• gage

  • Referenced in 1 article [sw25396]
  • gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray ... batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies ... pathways and GO terms. These funtions and data are also useful for gene set analysis...
  • PRS

  • Referenced in 1 article [sw29380]
  • Software. PRS software is a new pathway enrichment analysis tool with a MATLAB graphical user ... gene expression data and run a pathway enrichment analysis using two different approaches ... navigate through the maps of enriched pathways where significant genes are marked with different colours...
  • VIPER

  • Referenced in 1 article [sw28859]
  • most popular tools to take RNA-seq analysis from raw sequencing data, through alignment ... control, into downstream differential expression and pathway analysis. VIPER has been created in a modular...
  • ZFIQ

  • Referenced in 1 article [sw30480]
  • relationship between genotype and phenotype, for pathway analysis and systems biology. However, the tremendous amount...
  • CAVER

  • Referenced in 1 article [sw20702]
  • properties of transport pathways change significantly in time; therefore, the analysis of a trajectory from ... pathways. The identification and analysis of transport pathways are challenging because of the high complexity ... identification and analysis of properties of transport pathways both in static and dynamic structures. Moreover...
  • BiGG

  • Referenced in 10 articles [sw17247]
  • number of such reconstructions and analysis methods increases, there is a greater need for data ... metabolic pathway maps, and export SBML files of the models for further analysis by external...
  • PIGE

  • Referenced in 1 article [sw27011]
  • Analysis for Gene- And Pathway-Environment Interaction Analysis. Extension of the ’ARTP’ package ... /gepi.20422>) for gene- and pathway-environment interaction. A permutation and a parametric bootstrap approaches have ... implemented for investigating gene- and pathway-environment interaction analysis (Truong...
  • GenMAPP

  • Referenced in 7 articles [sw12317]
  • analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs...
  • Ginsim

  • Referenced in 29 articles [sw09090]
  • approach is illustrated by a preliminary model analysis of the inter-cellular regulatory network activating ... simulations qualitatively reproduce the wild-type developmental pathway, as well as the outcome of various...
  • sigora

  • Referenced in 0 articles [sw15595]
  • package sigora: Signature Overrepresentation Analysis. Pathway Analysis is the process of statistically linking observations ... molecular level to biological processes or pathways on the systems ... organism, organ, tissue, cell) level. Traditionally, pathway analysis methods regard pathways as collections of single ... pathways. The current version allows for pathway analysis of human and mouse data sets...
  • clipper

  • Referenced in 1 article [sw23836]
  • clipper: Gene Set Analysis Exploiting Pathway Topology. Implements topological gene set analysis using ... first step clipper selects significant pathways according to statistical tests on the means...
  • iMod

  • Referenced in 4 articles [sw35118]
  • studies, including standard vibrational analysis, Monte-Carlo simulations or pathway exploration. Examples of these approaches...
  • LncADeep

  • Referenced in 1 article [sw34142]
  • Furthermore, LncADeep integrates KEGG and Reactome pathway enrichment analysis and functional module detection with...
  • DINGO

  • Referenced in 2 articles [sw29317]
  • DINGO: differential network analysis in genomics. Motivation: Cancer progression and development are initiated by aberrations ... through coordinated changes across multiple genes and pathways. It is important to understand how these ... groups. Method: We propose a pathway-based differential network analysis in genomics (DINGO) model ... approaches. We apply DINGO to key signaling pathways in glioblastoma to build differential networks...
  • COMPADRE

  • Referenced in 1 article [sw24134]
  • resource for pathway activity analysis by component decompositions. The analysis of biological networks has become ... principal component analysis (PCA), Isomaps, independent component analysis (ICA) and non-negative matrix factorization ... Supplementary Information suggest that Compadre detects more pathways than over-representation tools like David, Babelomics...
  • TPEA

  • Referenced in 0 articles [sw17396]
  • package TPEA. A Novel Topology-Based Pathway Enrichment Analysis Approach. We described a novel Topology ... based pathway enrichment analysis, which integrated the global position of the nodes and the topological ... property of the pathways in Kyoto Encyclopedia of Genes and Genomes Database. We also provide ... latest information about pathways to finish pathway enrichment analysis using this method...
  • MUFFINN

  • Referenced in 1 article [sw23967]
  • associated pathways, which suggest potentials in pathway-centric analysis of mutation data. MUFFINN...
  • NeAT

  • Referenced in 1 article [sw21914]
  • biological networks, clusters, classes and pathways. he network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide...
  • StSNP

  • Referenced in 3 articles [sw30039]
  • links to metabolic pathway information, along with real-time visual comparative analysis of the modeled...
  • ReactomeFIViz

  • Referenced in 1 article [sw25625]
  • Cytoscape app for pathway and network-based data analysis. High-throughput experiments are routinely performed ... challenging task for biologists. Projecting data onto pathway and network contexts is a powerful ... assist biologists in performing pathway- and network-based data analysis in a biologically intuitive ... this app to uncover network and pathway patterns related to their studies, search for gene...