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 miRNA-1\_0\_probe\_tab.

Affymetrix mogene11 annotation data (chip mogene11sttranscriptcluster) 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).

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.

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

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

The Molecular Degree of Perturbation webtool quantifies the heterogeneity of samples. It takes a data.frame of omic data that contains at least two classes (control and test) and assigns a score to all samples based on how perturbed they are compared to the controls. It is based on the Molecular Distance to Health (Pankla et al. 2009), and expands on this algorithm by adding the options to calculate the z-score using the modified z-score (using median absolute deviation), change the z-score zeroing threshold, and look at genes that are most perturbed in the test versus control classes.

Easily visualize and inspect microarrays for spatial artifacts.

Codelink Mouse Inflammation 16 Bioarray annotation data (chip mi16cod) assembled using data from public repositories.

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.

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

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

Multi-omic Pathway Analysis of Cells (MPAC), integrates multi-omic data for understanding cellular mechanisms. It predicts novel patient groups with distinct pathway profiles as well as identifying key pathway proteins with potential clinical associations. From CNA and RNA-seq data, it determines genes’ DNA and RNA states (i.e., repressed, normal, or activated), which serve as the input for PARADIGM to calculate Inferred Pathway Levels (IPLs). It also permutes DNA and RNA states to create a background distribution to filter IPLs as a way to remove events observed by chance. It provides multiple methods for downstream analysis and visualization.

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

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

FHCRC Nelson Lab mpedbarray Annotation Data (mpedbarray) assembled using data from public repositories.

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.

MBttest method was developed from beta t-test method of Baggerly et al(2003). Compared to baySeq (Hard castle and Kelly 2010), DESeq (Anders and Huber 2010) and exact test (Robinson and Smyth 2007, 2008) and the GLM of McCarthy et al(2012), MBttest is of high work efficiency,that is, it has high power, high conservativeness of FDR estimation and high stability. MBttest is suit- able to transcriptomic data, tag data, SAGE data (count data) from small samples or a few replicate libraries. It can be used to identify genes, mRNA isoforms or tags differentially expressed between two conditions.

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.

The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile.

This package provides a package containing an environment representing the Mu11KsubB.CDF file.

Affymetrix mogene11 annotation data (chip mogene11stprobeset) assembled using data from public repositories.

Affymetrix mogene21 annotation data (chip mogene21sttranscriptcluster) assembled using data from public repositories.