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Pathway resources and types of pathway analysis using databases like KEGG, Reactome and WikiPathways. [1]Pathway is the term from molecular biology for a curated schematic representation of a well characterized segment of the molecular physiological machinery, such as a metabolic pathway describing an enzymatic process within a cell or tissue or a signaling pathway model representing a ...
tool for displaying and editing biological pathways multiplatform (Java-based) Apache License: InCroMAP: tool for the integration of omics data and joint visualization of experimental data in pathways multiplatform (Java-based) LGPL: Pathview: pathway based data integration and visualization, easy to use and integrate into pathway analysis
PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways. Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible. [1] [2] [3]
Reactome also has a ReactomeGSA [6] tool, integrated into the Reactome Analysis Tools that allows comparative pathway analyses of multi-omics datasets, with compatibility with single-cell RNA-seq data. Public data from EBI Expression Atlas, Single Cell Expression Atlas, and NCBI GREIN GEO data can be integrated into the analysis.
FunRichFunctional Enrichment analysis tool. GAGE is applicable independent of sample sizes, experimental design, assay platforms, and other types of heterogeneity. [148] This Biocondutor package also provides functions and data for pathway, GO and gene set analysis in general.
WikiPathways is originally built using MediaWiki software, [4] a custom graphical pathway editing tool (PathVisio [5]) and integrated BridgeDb [6] databases covering major gene, protein, and metabolite systems. WikiPathways was founded in 2008 by Thomas Kelder, Alex Pico, Martijn Van Iersel, Kristina Hanspers, Bruce Conklin and Chris Evelo.
Metascape is a free gene annotation and analysis resource that helps biologists make sense of one or multiple gene lists. Metascape provides automated meta-analysis tools to understand either common or unique pathways and protein networks within a group of orthogonal target-discovery studies.
COPASI includes features to define models of biological processes, simulate and analyze these models, generate analysis reports, and import/export models in SBML format. Model definition: Models are defined as chemical reactions between molecular species. The dynamics of the model is determined by Rate law associated with individual reactions ...