We can use the estimated RR to determine the sample size of the replication study, and to check the consistency between the results of the primary study and those of the replication study.

Datasets and utility functions to support the book "R for Plant Disease Epidemiology" (R4PDE). It includes functions for quantifying disease, assessing spatial patterns, and modeling plant disease epidemics based on weather predictors. These tools are intended for teaching and research in plant disease epidemiology. Several functions are based on classical and contemporary methods, including those discussed in Laurence V. Madden, Gareth Hughes, and Frank van den Bosch (2007) <doi:10.1094/9780890545058>.

Runitor runs the supplied command, captures its output, and based on its exit code reports successful or failed execution to https://healthchecks.io or your private instance.

ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty.

Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using a negative bionomial generalized linear model.