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

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

This package provides a package containing an environment representing the MOE430B.CDF file.

The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages.

Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.

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.

This package provides a model-based background correction method, which incorporates the negative control beads to pre-process Illumina BeadArray data.

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-U74Bv2\_probe\_tab.

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

multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.

The matchBox package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing statistical significance.

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

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

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

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.

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

The Mergeomics pipeline serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts, 1) Marker set enrichment analysis (MSEA); 2) Weighted Key Driver Analysis (wKDA).

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

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

Affymetrix Affymetrix MOE430B Array annotation data (chip moe430b) assembled using data from public repositories.

This package provides a package containing an environment representing the MG_U74Av2.CDF file.

MetaPhOR was developed to enable users to assess metabolic dysregulation using transcriptomic-level data (RNA-sequencing and Microarray data) and produce publication-quality figures. A list of differentially expressed genes (DEGs), which includes fold change and p value, from DESeq2 or limma, can be used as input, with sample size for MetaPhOR, and will produce a data frame of scores for each KEGG pathway. These scores represent the magnitude and direction of transcriptional change within the pathway, along with estimated p-values.MetaPhOR then uses these scores to visualize metabolic profiles within and between samples through a variety of mechanisms, including: bubble plots, heatmaps, and pathway models.

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

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