Convert Gene IDs Between Each Other and Fetch Annotations from Biomart

Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() for the most common use cases in data analysis. The main function in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the 'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes" can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol() attempts to determine the most likely current Gene Symbol.

Automated Transcriptome Classifier Pipeline: Comprehensive Transcriptome Analysis

An unsupervised fully-automated pipeline for transcriptome analysis or a supervised option to identify characteristic genes from predefined subclasses. We rely on the 'pamr' < http://www.bioconductor.org/packages//2.7/bioc/html/pamr.html> clustering algorithm to cluster the Data and then draw a heatmap of the clusters with the most significant genes and the least significant genes according to the 'pamr' algorithm. This way we get easy to grasp heatmaps that show us for each cluster which are the clusters most defining genes.

An Efficient and Deterministic Method for Identifying Topological Domains in Genomes

The 'TopDom' method identifies topological domains in genomes from Hi-C sequence data (Shin et al., 2016 ). The authors published an implementation of their method as an R script (two different versions; also available in this package). This package originates from those original 'TopDom' R scripts and provides help pages adopted from the original 'TopDom' PDF documentation. It also provides a small number of bug fixes to the original code.

Continuous Time Stochastic Modelling using Template Model Builder

Perform state and parameter inference, and forecasting, in stochastic state-space systems using the 'ctsmTMB' R6 class. This class provides a user-friendly interface for working with stochastic state space models. Inference is based on maximum likelihood estimation, with derivatives efficiently computed through automatic differentiation enabled by the 'TMB'/'RTMB' packages (Kristensen et al., 2016) . The available inference methods include Kalman filters, in addition to a Laplace approximation-based smoothing method. For further details of these methods refer to the documentation of the 'CTSMR' package < https://ctsm.info/ctsmr-reference.pdf> and Thygesen (2025) . Forecasting capabilities include moment predictions and stochastic path simulations implemented in 'C++' using 'Rcpp' (Eddelbuettel et al., 2018) for computational efficiency.

Estimate Global Clustering in Infectious Disease

Implements various novel and standard clustering statistics and other analyses useful for understanding the spread of infectious disease.

Ensemble Clustering using K Means and Hierarchical Clustering

Implements an ensemble algorithm for clustering combining a k-means and a hierarchical clustering approach.

R Interface with Google Compute Engine

Interact with the 'Google Compute Engine' API in R. Lets you create, start and stop instances in the 'Google Cloud'. Support for preconfigured instances, with templates for common R needs.

Robust Bayesian T-Test

An implementation of Bayesian model-averaged t-tests that allows users to draw inferences about the presence versus absence of an effect, variance heterogeneity, and potential outliers. The 'RoBTT' package estimates ensembles of models created by combining competing hypotheses and applies Bayesian model averaging using posterior model probabilities. Users can obtain model-averaged posterior distributions and inclusion Bayes factors, accounting for uncertainty in the data-generating process (Maier et al., 2024, ). The package also provides a truncated likelihood version of the model-averaged t-test, enabling users to exclude potential outliers without introducing bias (Godmann et al., 2024, ). Users can specify a wide range of informative priors for all parameters of interest. The package offers convenient functions for summary, visualization, and fit diagnostics.

Automated and Early Detection of Disease Outbreaks

A powerful tool for automating the early detection of disease outbreaks in time series data. 'aeddo' employs advanced statistical methods, including hierarchical models, in an innovative manner to effectively characterize outbreak signals. It is particularly useful for epidemiologists, public health professionals, and researchers seeking to identify and respond to disease outbreaks in a timely fashion. For a detailed reference on hierarchical models, consult Henrik Madsen and Poul Thyregod's book (2011), ISBN: 9781420091557.

Fitting (Exponential/Diffusion) RT-MPT Models

Fit (exponential or diffusion) response-time extended multinomial processing tree (RT-MPT) models by Klauer and Kellen (2018) and Klauer, Hartmann, and Meyer-Grant (submitted). The RT-MPT class not only incorporate frequencies like traditional multinomial processing tree (MPT) models, but also latencies. This enables it to estimate process completion times and encoding plus motor execution times next to the process probabilities of traditional MPTs. 'rtmpt' is a hierarchical Bayesian framework and posterior samples are sampled using a Metropolis-within-Gibbs sampler (for exponential RT-MPTs) or Hamiltonian-within-Gibbs sampler (for diffusion RT-MPTs).