Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'.

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.

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

This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.

MetaDICT is a method for the integration of microbiome data. This method is designed to remove batch effects and preserve biological variation while integrating heterogeneous datasets. MetaDICT can better avoid overcorrection when unobserved confounding variables are present.

"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.

This package provides several functions to explore miRNA sponge (also called ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and transcriptomics data (including bulk, single-cell and spatial gene expression data). It provides eight popular methods for identifying miRNA sponge interactions, and an integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct survival analysis of miRNA sponge modules. By using a sample control variable strategy, it provides a function to infer sample-specific miRNA sponge interactions. In terms of sample-specific miRNA sponge interactions, it implements three similarity methods to construct sample-sample correlation network.

mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis between mRNA and miRNA expriments. These experiments can be time point experiments, and or condition expriments.

Affymetrix mta10 annotation data (chip mta10probeset) assembled using data from public repositories.

Agilent Mouse annotation data (chip mgug4121a) assembled using data from public repositories.

This package provides tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.

The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences.

Affymetrix Affymetrix Mouse430_2 Array annotation data (chip mouse4302) assembled using data from public repositories.

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

Affymetrix Affymetrix Mouse430A_2 Array annotation data (chip mouse430a2) assembled using data from public repositories.

Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework.

affy and illumina raw data for assessing outlier detector performance.

The package is unified implementation of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db and also is interface to construct Gene-MeSH package (MeSH.XXX.eg.db). loadMeSHDbiPkg import sqlite file and generate MeSH.XXX.eg.db.

This package provides a package containing an environment representing the MG_U74Cv2.CDF file.

The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.

This package provides a seamless interface to the MEME Suite family of tools for motif analysis. memes provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. memes functions and data structures are amenable to both base R and tidyverse workflows.

To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.

Annotation data file for mouseCHRLOC assembled using data from public data repositories.

This package provides a package containing an environment representing the Mouse430A_2.cdf file.