Results 1 - 17 of 17 results out of about 3870 pages. (2.04 seconds)
- Software . . . 22 matches
- ...and analyze.'''
<<TableOfContents>>
= Biological Network Analysis and Visualization Software =
== Cytoscape ==
Cytoscape is a bioinformatics software platform for visualizing mol...
- Software/MCODE . . . 12 matches
- ...tp://cytoscape.org|Cytoscape]] is freely available network visualization and analysis software.
* Coming Soon: Run MCODE v1.3 using Java !WebStart
MCODE is a relatively fast met...
- Software/EnrichmentMap . . . 5 matches
- ...
## page was renamed from Software/EnrichmentMaps
## IMPORTANT EDITING NOTE (by Daniele Merico, 12/10/2010)
## - links to this page and its subsection have been included in a book...
- Software/WordCloudPlugin/BasicTutorial . . . 4 matches
- ... the WordCloud plugin using the Cytoscape session file provided. See the WordCloud [[Software/WordCloudPlugin/ParameterTutorial|Parameter Tutorial]] for a more detailed examples o...
- Software/EnrichmentMap/Tutorial_originalgseatutorial_outofdate . . . 4 matches
- ...
{{attachment:Software/EnrichmentMap/UserManual/enrichmentmap_logo3.png|Enrichment Map Logo|align="right"}}<<BR>>
= Enrichment Map Tutorial =
== Outline ==
This quick tutorial w...
- Software/EnrichmentMap/Description . . . 4 matches
- ...
{{attachment:Software/EnrichmentMap/UserManual/enrichmentmap_logo3.png|Enrichment Map Logo|align="right"}}<<BR>>
= The Enrichment Map Plugin =
== Concept ==
Enrichment analysis (...
- Software/GOSlimmer . . . 3 matches
- ...loped GOSlimmer, a plug-in built for use with Cytoscape. Cytoscape is an open source software platform for biological network visualization and analysis available from http://www....
- Software/EnrichmentMap/CollapseExpressionMatrix . . . 3 matches
- ...t (RNK format) to perform a "preRanked GSEA" that you later on want to analyze with [[Software/EnrichmentMap|EnrichmentMap]] and want to see an expression heatmap for the genesets,...
- Software/WordCloudPlugin/UserManual . . . 2 matches
- ...oscape.org/ and install it on your computer.
* Download the WordCloud Plugin from [[Software/WordCloudPlugin|here]] and manually place the file 'WordCloud.jar' in the 'Cytoscape/...
- Publications . . . 30 matches
- ...lm.nih.gov/34860157/|PubMed Abstract]] - [[attachment:Elife_Dec2021.pdf|PDF]]<<BR>>'''SOFTWARE'''<<BR>><<BR>>
1. '''Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the...
- GSoC2010_Directory . . . 6 matches
- ... Annotations]]
* [[GO_1|Refined Gene Ontology example]]
* Project Development
* [[Software/WordCloudPlugin/UserManual|User Manual]]
* [[Software/WordCloudPlugin|Software Downl...
- Research . . . 5 matches
- ...types can be compared to identify important components. Three research tracks and one software infrastructure track are actively developing to reach this goal.
General references:...
- CSCPathwayAnalysisService/Tutorials . . . 5 matches
- ...alysis (GSEA)]] [[http://www.ncbi.nlm.nih.gov/pubmed/21085593|Enrichment Map]]
* [[ Software/EnrichmentMap/Description | EnrichmentMap Description ]]
*Metabolic adaptation to ch...
- WordCloud . . . 3 matches
- ... a user-defined node selection, summarizing an attribute of choice.
Resources:
* [[Software/WordCloudPlugin|Plugin Download]]
* [[Software/WordCloudPlugin/BasicTutorial|Quick S...
- RonAmmar . . . 2 matches
- ...act on choice of drug dosing in many medical contexts. I am working on an open-source software tool, the Pharmacogenomics app for MedSavant. The app interprets pharmacogenomic vari...
- RuthIsserlin . . . 1 match
- ...nd Interactions]]
1. [[UpToDateGeneSets| Automatically updated Gene sets]]
1. [[Software/EnrichmentMap|Enrichment Map]]
1. [[PathwayAnalysis| Pathway Analysis ]]
Curre...
- GSoC2010_OriginalDescription . . . 1 match
- ...more details on the lab research areas, and at our home-pages for our own research interests. [[Software/EnrichmentMap|Here]] is also a Cytoscape plugin we have recently developed....