Describe distributions of EBImage Data

[gwaybio]

It will be great for some initial data science be applied to the EBImage data features - exploring distributions, identifying sources of variation (PCA, UMAP, etc.), determining MOA heterogeneity, etc.

This can live in the 2.process-data folder.

[pearsy]

I can do this, and anything related to this!

[gwaybio]

Fantastic! 🎉 This is probably most suitably written in R.

I would also recommend making some of the code modular. We may want to apply parts of this code to exploring the internal CNN representations trained on single cell images. (e.g. CNN activation layer distributions across targets, UMAP in different layer spaces, etc.)

[pearsy]

Sounds great!

…

On Sun, Dec 15, 2019 at 12:05 AM Greg Way ***@***.***> wrote: Fantastic! 🎉 This is probably most suitably written in R. I would also recommend making some of the code modular. We may want to apply parts of this code to exploring the internal CNN representations trained on single cell images. (e.g. CNN activation layer distributions across targets, UMAP in different layer spaces, etc.) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cytodata_single-2Dcell-2Dclassifier_issues_22-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DANT7UDAQ7RQZ2YSVMW2AZATQYU367A5CNFSM4JOV7OE2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEG4KJGA-23issuecomment-2D565748888&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=DP3POD-Bz5Q3NHpPPMYmng&m=SQ1KIrfZRw3JMT_paP-aruYZUOKVhj5D47gbrkhxN1Q&s=Ci_2Y0v3gdbHVUW4o3SeWwr3KnKZM3LjYqP0sz0-J24&e=>, or unsubscribe <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ANT7UDB7GCUYFME7KS2CTELQYU367ANCNFSM4JOV7OEQ&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=DP3POD-Bz5Q3NHpPPMYmng&m=SQ1KIrfZRw3JMT_paP-aruYZUOKVhj5D47gbrkhxN1Q&s=xxdRNX4wyR62kWMXeu-b5GGV0BSsPgADmISiB3QkwpQ&e=> .

[pearsy]

I tried to create a folder inside 2.process-data, but it said

You’re creating a file in a project you don’t have write access to.
We’ve created a fork of this project for you to commit your proposed changes to.
Submitting a change will create the file in a new branch in your fork, so you can send a pull request.

Do I follow this process to create a folder for different parts of the analysis pipeline?

I'm a little rusty on all things Git and Github, but will try to figure it out!

[wagenrace]

Hey @pearsy,
You do not have writing right to this project itself. The best thing to do is copying it to your own account (creating a fork).
In you own fork you can make the changes, when you're happy with changes you can make a pull request so the changes can be pulled into this project.
Hope this helps

[pearsy]

Ok, thank you, will do that.

…

On Thu, Jan 9, 2020, 5:50 PM wagenrace ***@***.***> wrote: Hey @pearsy <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pearsy&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=DP3POD-Bz5Q3NHpPPMYmng&m=TivAUAodcV_iVFHgfyeZSD8Gs8svt6120kdQhiZz1SA&s=t2b1qXGe5k0ogmWgbVH4SMS2t6FWLQ40dUYlUMcQckw&e=> , You do not have writing right to this project itself. The best thing to do is copying it to your own account (creating a fork). In you own fork you can make the changes, when you're happy with changes you can make a pull request so the changes can be pulled into this project. Hope this helps — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cytodata_single-2Dcell-2Dclassifier_issues_22-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DANT7UDFCMJNJTDBL3ABNXV3Q44TSJA5CNFSM4JOV7OE2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEIQLSHI-23issuecomment-2D572569885&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=DP3POD-Bz5Q3NHpPPMYmng&m=TivAUAodcV_iVFHgfyeZSD8Gs8svt6120kdQhiZz1SA&s=L9Gn3Mv3BGAAvRPBUg2qhc2eRDR2mvRDM4Do1ReU63c&e=>, or unsubscribe <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ANT7UDBMCWKH2ADIGPSY5M3Q44TSJANCNFSM4JOV7OEQ&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=DP3POD-Bz5Q3NHpPPMYmng&m=TivAUAodcV_iVFHgfyeZSD8Gs8svt6120kdQhiZz1SA&s=FQIQ3qMiPMyCoy5ehFd0HEoNKmscQP8GTi5gde1uqWA&e=> .

[gwaybio]

github can definitely be frustrating at times...

I wrote this a couple years ago, and it might be helpful. If it's not, then we can work something else out

[pearsy]

ok super, I will check it out. Thanks!

…

On Thu, Jan 9, 2020 at 6:50 PM Greg Way ***@***.***> wrote: github can definitely be frustrating at times... I wrote this <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_PennGCB_sandbox&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=DP3POD-Bz5Q3NHpPPMYmng&m=Jr1ZN2wymicj_mHLEjJqrsC99dzTMbyeOUqoWEMPPkI&s=BeNRSAg7YQSldyZW3XZR1Ic5IXnxq1_CBEFjN_-yt_E&e=> a couple years ago, and it might be helpful. If it's not, then we can work something else out — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cytodata_single-2Dcell-2Dclassifier_issues_22-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DANT7UDGL6Q3J5KS2JWNZBATQ442SNA5CNFSM4JOV7OE2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEIQRWAA-23issuecomment-2D572594944&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=DP3POD-Bz5Q3NHpPPMYmng&m=Jr1ZN2wymicj_mHLEjJqrsC99dzTMbyeOUqoWEMPPkI&s=b5hev3t4SgJp5X20yzIiHEn4_jB-clSEWzDB69jbJXU&e=>, or unsubscribe <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ANT7UDEPIJRFBNAWSUWKCNTQ442SNANCNFSM4JOV7OEQ&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=DP3POD-Bz5Q3NHpPPMYmng&m=Jr1ZN2wymicj_mHLEjJqrsC99dzTMbyeOUqoWEMPPkI&s=c3kQIgVDfgyxzEjtIeWhxJYYdZu6OW2GAMoeB9FXPGs&e=> .