Predicts the sex of samples in gene expression microarray datasets.

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.

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.

Fragmentation spectral libraries and data to test the msPurity package.

Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.

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.

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

Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0) for the human genome version GRCh38.

Assorted utilities for multi-modal analyses of single-cell datasets. Includes functions to combine multiple modalities for downstream analysis, perform MNN-based batch correction across multiple modalities, and to compute correlations between assay values for different modalities.

Agilent annotation data (chip mgug4104a) assembled using data from public repositories.

Codelink Mouse Whole Genome Bioarray (~36 000 mouse gene targets) annotation data (chip mwgcod) assembled using data from public repositories.

Example CDF data for the metaMS package.

Affymetrix Affymetrix MOE430A Array annotation data (chip moe430a) assembled using data from public repositories.

This package provides functions for interfacing with the Metabolomics Workbench RESTful API. Study, compound, protein and gene information can be searched for using the API. Methods to obtain study data in common Bioconductor formats such as SummarizedExperiment and MultiAssayExperiment are also included.

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

The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available.

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

This package provides functions for the analysis of data generated by the multiplex substrate profiling by mass spectrometry for proteases (MSP-MS) method. Data exported from upstream proteomics software is accepted as input and subsequently processed for analysis. Tools for statistical analysis, visualization, and interpretation of the data are provided.

Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.

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

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

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 Mouse430\_2\_probe\_tab.

Easily visualize and inspect microarrays for spatial artifacts.

This package provides a package containing an environment representing the MOE430A.CDF file.