search

hubmapconsortium / ccf-asct-reporter

HRA ASCT+B Reporter
https://hubmapconsortium.github.io/ccf-asct-reporter/
10 stars 5 forks source link

New feature: Report output needed for Antibody #290

Open emquardokus opened 2 years ago

emquardokus commented 2 years ago

We really NEED for the collaboration with Neil Kelleher’s affinity reagents working group for the Organ Mapping Antibody Panels (OMAP), is an output in the ASCT+B reporter that would perhaps give 3 columns of information:
column 1: protein biomarker name, column 2 : number of cell types in organ table that have that biomarker, column 3, comma delimited list of the cell type names. It seems like this might be “easy” to do? It is NOT currently able to do this.

We could then use this proposed output to help OMAP table authors determine which protein biomarkers would be best to use for their panels.

It would be good to have it for each organ table, but also the ability to do this across ALL organs.

emquardokus commented 2 years ago

Related project that would be good to complete: https://github.com/hubmapconsortium/ccf-asct-reporter/issues/187

Need HGNC to UniProt translation support

katyb commented 2 years ago

I agree. Can use students to get all release 2 data in this format quickly. k

From: emquardokus @.> Sent: Thursday, December 2, 2021 10:41 AM To: hubmapconsortium/ccf-asct-reporter @.> Cc: Subscribed @.***> Subject: [hubmapconsortium/ccf-asct-reporter] New feature: Report output needed for Antibody (Issue #290)

We really NEED for the collaboration with Neil Kelleher’s affinity reagents working group for the Organ Mapping Antibody Panels (OMAP), is an output in the ASCT+B reporter that would perhaps give 3 columns of information: column 1: protein biomarker name, column 2 : number of cell types in organ table that have that biomarker, column 3, comma delimited list of the cell type names. It seems like this might be “easy” to do? It is NOT currently able to do this.

We could then use this proposed output to help OMAP table authors determine which protein biomarkers would be best to use for their panels.

It would be good to have it for each organ table, but also the ability to do this across ALL organs.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/hubmapconsortium/ccf-asct-reporter/issues/290, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAP6S74BLLRBT6FX6OAXRTLUO6HQDANCNFSM5JHN7SDA. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.