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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.
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.
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
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 ...
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 ...
Suite of tools for assembly, alignment, and analysis of short read next generation sequencing data Unix/Linux, macOS: GPL: BGI: Staden Package: Sequence assembly, editing, and analysis, mainly consisting of gap4, gap5, and spin. Written in C, C++, Fortran and Tcl. Linux, macOS, Windows: BSD: Wellcome Trust Sanger Institute, Medical Research Council
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.
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 ...