Software, methods: Difference between revisions

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Trying to list software/methods/database systems provided to FANTOM5. Feel free to add anything

== Read alignment with genome ==
* Delve - contact: Timo Lassmann


== Tag clustering / peak calls ==
== Tag clustering / peak calls ==
* see [[Clustering_evaluation]]


== Genome Browser ==
see here
* see the left section (side bar) - ZENBU and UCSC RIKEN mirror


== Expression ==
== Expression ==
* BioLayout http://www.biolayout.org/fantom5/
* Pathway fingerprinting - see [fantom5:00982] http://compbio.sph.harvard.edu/hidelab/pathprint/Pathprint/Pathway_Fingerprint.html
* Pathway fingerprinting - see [fantom5:00982] http://compbio.sph.harvard.edu/hidelab/pathprint/Pathprint/Pathway_Fingerprint.html

* SwitchEngine See [[October_meeting]]
* SwitchEngine See [[October_meeting]]

== Sample exploration ==
* FONSE (the Fantom ONtology Sample Explorer) http://yuri.lbl.gov:8600/fonse/ - see [fantom5:00967] for username and password
* resource_wiki https://fantom5-collaboration.gsc.riken.jp/resource_wiki/

Latest revision as of 16:37, 18 October 2011

Trying to list software/methods/database systems provided to FANTOM5. Feel free to add anything

Read alignment with genome

  • Delve - contact: Timo Lassmann

Tag clustering / peak calls

Genome Browser

  • see the left section (side bar) - ZENBU and UCSC RIKEN mirror

Expression

Sample exploration

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