search

dynverse / dyno

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
https://dynverse.github.io/dyno
Other
163 stars 32 forks source link

How to import an integrated data from seurat V3 to dyno? #95

Open Dongxu-Zheng opened 3 years ago

Dongxu-Zheng commented 3 years ago

Hi, thanks for developing such a great package for trajectory analysis. Maybe this is a problem not a issue. If I post it in a wrong place, just let me know and show me a right direction.

I have 4 samples and they do have some batch effect. So I use scTransform workflow to integrate them together using seurat V3. My question is how to import a integrated data to dyno? If I still use the original read count matrix, the batch effect will also be introduced into dyno. Or is there any way to remove the batch effect in dyno?

Thanks for any suggestions and advices in advance!

Issac

wfma commented 3 years ago

also want to know this^

rcannood commented 3 years ago

Hello @Dongxu-Zheng !

Can you send me an example data object you wish to run with dyno?

Kind regards, Robrecht

Dongxu-Zheng commented 3 years ago

Hello @Dongxu-Zheng !

Can you send me an example data object you wish to run with dyno?

Kind regards, Robrecht

Hi Robrecht,

Thanks for your reply. I am not allowed to send the whole dataset to you due to confidentiality. But I can send you a subset of the integrated object created by Seurat V3. By the way, where to find your email or how to share it with you?

Thanks! Dongxu

rcannood commented 3 years ago

No need to send me the whole dataset, a tiny part of it is okay.

You can send it to 'rcannood@gmail.com'.

VeredasCA commented 2 years ago

Hi! I'm interested in this question. Was it solved? If so, could you share the solution? Thank you!

Veredas

Dongxu-Zheng commented 2 years ago

Hi, unfortunately, I didn’t get any reply. To remove the batch effect, my suggestion is to use a UMAP embedding matrix for trajectory analysis.

From: VeredasCA @.> Sent: vrijdag 27 augustus 2021 11:49 To: dynverse/dyno @.> Cc: Zheng, D. (HG) @.>; Mention @.> Subject: Re: [dynverse/dyno] How to import an integrated data from seurat V3 to dyno? (#95)

Hi! I'm interested in this question. Was it solved? If so, could you share the solution? Thank you!

Veredas

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/dynverse/dyno/issues/95#issuecomment-907075352, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APVO5HXO2HRUSMRDPOUFKI3T65NQJANCNFSM4TARO2MA. 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.

VeredasCA commented 2 years ago

Oh, I see.. Thank you @Dongxu-Zheng for your quick answer and for your suggestion!