Affymetrix Affymetrix MG_U74A Array annotation data (chip mgu74a) assembled using data from public repositories.

affy and illumina raw data for assessing outlier detector performance.

This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.

microbiomeDataSets is a collection of microbiome datasets loaded from Bioconductor'S ExperimentHub infrastructure. The datasets serve as reference for workflows and vignettes published adjacent to the microbiome analysis tools on Bioconductor. Additional datasets can be added overtime and additions from authors are welcome.

Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.

MetNet contains functionality to infer metabolic network topologies from quantitative data and high-resolution mass/charge information. Using statistical models (including correlation, mutual information, regression and Bayes statistics) and quantitative data (intensity values of features) adjacency matrices are inferred that can be combined to a consensus matrix. Mass differences calculated between mass/charge values of features will be matched against a data frame of supplied mass/charge differences referring to transformations of enzymatic activities. In a third step, the two levels of information are combined to form a adjacency matrix inferred from both quantitative and structure information.

This package provides a package containing an environment representing the Mu6500subD.CDF file.

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

This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by LC-MS.

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'.

This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART to RNA-Seq data.

Affymetrix mogene21 annotation data (chip mogene21stprobeset) assembled using data from public repositories.

The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method.

This package implements the inference of candidate master regulator proteins from multi-omics data (MOMA) algorithm, as well as ancillary analysis and visualization functions.

Affymetrix Affymetrix Mu19KsubB Array annotation data (chip mu19ksubb) assembled using data from public repositories.

Simple and efficient workflow for time-course gene expression data, built on publictly available open-source projects hosted on CRAN and bioconductor. moanin provides helper functions for all the steps required for analysing time-course data using functional data analysis: (1) functional modeling of the timecourse data; (2) differential expression analysis; (3) clustering; (4) downstream analysis.

Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses.

Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata.

This package provides a tool to estimate the cell composition of DNA methylation whole blood sample measured on any platform technology (microarray and sequencing).

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

Agilent "Mouse Genome, Whole" annotation data (chip mgug4122a) assembled using data from public repositories.

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

Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.

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