Calculates k-best solutions and costs for an assignment problem following the method outlined in Murty (1968) <doi:10.1287/opre.16.3.682>.

MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It contains modules for a large number of common bioinformatics tools.

This package implements contamination bias diagnostics and alternative estimators for regressions with multiple treatments. The implementation is based on Goldsmith-Pinkham, Hull, and Kolesár (2024) <doi:10.48550/arXiv.2106.05024>.

Tools for performing model selection and model averaging. Automated model selection through subsetting the maximum model, with optional constraints for model inclusion. Model parameter and prediction averaging based on model weights derived from information criteria (AICc and alike) or custom model weighting schemes.

Generates mid upper arm circumference (MUAC) and body mass index (BMI) for age z-scores and percentiles based on LMS method for children and adolescents up to 19 years that can be used to assess nutritional and health status and define risk of adverse health events.

Predictive multivariate modelling for metabolomics. Types: Classification and regression. Methods: Partial Least Squares, Random Forest ans Elastic Net Data structures: Paired and unpaired Validation: repeated double cross-validation (Westerhuis et al. (2008)<doi:10.1007/s11306-007-0099-6>, Filzmoser et al. (2009)<doi:10.1002/cem.1225>) Variable selection: Performed internally, through tuning in the inner cross-validation loop.

Allows the user to create graphs with multiple layers. The user can also modify the layers, the nodes, and the edges. The graph can also be visualized. Zaynab Hammoud and Frank Kramer (2018) <doi:10.3390/genes9110519>. More about multilayered graphs and their usage can be found in our review paper: Zaynab Hammoud and Frank Kramer (2020) <doi:10.1186/s41044-020-00046-0>.

Background - Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. Results - mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 22 ontology types from 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (e.g., MSigDB or Enrichr), expanding its applicability across diverse research areas. Conclusions - mulea is distributed as a CRAN R package. It offers researchers a powerful and flexible toolkit for functional enrichment analysis, addressing limitations of traditional tools with its progressive eFDR and by supporting a variety of ontologies. Overall, mulea fosters the exploration of diverse biological questions across various model organisms.

muParser is an extensible high performance math parser library. It is based on transforming an expression into a bytecode and precalculating constant parts of it.

This package is designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying mutossGUI package.

Allows to perform the multivariate version of the Diebold-Mariano test for equal predictive ability of multiple forecast comparison. Main reference: Mariano, R.S., Preve, D. (2012) <doi:10.1016/j.jeconom.2012.01.014>.

An ensemble classifier for multiclass classification. This is a novel classifier that natively works as an ensemble. It projects data on a large number of matrices, and uses very simple classifiers on each of these projections. The results are then combined, ideally via Dempster-Shafer Calculus.

Equivalence tests and related confidence intervals for the comparison of two treatments, simultaneously for one or many normally distributed, primary response variables (endpoints). The step-up procedure of Quan et al. (2001) is both applied for differences and extended to ratios of means. A related single-step procedure is also available.

This is a companion to the book Cook, D. and Laa, U. (2023) <https://dicook.github.io/mulgar_book/> "Interactively exploring high-dimensional data and models in R". by Cook and Laa. It contains useful functions for processing data in preparation for visualising with a tour. There are also several sample data sets.

Computes efficient data distributions from highly inconsistent datasets with many missing values using multi-set intersections. Based upon hash functions, mulset can quickly identify intersections from very large matrices of input vectors across columns and rows and thus provides scalable solution for dealing with missing values. Tomic et al. (2019) <doi:10.1101/545186>.

This package provides tools necessary to reconstruct clonal affiliations from temporally and/or spatially separated measurements of viral integration sites. For this means it utilizes correlations present in the relative readouts of the integration sites. Furthermore, facilities for filtering of the data and visualization of different steps in the pipeline are provided with the package.

This package muscat provides various methods and visualization tools for DS(differential splicing) analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated "pseudobulk" data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.

Muchsync brings Notmuch to all of your computers by synchronizing your mail messages and Notmuch tags across machines. The protocol is heavily pipelined to work efficiently over high-latency networks such as mobile broadband. Muchsync supports arbitrary pairwise synchronization among replicas. A version-vector-based algorithm allows it to exchange only the minimum information necessary to bring replicas up to date regardless of which pairs have previously synchronized.

Estimation of multivariate differences between two groups (e.g., multivariate sex differences) with regularized regression methods and predictive approach. See Lönnqvist & Ilmarinen (2021) <doi:10.1007/s11109-021-09681-2> and Ilmarinen et al. (2023) <doi:10.1177/08902070221088155>. Includes tools that help in understanding difference score reliability, predictions of difference score variables, conditional intra-class correlations, and heterogeneity of variance estimates. Package development was supported by the Academy of Finland research grant 338891.

This package provides a set of functions for some multivariate analyses utilizing a structural equation modeling (SEM) approach through the OpenMx package. These analyses include canonical correlation analysis (CANCORR), redundancy analysis (RDA), and multivariate principal component regression (MPCR). It implements procedures discussed in Gu and Cheung (2023) <doi:10.1111/bmsp.12301>, Gu, Yung, and Cheung (2019) <doi:10.1080/00273171.2018.1512847>, and Gu et al. (2023) <doi:10.1080/00273171.2022.2141675>.

A simple Unix utility in C to run multiple commands concurrently.

• A very light alternative to classic init processes or supervisord to run multiple services in the same Docker container.

• Is dead-simple to use.

• Can be run without root permissions.

• Cleanly kills all the processes it starts, including their subprocesses.

• Delegates the restart duty to the upper level.

• Forwards stdout and stderr for proper logging with Docker or systemd.

qr_mumps is a software package for the solution of sparse, linear systems on multicore computers based on the QR factorization of the input matrix. Therefore, it is suited to solving sparse least-squares problems and to computing the minimum-norm solution of sparse, underdetermined problems. It can obviously be used for solving square problems in which case the stability provided by the use of orthogonal transformations comes at the cost of a higher operation count with respect to solvers based on, e.g., the LU factorization. qr_mumps supports real and complex, single or double precision arithmetic. This is an experimental version of the package for distributed memory.

Musikcube is a terminal-based music player, library, and streaming audio server.

The Munsell package contains functions for exploring and using the Munsell colour system.