MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.

MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis.

gene target tabale of miRNA for human/mouse used for MiRaGE package.

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.

This package provides tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.

MIRit is an R package that provides several methods for investigating the relationships between miRNAs and genes in different biological conditions. In particular, MIRit allows to explore the functions of dysregulated miRNAs, and makes it possible to identify miRNA-gene regulatory axes that control biological pathways, thus enabling the users to unveil the complexity of miRNA biology. MIRit is an all-in-one framework that aims to help researchers in all the central aspects of an integrative miRNA-mRNA analyses, from differential expression analysis to network characterization.

The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. This package is an R wrapper of the lastest MACS3.

Graphically displays correlation in microarray data that is due to insufficient normalization.

This package provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

Codelink UniSet Mouse 20k I Bioarray annotation data (chip m20kcod) assembled using data from public repositories.

This package provides a set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments.

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-U74A\_probe\_tab.

This package provides functions for preprocessing, automated gating and meta-analysis of cytometry data. It also provides functions that facilitate the collection of cytometry data from the ImmPort database.

This package contains example data for the MUGA array that is used by the R package DOQTL.

This package provides tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA).

Store minor allele frequency data from NHLBI TOPMed for the human genome version hg38.

Our R package MultiRNAflow provides an easy to use unified framework allowing to automatically make both unsupervised and supervised (DE) analysis for datasets with an arbitrary number of biological conditions and time points. In particular, our code makes a deep downstream analysis of DE information, e.g. identifying temporal patterns across biological conditions and DE genes which are specific to a biological condition for each time.

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

This package implements methods for testing multiple mediators.

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

MeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups. meshes implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports more than 70 species.

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

The package aims to identify miRNA sponge or ceRNA modules in heterogeneous data. It provides several functions to study miRNA sponge modules at single-sample and multi-sample levels, including popular methods for inferring gene modules (candidate miRNA sponge or ceRNA modules), and two functions to identify miRNA sponge modules at single-sample and multi-sample levels, as well as several functions to conduct modular analysis of miRNA sponge modules.

This package provides a package containing an environment representing the miRNA-1_0.CDF file.