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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
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For computed cluster markers, no link outs to gene resources #70

Open matthewspeir opened 5 years ago

matthewspeir commented 5 years ago

It would be nice if the Marker Genes pop-up included links to external resources (e.g. UCSC GB, GeneCards, HGNC) when the markers are computed.

I think you're using GENCODE to define genes, so it seems like we could incorporate GENCODE metadata files (e.g. https://www.gencodegenes.org/human/release_29.html) to make link outs to a few different resources as well. I guess this assumes a more human-focused Cell Browser, but maybe there could be an option to not include these links.

maximilianh commented 5 years ago

I don't want to add too many links as people are quickly getting tired of seeing the same information everywhere. Which links do you think would be useful to have?

On Tue, Feb 5, 2019 at 10:36 AM Matt Speir notifications@github.com wrote:

It would be nice if the Marker Genes pop-up included links to external resources (e.g. UCSC GB, GeneCards, HGNC) when the markers are computed.

I think you're using GENCODE to define genes, so it seems like we could incorporate GENCODE metadata files (e.g. https://www.gencodegenes.org/human/release_29.html) to make link outs to a few different resources as well. I guess this assumes a more human-focused Cell Browser, but maybe there could be an option to not include these links.

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matthewspeir commented 5 years ago

I think GeneCards would be best as it contains a lot of information. Basically, I just want a link to a place with info about gene function.

Thanks!

maximilianh commented 5 years ago

Let me know how cbMarkerAnnotate works for you. It may be what you wanted. In that case, we can close this ticket.

What this brings up is that cbMarkerAnnotate has no docs right now. Where do you think should I doc it?

matthewspeir commented 5 years ago

I'll play with cbMarkerAnnotate a little bit and let you know how it goes.

And let me think about cbMarkerAnnotate documentation a little bit more. I need to go through the current documentation first and then think about how this new documentation might fit into this.

matthewspeir commented 5 years ago

cbMarkerAnnotate is great. Maybe you can add 'GeneCards' to cbMarkerAnnotate? I feel that would be satisfactory.

I do still think it would nice to add GeneCards to the output 'markers.tsv' by default with the ability to add more link outs with cbMarkerAnnotate, but I'm sure that's more work, haha.

maximilianh commented 5 years ago

Good idea. What do you think: How would that link look like in the table ?

On Wed 13 Mar 2019 at 22:18, Matt Speir notifications@github.com wrote:

cbMarkerAnnotate is great. Maybe you can add 'GeneCards' to cbMarkerAnnotate? I feel that would be satisfactory.

I do still think it would nice to add GeneCards to the output 'markers.tsv' by default with the ability to add more link outs with cbMarkerAnnotate, but I'm sure that's more work, haha.

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matthewspeir commented 5 years ago

Hmm, maybe the 'Gene Lists' column should be renamed to something like 'Phenotype and Disease' or something as the sites in that column (OMIM, HPO, and COSMIC) are phenotype/disease databases?

The 'Gene Lists' column could then be repurposed to contain links out to things like GeneCards? Or maybe it could be in a column named 'Gene Details'?

maximilianh commented 5 years ago

Ah nice! Yes, it should be called Phenotype & Disease. Yay browser QA!

The problem is that the normal markers.tsv doesn't have a gene list column... I could add one... I could add a Gene Details column, always. But details is also very vague... How about a column "Gene Cards" and a little "GC" link? Or some Icon. e.g. genecard's logo, the little double helix (how unusual! :-)

On Wed, Mar 13, 2019 at 10:48 PM Matt Speir notifications@github.com wrote:

Hmm, maybe the 'Gene Lists' column should be renamed to something like 'Phenotype and Disease' or something as the sites in that column (OMIM, HPO, and COSMIC) are phenotype/disease databases?

The 'Gene Lists' column could then be repurposed to contain links out to things like GeneCards? Or maybe it could be in a column named 'Gene Details'?

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matthewspeir commented 5 years ago

I think just a Gene Cards column with the GeneCards logo being the link (or maybe even 'GC {LOGO}') would be good.