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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]
Users can also download the current data set or individual pathways and reactions in a variety of formats including PDF, BioPAX, and SBML [5] 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 ...
curated resource of human signal transduction pathways MEGA: free, online, open-source, phylogenetic analysis, drawing dendrograms etc. REACTOME free, online, open-source, curated pathway database encompassing many areas of human biology WikiPathways: curate biological pathways MetaboMAPS: visualize omics data on shared metabolic pathways [1]
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 ...
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.
PathwaySeq [154] Pathway analysis for RNA-Seq data using a score-based approach. petal Co-expression network modelling in R. ToPASeq: [155] an R package for topology-based pathway analysis of microarray and RNA-Seq data. RNA-Enrich A cut-off free functional enrichment testing method for RNA-seq with improved detection power.
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.
COPASI [1] (COmplex PAthway SImulator) is an open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others.