Difference between revisions of "Cytoscape"
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==Contents== | ==Contents== | ||
− | + | Cytoscape is now [http://cytoscape.org/ available as '''version 3'''] and should be straightforward to download and install. | |
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==Exercises== | ==Exercises== | ||
− | <section begin= | + | <section begin=exercises_I /> |
+ | <div class="reference-box">Cytoscape 3 tutorials <small>([http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3])</small> | ||
+ | * [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3 Introduction to Cytoscape 3: User Interface] | ||
+ | * [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3.1-part2 Introduction to Cytoscape 3.1: Part 2 - importing networks] | ||
+ | * [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3-part3 Introduction to Cytoscape 3: Part 3 - Web import] | ||
+ | * [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Filtering_and_Editing_in_Cytoscape_3 Cytoscape 3: Filtering and editing] | ||
+ | </div> | ||
+ | <section end=exercises_I /> | ||
+ | <!-- section begin=exercises_II /> | ||
+ | <div class="reference-box">Cytoscape tutorials <small>([http://wiki.cytoscape.org/Presentations/Basic])</small> | ||
+ | * Browse over the [http://wiki.cytoscape.org/Presentations/03_Download_Data Cytoscape Downloading Data tutorial] | ||
+ | * Work through the [http://irefindex.uio.no/wiki/iRefScape '''iRefScape''' — iRefIndex Cytoscape plugin tutorial:] Installation, data selection and use. | ||
+ | * Work through the [http://wiki.cytoscape.org/Presentations/04_Expression_Data Cytoscape Basic expression analysis tutorial] | ||
+ | </div --> | ||
+ | <section end=exercises_II /> | ||
+ | <section begin=exercises_III /> | ||
+ | <section end=exercises_III /> | ||
+ | <section begin=exercises_IV /> | ||
+ | <section end=exercises_IV /> | ||
+ | <section begin=exercises_V /> | ||
+ | <section end=exercises_V /> | ||
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+ | ;Further reading | ||
{{#pmid:20926419}} | {{#pmid:20926419}} | ||
{{#pmid:21877285}} | {{#pmid:21877285}} | ||
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==Further reading and resources== | ==Further reading and resources== | ||
<div class="reference-box">The [http://wiki.cytoscape.org/Welcome '''Cytoscape wiki''' and manual], and the [http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats Cytoscape manual page on '''network formats'''].</div> | <div class="reference-box">The [http://wiki.cytoscape.org/Welcome '''Cytoscape wiki''' and manual], and the [http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats Cytoscape manual page on '''network formats'''].</div> |
Latest revision as of 00:49, 12 March 2014
Cytoscape
This page is a placeholder, or under current development; it is here principally to establish the logical framework of the site. The material on this page is correct, but incomplete.
Cytoscape is a program originally written in Trey Ideker's lab at the Institue for Systems Biology, that is now a thriving, open-source community project for the development of a biology-oriented network display and analysis tool.
Introductory reading
Kohl et al. (2011) Cytoscape: software for visualization and analysis of biological networks. Methods Mol Biol 696:291-303. (pmid: 21063955) |
Contents
Cytoscape is now available as version 3 and should be straightforward to download and install.
Exercises
Cytoscape 3 tutorials ([1])
- Further reading
Montojo et al. (2010) GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics 26:2927-8. (pmid: 20926419) |
Merico et al. (2011) Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map. Methods Mol Biol 781:257-77. (pmid: 21877285) |
Further reading and resources
- Platform
Shannon et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-504. (pmid: 14597658) |
Cline et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366-82. (pmid: 17947979) |
Killcoyne et al. (2009) Cytoscape: a community-based framework for network modeling. Methods Mol Biol 563:219-39. (pmid: 19597788) |
Smoot et al. (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431-2. (pmid: 21149340) |
- Plugins
Rivera et al. (2010) NeMo: Network Module identification in Cytoscape. BMC Bioinformatics 11 Suppl 1:S61. (pmid: 20122237) |
Montojo et al. (2010) GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics 26:2927-8. (pmid: 20926419) |
Oesper et al. (2011) WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code Biol Med 6:7. (pmid: 21473782) |
Razick et al. (2011) iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex. BMC Bioinformatics 12:388. (pmid: 21975162) |
Morris et al. (2011) clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics 12:436. (pmid: 22070249) |