Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.

Documentation at https://melpa.org/#/multi

Documentation at https://melpa.org/#/muban

Documentation at https://melpa.org/#/mugur

muon is a multimodal omics Python framework.

This is the VPN client software for the Mullvad VPN service.

Estimates gene expressions from several laser scans of the same microarray.

This package provides a graphical user interface for the MuToss Project.

FHCRC Genomics Shared Resource Mu22v3 Annotation Data (Mu22v3) assembled using data from public repositories.

FHCRC Genomics Shared Resource Mu15v1 Annotation Data (Mu15v1) assembled using data from public repositories.

Data package containing a multi-sample multi-group spatial dataset in SpatialExperiment Bioconductor object format.

MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a sparse system of linear equations A x = b using Gaussian elimination.

This package performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).

GNOME Music is the new GNOME music playing application that aims to combine an elegant and immersive browsing experience with simple and straightforward controls.

This is a Common Lisp implementation for the Mustache template system. More details on the standard are available at https://mustache.github.io.

This package provides a set of tools to permute multisets without loops or hash tables and to generate integer partitions. Cool-lex order is similar to colexicographical order.

Extracted features from pathways derived from 8 different databases (KEGG, Reactome, Biocarta, etc.) can be used on transcriptomic, proteomic, and/or metabolomic level to calculate a combined GSEA-based enrichment score.

This library implements an efficient loopless multiset combination generation algorithm which is (approximately) described in "Loopless algorithms for generating permutations, combinations, and other combinatorial configurations.", G. Ehrlich - Journal of the ACM (JACM), 1973. (Algorithm 7.)

Computes the third multivariate cumulant of either the raw, centered or standardized data. Computes the main measures of multivariate skewness, together with their bootstrap distributions. Finally, computes the least skewed linear projections of the data.

Analyze multilevel networks as described in Lazega et al (2008) <doi:10.1016/j.socnet.2008.02.001> and in Lazega and Snijders (2016, ISBN:978-3-319-24520-1). The package was developed essentially as an extension to igraph'.

Model fitting and simulation for Gaussian and logistic inner product MultiNeSS models for multiplex networks. The package implements a convex fitting algorithm with fully adaptive parameter tuning, including options for edge cross-validation. For more details see MacDonald et al. (2020).

Implementation of the methodology of Aleshin-Guendel & Sadinle (2022) <doi:10.1080/01621459.2021.2013242>. It handles the general problem of multifile record linkage and duplicate detection, where any number of files are to be linked, and any of the files may have duplicates.

Different examples and methods for testing (including different proposals described in Ameijeiras-Alonso et al., 2019 <DOI:10.1007/s11749-018-0611-5>) and exploring (including the mode tree, mode forest and SiZer) the number of modes using nonparametric techniques <DOI:10.18637/jss.v097.i09>.

Wrapper around the Unix join facility which is more efficient than the built-in R routine merge(). The package enables the joining of multiple files on disk at once. The files can be compressed and various filters can be deployed before joining. Compiles only under Unix.