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welch-lab / MultiVelo

Multi-omic velocity inference
BSD 3-Clause "New" or "Revised" License
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How to build GRN #3

Open Dan-121 opened 2 years ago

Dan-121 commented 2 years ago

Hi,professor welch: MultiVelo is really great and I want to apply it to my own data. But I haven't see the code that build GRN and analysis with GWAS. I will be appreciate if you can share the code. Thanks a lot. Yours Dan

danielee0707 commented 2 years ago

Hi Dan. By GRN, are you referring to the motif analysis we did for the human brain? It follows the steps of chromVAR, or similarly, RunChromVAR section in the Seurat weighted nearest neighbor vignette. The list of GWAS SNPs were downloaded directly from Ensembl GWAS Catalog as mentioned in the preprint.

An example R script about how to run DTW time delay analysis was uploaded to multivelo_demo as well.

Dan-121 commented 2 years ago

Thanks for your reply.I will have a try.

发自我的iPhone

------------------ Original ------------------ From: Chen Li @.> Date: Thu,Mar 17,2022 5:36 AM To: welch-lab/MultiVelo @.> Cc: Dan @.>, Author @.> Subject: Re: [welch-lab/MultiVelo] How to build GRN (Issue #3)

Hi Dan. By GRN, are you referring to the motif analysis we did for the human brain? It follows the steps of chromVAR, or similarly, RunChromVAR section in the Seurat weighted nearest neighbor vignette. The list of GWAS SNPs were downloaded directly from Ensembl GWAS Catalog as mentioned in the preprint.

An example R script about how to run DTW time delay analysis was uploaded to multivelo_demo as well.

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