This package provides a package containing an environment representing the Mu11KsubA.CDF file.

MEIGOR provides a comprehensive environment for performing global optimization tasks in bioinformatics and systems biology. It leverages advanced metaheuristic algorithms to efficiently search the solution space and is specifically tailored to handle the complexity and high-dimensionality of biological datasets. This package supports various optimization routines and is integrated with Bioconductor's infrastructure for a seamless analysis workflow.

implements a MsBackend for the Spectra package using Thermo Fisher Scientific's NewRawFileReader .Net libraries. The package is generalizing the functionality introduced by the rawrr package Methods defined in this package are supposed to extend the Spectra Bioconductor package.

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

Affymetrix Affymetrix MG_U74Cv2 Array annotation data (chip mgu74cv2) assembled using data from public repositories.

This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.

maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.

This package provides a package containing an environment representing the Mu6500subD.CDF file.

This package provides a package containing an environment representing the miRNA-1_0_2Xgain.CDF file.

MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression. References: Gevaert 0. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8.

Affymetrix Affymetrix Mu19KsubB Array annotation data (chip mu19ksubb) assembled using data from public repositories.

It contains functions for estimating the DNA copy number profile using mBPCR with the aim of detecting regions with copy number changes.

This package provides a package containing an environment representing the Mu6500subA.CDF file.

This package provides a collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium.

MetaboDynamics is an R-package that provides a framework of probabilistic models to analyze longitudinal metabolomics data. It enables robust estimation of mean concentrations despite varying spread between timepoints and reports differences between timepoints as well as metabolite specific dynamics profiles that can be used for identifying "dynamics clusters" of metabolites of similar dynamics. Provides probabilistic over-representation analysis of KEGG functional modules and pathways as well as comparison between clusters of different experimental conditions.

Affymetrix moex10 annotation data (chip moex10sttranscriptcluster) assembled using data from public repositories.

This package provides a collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models.

Data sets for the book Modern Statistics for Modern Biology', S.P. Holmes and W. Huber.

Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation.

An integrated pipeline to predict the potential synthetic lethality partners (SLPs) of tumour mutations, based on gene expression, mutation profiling and cell line genetic screens data. It has builtd-in support for data from cBioPortal. The primary SLPs correlating with muations in WT and compensating for the loss of function of mutations are predicted by random forest based methods (GENIE3) and Rank Products, respectively. Genetic screens are employed to identfy consensus SLPs leads to reduced cell viability when perturbed.

This package implements functions for calling methylation for all cytosines in the genome.

This package estimates epigenetic age in skeletal muscle, using DNA methylation data generated with the Illumina Infinium technology (HM27, HM450 and HMEPIC).

This package provides a package to merge, filter sort, organise and otherwise mash together metabolite annotation tables. Metabolite annotations can be imported from multiple sources (software) and combined using workflow steps based on S4 class templates derived from the `struct` package. Other modular workflow steps such as filtering, merging, splitting, normalisation and rest-api queries are included.

Clontech BD Atlas Long Oligos Mouse 5K annotation data (chip mguatlas5k) assembled using data from public repositories.