:: DESCRIPTION
KEGGscape is a pathway data integration and visualization app for Cytoscape.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
KEGGscape: a Cytoscape app for pathway data integration.
Nishida K, Ono K, Kanaya S, Takahashi K.
F1000Res. 2014 Jul 1;3:144. doi: 10.12688/f1000research.4524.1
:: DESCRIPTION
NetworkPainter is a web-based program for visually analyzing data stored in Cytobank. NetworkPainter enables researchers to draw signaling network diagrams and animate them with time-lapsed experimental data such as flow and mass cytometry. NetworkPainter can be used to analyze any data contained within Cytobank.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
NetworkPainter: dynamic intracellular pathway animation in Cytobank.
Karr JR, Guturu H, Chen EY, Blair SL, Irish JM, Kotecha N, Covert MW.
BMC Bioinformatics. 2015 May 25;16:172. doi: 10.1186/s12859-015-0602-4.
:: DESCRIPTION
Caleydo is an open source visual analysis framework targeted at biomolecular data. The biggest strength of Caleydo is the visualization of interdependencies between multiple datasets. Caleydo can load tabular data and groupings/clusterings. You can explore relationships between multiple groupings, between different datasets and see how your data maps onto pathways.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2009 Oct 15;25(20):2760-1. doi: 10.1093/bioinformatics/btp432. Epub 2009 Jul 20.
Caleydo: connecting pathways and gene expression.
Streit M, Lex A, Kalkusch M, Zatloukal K, Schmalstieg D.
:: DESCRIPTION
APP （Advanced Pathway Painter）visualizes pathways (KEGG, GenMAPP, BioCarta…). The user has the possibility to display any kind of quantitative data from gene and protein experiments (e.g. microarrays from affymetrix) directly within the pathways (colours represent the value). The linking between the pathway items and the experiment data is done over the gene or protein names and their accession numbers. Furthermore the user has a quick overview on the gene/protein with the collected links in the web-interface。
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Katsura tool is a free open source Java application designed to overlay gene expression data, comparative genomics data, or quantitative shotgun proteomics data onto metabolic pathways. Katsura uses data from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Kanehisa Laboratory at Kyoto University, to build a small database containing KEGG pathway and enzyme data relating to one or more user specified organisms. Katsura manages the local database allowing users to update core information, add genomes of interest, backup the database and display database status reports. Gene expression data is input to allow visualization of pathway level expression trends over time or over a series of experimental conditions. A separate table visualizes the individual enzymes and associated gene expression values for each pathway. Capabilities such as bookmarking pathways to annotate findings, saving results to reloadable files, and the ability to output pdf reports and summary files help to capture key research findings.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
This application is released under the GPL v3 License: View License
Citation:
:: DESCRIPTION
FacPad is an R package implementing a Bayesian sparse factor model for the inference of pathways responsive to drug treatment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Oct 15;28(20):2662-70. doi: 10.1093/bioinformatics/bts502. Epub 2012 Aug 24.
FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment.
Ma H, Zhao H.
:: DESCRIPTION
MetaMapR integrates enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate richly connected metabolic networks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MetaMapR: Pathway Independent Metabolomic Network Analysis Incorporating Unknowns.
Grapov D, Wanichthanarak K, Fiehn O.
Bioinformatics. 2015 Apr 5. pii: btv194.
:: DESCRIPTION
pwOmics performs pathway-based level-specific data comparison of matching omics data sets based on pre-analysed user-specified lists of differential genes/transcripts and proteins.
::DEVELOPER
Astrid Wachter <Astrid.Wachter at med.uni-goettingen.de>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
pwOmics: An R package for pathway-based integration of time-series omics data using public database knowledge.
Wachter A, Beissbarth T.
Bioinformatics. 2015 May 21. pii: btv323.
:: DESCRIPTION
KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.
::DEVELOPER
Jitao David Zhang <jitao_david.zhang at roche.com>, Stefan Wiemann
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2009 Jun 1;25(11):1470-1. doi: 10.1093/bioinformatics/btp167. Epub 2009 Mar 23.
KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor.
Zhang JD, Wiemann S.
:: DESCRIPTION
MEPSA is a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MEPSA: minimum energy pathway analysis for energy landscapes.
Marcos-Alcalde I, Setoain J, Mendieta-Moreno JI, Mendieta J, Gómez-Puertas P.
Bioinformatics. 2015 Jul 31. pii: btv453.