Models

oposSOM is a comprehensive, machine learning based open-source data analysis software combining functionalities such as diversity analyses, biomarker selection, function mining, and visualization. These functionalities are now available as interactive web-browser application for a broader user audience interested in extracting detailed information from high-throughput omics data sets pre-processed by oposSOM. It enables interactive browsing of single-gene and gene set profiles, of molecular ...

The Pathway Signal Flow (PSF) toolkit is an R package designed for pathway editing and signal flow analysis. It enables users to perform PSF analysis on functional -omics data, facilitating the study of signaling pathways in various biological contexts.

Key Features:

• Pathway Editing: Allows customization and editing of biological pathways to suit specific research needs.

• Signal Flow Calculation: Computes signal flow within pathways based on gene expression data, aiding in the ...

KEGG pathway database is a collection of manually drawn pathway maps representing current knowledge on molecular interaction and reaction networks, accompanied with KGML (KEGG pathway xml format) files for automatic computational analyses and modeling of metabolic and signaling networks. In a KGML file the pathway is represented as a graph object with entry elements (gene products, compounds, pathways) as its nodes, and relations between elements as edges. However, in most cases there is a lack ...