User: 623202215

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62320221530
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Posts by 623202215

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Comment: C: How to choose method to integrate different patient sample together in Seurat
... I will explore it, thanks a lot for patient and timely help! ...
written 6 months ago by 62320221530
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Comment: C: How to choose method to integrate different patient sample together in Seurat
... Hi jared, Thanks very much, I learn a lot from your answer. I agree with you, subset and run integrate pipeline again maybe better. I also test the dimension of FindIntegrationAnchors() and IntegrateData(), the one is use from the CCA to specify the neighbor search space, the another one is number ...
written 6 months ago by 62320221530
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Comment: C: How to choose method to integrate different patient sample together in Seurat
... Hi jared, Thanks for your reply. I get a one more question, if you don't mind, I hope you can give me some suggestions. Sorry to bother you again! 1. When we use seurat integrate pipeline, how can we do sub-clustering on a specific cluster, for example, I want to study the heterogeneity of T cell ...
written 7 months ago by 62320221530
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What's best way to perform sub-clustering in seurat integrate pipeline?
... Hi, In seurat integrate pipeline, if I want to do **subclusterring** for a specific cluster in an **integrate** object, what's the reasonable way to do it? I have notice that there are some discussion, but it seems that it is still unsolved. [#1883][1] [#4][2] Thanks in advance if some one can sh ...
scrna seurat clustering integrate written 7 months ago by 62320221530
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Comment: C: How to choose method to integrate different patient sample together in Seurat
... Hi jared, Thanks for your tiemly help, I will explore the related parper and github. Thanks again! Best, Wei ...
written 7 months ago by 62320221530
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Comment: C: How to choose method to integrate different patient sample together in Seurat
... Hi jared, Thanks very much, it's very helpful. I will try it and see what's the "best" solution. In addition, I met several technicial problems when I perform seurat integrate pipeline, I would be appreciated if you can make some commnet. 1. For the seurat's integrate pipeline, they **normalize** ...
written 7 months ago by 62320221530
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Comment: C: Harmony batch correction vs. regressing out donor effect in Seurat
... Hi jared, I have post a new question, hope to get your suggestions!Thanks a lot! [Here is the new post][1] Best, Wei [1]: https://www.biostars.org/p/422409/ ...
written 7 months ago by 62320221530
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How to choose method to integrate different patient sample together in Seurat
... Hi, I have 3 patients with normal and tumor tissue sample(10× technology), there are six samples in total. I want combine them and find whether there is some difference between normal and tumor sample in specific cell type (such as immune cell). Due to different patients, it may have batch effect. ...
harmony batch effect scrna seurat integrate written 7 months ago by 62320221530
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Comment: C: Harmony batch correction vs. regressing out donor effect in Seurat
... Hi, I have 3 patients with normal and tumor tissue sample(10× technology), there are six samples in total. I want combine them and find whether there is some difference between normal and tumor sample in specific cell type (such as immune cell). I am struggle to choose integrate method. For the seu ...
written 7 months ago by 62320221530

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