Affymetrix mogene20 annotation data (chip mogene20sttranscriptcluster) assembled using data from public repositories.

The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available.

This package finds optimal sets of genes that seperate samples into two or more classes.

Simulate a multigeneration methylation case versus control experiment with inheritance relation using a real control dataset.

Annotation package containing all available miRNA names from 22 versions (data from http://www.mirbase.org/).

This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes.

This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by LC-MS.

mitology allows to study the mitochondrial activity throught high-throughput RNA-seq data. It is based on a collection of genes whose proteins localize in to the mitochondria. From these, mitology provides a reorganization of the pathways related to mitochondria activity from Reactome and Gene Ontology. Further a ready-to-use implementation of MitoCarta3.0 pathways is included.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74B\_probe\_tab.

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

Affymetrix Affymetrix MG_U74A Array annotation data (chip mgu74a) assembled using data from public repositories.

Example data for M3Drop package.

This package provides a comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends.

MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.

Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.

This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.

Base annotation databases for malaria, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Maize\_probe\_tab.

Data used by the barcode package for microarrays of type mouse4302.

The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.

Affymetrix mogene10 annotation data (chip mogene10sttranscriptcluster) assembled using data from public repositories.

Affymetrix Affymetrix Mu11KsubB Array annotation data (chip mu11ksubb) assembled using data from public repositories.

MSstatsQC is an R package which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.

MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectra object infrastructure defined in the package Spectra that stores MS/MS spectra. MetCirc offers functionality to calculate similarity between precursors based on the normalised dot product, neutral losses or user-defined functions and visualise similarities in a circular layout. Within the interactive framework the user can annotate MS/MS features based on their similarity to (known) related MS/MS features.