This package provides efficient batch-effect adjustment of data with missing values. BERT orders all batch effect correction to a tree of pairwise computations. BERT allows parallelization over sub-trees.

Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.

Estimate diagnosis performance (Sensitivity, Specificity, Positive predictive value, Negative predicted value) of a diagnostic test where can not measure the golden standard but can estimate it using the attributable fraction.

This package performs least squares constrained optimization on a linear objective function. It contains a number of algorithms to choose from and offers a formula syntax similar to lm().

This package provides the source and examples for James P. Howard, II, "Computational Methods for Numerical Analysis with R," <https://jameshoward.us/cmna/>, a book on numerical methods in R.

Fit logistic functions to observed dose-response continuous data and evaluate goodness-of-fit measures. See Malyutina A., Tang J., and Pessia A. (2023) <doi:10.18637/jss.v106.i04>.

Bayesian networks with continuous and/or discrete variables can be learned and compared from data. The method is described in Boettcher and Dethlefsen (2003), <doi:10.18637/jss.v008.i20>.

This package contains data sets, examples and software from the Second Edition of "Design of Observational Studies"; see Rosenbaum, P.R. (2010) <doi:10.1007/978-1-4419-1213-8>.

Background correction of spectral like data. Handles variations in scaling, polynomial baselines, interferents, constituents and replicate variation. Parameters for corrections are stored for further analysis, and spectra are corrected accordingly.

This package provides tools for fluctuations analysis of mutant cells counts. Main reference is A. Mazoyer, R. Drouilhet, S. Despreaux and B. Ycart (2017) <doi:10.32614/RJ-2017-029>.

This package implements common geostatistical methods in a clean, straightforward, efficient manner. The methods are discussed in Schabenberger and Gotway (2004, <ISBN:9781584883227>) and Waller and Gotway (2004, <ISBN:9780471387718>).

This package implements assessment of benefit-risk balance using Bayesian Discrete Choice Experiment. For more details see the article by Mukhopadhyay et al. (2019) <DOI:10.1080/19466315.2018.1527248>.

Smoothing techniques and computing bandwidth selectors of the nth derivative of a probability density for one-dimensional data (described in Arsalane Chouaib Guidoum (2020) <arXiv:2012.06102> [stat.CO]).

Analyzing data under multivariate mixed effects model using multivariate REML and multivariate Henderson3 methods. See Meyer (1985) <doi:10.2307/2530651> and Wesolowska Janczarek (1984) <doi:10.1002/bimj.4710260613>.

Generates multivariate subgaussian stable probabilities using the QRSVN algorithm as detailed in Genz and Bretz (2002) <DOI:10.1198/106186002394> but by sampling positive stable variates not chi/sqrt(nu).

This package implements orbit counting using a fast combinatorial approach. Counts orbits of nodes and edges from edge matrix or data frame, or a graph object from the graph package.

Transforms datetime data into a format ready for analysis. It offers two core functionalities; aggregating data to a higher level interval (thicken) and imputing records where observations were absent (pad).

This package provides functions to generate ensembles of generalized linear models using a greedy projected subset gradient descent algorithm. The sparsity and diversity tuning parameters are selected by cross-validation.

This function produces both the numerical and graphical summaries of the QTL hotspot detection in the genomes that are available on the worldwide web including the flanking markers of QTLs.

This package provides a set of consistent, opinionated functions to quickly check function arguments, coerce them to the desired configuration, or deliver informative error messages when that is not possible.

This package provides tools to help developers and producers manipulate R objects and outputs. It includes tools for displaying results and objects, and for formatting them in the correct format.

This package provides functions for statistical analysis, modeling and simulation of time series with state space model, based on the methodology in Kitagawa (2020, ISBN: 978-0-367-18733-0).

ramr is an R package for detection of epimutations (i.e., infrequent aberrant DNA methylation events) in large data sets obtained by methylation profiling using array or high-throughput methylation sequencing. In addition, package provides functions to visualize found aberrantly methylated regions (AMRs), to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms.