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Sage-Bionetworks / fendR

Current workspace for development of drug efficacy prediction based on omic data
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Agreement on gene id type for networks #9

Closed mjrmason closed 7 years ago

mjrmason commented 7 years ago

All network files should have the same id type. Discuss

blogsdon commented 7 years ago

I vote for ENSEMBL ids

mjrmason commented 7 years ago

I prefer entrez but but I can do ensembl.

On Thu, Oct 27, 2016 at 12:39 PM, Ben Logsdon notifications@github.com wrote:

I vote for ENSEMBL ids

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sgosline commented 7 years ago

What do you guys have against HUGO? Human-readable http://www.genenames.org

blogsdon commented 7 years ago

Isoforms! Pseudogenes! Oh my!

mjrmason commented 7 years ago

human readable = human mess-up-able

On Thu, Oct 27, 2016 at 2:31 PM, Ben Logsdon notifications@github.com wrote:

Isoforms! Pseudogenes! Oh my!

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mjrmason commented 7 years ago

Wait is this like slack? can I delete things I've posted? darn

On Thu, Oct 27, 2016 at 2:38 PM, Michael Mason michael.mason@sagebase.org wrote:

human readable = human fuck-up-able

On Thu, Oct 27, 2016 at 2:31 PM, Ben Logsdon notifications@github.com wrote:

Isoforms! Pseudogenes! Oh my!

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mjrmason commented 7 years ago

Man! kenny's looking great these days!

On Thu, Oct 27, 2016 at 3:03 PM, Kenneth Daily notifications@github.com wrote:

@mjrmason https://github.com/mjrmason:

[image: finger wag] https://camo.githubusercontent.com/ba82ebd317f6af6dbc70ec9b890676c3dc03054c/68747470733a2f2f6d656469612e67697068792e636f6d2f6d656469612f4532674a396b4e6a43674c36672f67697068792e676966

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kdaily commented 7 years ago

@mjrmason, James says:

finger wag

sgosline commented 7 years ago

Who invited @kdaily?? (Unless he votes for HUGO, then he can stay)

kdaily commented 7 years ago

mygene.info

mjrmason commented 7 years ago

Thanks!

On Thu, Oct 27, 2016 at 3:14 PM, Kenneth Daily notifications@github.com wrote:

mygene.info

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mjrmason commented 7 years ago

where did Queen B go?

Also I'd like to propose only going to 3 digits in networks in order to use less memory. Thoughts?

sgosline commented 7 years ago

Are you referring to precision on the edge weights? If so I agree.

mjrmason commented 7 years ago

yes indeed

On Tue, Nov 1, 2016 at 7:54 AM, Sara JC Gosline notifications@github.com wrote:

Are you referring to precision on the edge weights? If so I agree.

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kdaily commented 7 years ago

Floating points take up 8-bytes (in R) if they have 3 digits or 10...

mjrmason commented 7 years ago

yes but I think feather optimizes that for you

On Tue, Nov 1, 2016 at 9:20 AM, Kenneth Daily notifications@github.com wrote:

Floating points take up 8-bytes (in R) if they have 3 digits or 10...

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sgosline commented 7 years ago

We agreed on HGNC due to usage in Broad/CTRP data.