GraphST with multiple samples, general question

[kguion1]

Hi! Congrats on an awesome tool!

I have multiple Visium samples from multiple subjects, so they are not spatially aligned in any way. However, we want to analyze them concurrently. Is there a way to use GraphST to do this? Or do the samples need to spatially align.

Thank you
Kate

[peterkilfeather]

I'm getting started using this package, but from the looks of the manuscript, they use PASTE to align sections:
https://paste-bio.readthedocs.io/en/latest/notebooks/getting-started.html

Methods of paper:
https://www.nature.com/articles/s41467-023-36796-3#Sec12

[jinmiaochen]

Hi Kate, Thank you for you our interest in grapST. For slides that cannot be aligned, we use SEDR to generate a shared latent representation then use harmony to remove the batch effects. Hi xu hang, Let's share the sedr codes and tutorials with Kate. Thanks. Best Jinmiao Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: Peter Kilfeather ***@***.***> Sent: Tuesday, October 10, 2023 2:36:45 AM To: JinmiaoChenLab/GraphST ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [JinmiaoChenLab/GraphST] GraphST with multiple samples, general question (Issue #14) This email is from a sender external to A*STAR. If you are unsure of the content, please check the source before you respond. I'm getting started using this package, but from the looks of the manuscript, they use PASTE to align sections: https://paste-bio.readthedocs.io/en/latest/notebooks/getting-started.html Methods of paper: https://www.nature.com/articles/s41467-023-36796-3#Sec12 — Reply to this email directly, view it on GitHub<#14 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACD33WX4JKDN7L4YYTJHH3DX6Q733AVCNFSM6AAAAAA5ZC3OBOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJTGQ3TGNZSGA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.

[jinmiaochen]

Hi Kate, Thank you for using our methods. The tutorial can be found here: https://sedr.readthedocs.io/en/latest/Tutorial3_Batch_integration.html. Do not hesitate to tell me if you have any problem when running SEDR. ​Best regards, XU Hang Research Fellow Singapore Immunology Network (SIgN) Agency for Science, Technology and Research (A*STAR) IMMUNOS bldg, Level 3, SINGAPORE 138648 Tel: 65-85791735 ***@***.******@***.***>

…

________________________________ From: Chen Jinmiao ***@***.***> Sent: Tuesday, 10 October 2023 07:51 To: JinmiaoChenLab/GraphST ***@***.***>; JinmiaoChenLab/GraphST ***@***.***>; Xu Hang ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [JinmiaoChenLab/GraphST] GraphST with multiple samples, general question (Issue #14) Hi Kate, Thank you for you our interest in grapST. For slides that cannot be aligned, we use SEDR to generate a shared latent representation then use harmony to remove the batch effects. Hi xu hang, Let's share the sedr codes and tutorials with Kate. Thanks. Best Jinmiao Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________ From: Peter Kilfeather ***@***.***> Sent: Tuesday, October 10, 2023 2:36:45 AM To: JinmiaoChenLab/GraphST ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [JinmiaoChenLab/GraphST] GraphST with multiple samples, general question (Issue #14) This email is from a sender external to A*STAR. If you are unsure of the content, please check the source before you respond. I'm getting started using this package, but from the looks of the manuscript, they use PASTE to align sections: https://paste-bio.readthedocs.io/en/latest/notebooks/getting-started.html Methods of paper: https://www.nature.com/articles/s41467-023-36796-3#Sec12 — Reply to this email directly, view it on GitHub<#14 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACD33WX4JKDN7L4YYTJHH3DX6Q733AVCNFSM6AAAAAA5ZC3OBOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJTGQ3TGNZSGA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person. This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.