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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.
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 ...
Academic Free: Collaborative project GenePattern: Scientific workflow system that provides access to hundreds of genomic analysis tools Unix-like (public server); Linux, macOS, Windows: MIT: Broad Institute, UC San Diego: Geworkbench: Genomic data integration platform Linux, macOS, Windows: GeWorkbench License [5] Columbia University: GMOD
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.
ICSYNTH – demo available; proprietary software; A computer aided synthesis design tool that enables chemists to generate synthetic pathways for a target molecule, and a multistep interactive synthesis tree; at its core is an algorithmic chemical knowledge base of transform libraries that are automatically generated from reaction databases. [9]
Over-representation analysis [ edit ] Using the web-interface of the database, one can perform overrepresentation analysis, based on biochemical pathways or on neighbourhood-based entity sets (NESTs) that constitute sub-networks of the overall interaction network containing all physical entities around a central one within a "radius" (number of ...