Question

RCytoscape using Cytoscape v3 REST interface?

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Robert M. Flight ▴ 280

@robert-m-flight-4158

Last seen 3 months ago

United States

Are there any plans to convert the RCytoscape package to use the REST interface in Cytoscape v3? There is an interesting proof of concept post from the Ideker lab now on Github here https://github.com/idekerlab/cy-rest-R

rcytoscape • 1.6k views

ADD COMMENT • link updated 9.4 years ago by Dan Tenenbaum ★ 8.2k • written 9.4 years ago by Robert M. Flight ▴ 280

Dan Tenenbaum · Answer 1 · 2015-06-17

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Dan Tenenbaum ★ 8.2k

@dan-tenenbaum-4256

Last seen 5 months ago

United States

RCy3 will probably be in the next Bioconductor release. It barely missed being in the current one.

It's not yet an officially supported Bioconductor package, and I believe it is not quite complete, but you can check it out here: https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape

ADD COMMENT • link 9.4 years ago Dan Tenenbaum ★ 8.2k

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Good to know. So I should wait another Bioconductor release before looking for it as a dependency for my own package?

ADD REPLY • link updated 9.4 years ago by Dan Tenenbaum ★ 8.2k • written 9.4 years ago by Robert M. Flight ▴ 280

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Well, if all goes well, it will be accepted into devel in the current release cycle. And then your package can depend on it. (Assuming your package is or is going to be a Bioconductor package; if not then you can do whatever you want). So I'd watch our twitter feed for the announcement that RCy3 has been added.

ADD REPLY • link 9.4 years ago Dan Tenenbaum ★ 8.2k