Platform Design Info for The Manufacturer's Name Maize.

Platform Design Info for The Manufacturer's Name Sugar_Cane.

Platform Design Info for The Manufacturer's Name Drosophila_2.

Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.

Platform Design Info for The Manufacturer's Name Plasmodium_Anopheles.

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

Platform Design Info for Affymetrix FinGene-1_1-st.

pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.

Platform Design Info for Affymetrix RCnGene-1_0-st.

Platform Design Info for Affymetrix RheGene-1_1-st.

This package provides functions to Analyze Microarray (Gene Expression) Data.

Platform Design Info for The Manufacturer's Name RG_U34C.

This package provides a package for processing protein mass spectrometry data.

The PIUMA package offers a tidy pipeline of Topological Data Analysis frameworks to identify and characterize communities in high and heterogeneous dimensional data.

Platform Design Info for The Manufacturer's Name Soybean.

Platform Design Info for The Manufacturer's Name Medicago.

Platform Design Info for The Manufacturer's Name Chicken.

PaIRKAT is model framework for assessing statistical relationships between networks of metabolites (pathways) and an outcome of interest (phenotype). PaIRKAT queries the KEGG database to determine interactions between metabolites from which network connectivity is constructed. This model framework improves testing power on high dimensional data by including graph topography in the kernel machine regression setting. Studies on high dimensional data can struggle to include the complex relationships between variables. The semi-parametric kernel machine regression model is a powerful tool for capturing these types of relationships. They provide a framework for testing for relationships between outcomes of interest and high dimensional data such as metabolomic, genomic, or proteomic pathways. PaIRKAT uses known biological connections between high dimensional variables by representing them as edges of ‘graphs’ or ‘networks.’ It is common for nodes (e.g. metabolites) to be disconnected from all others within the graph, which leads to meaningful decreases in testing power whether or not the graph information is included. We include a graph regularization or ‘smoothing’ approach for managing this issue.

This package provides a package containing metadata for POCRC arrays assembled using data from public repositories.

Platform Design Info for The Manufacturer's Name MG_U74Av2.

This package provides a data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples.

Platform Design Info for The Manufacturer's Name MOE430B.

peakCombiner, a fully R based, user-friendly, transparent, and customizable tool that allows even novice R users to create a high-quality consensus peak list. The modularity of its functions allows an easy way to optimize input and output data. A broad range of accepted input data formats can be used to create a consensus peak set that can be exported to a file or used as the starting point for most downstream peak analyses.

Platform Design Info for Affymetrix MTA-1_0.