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ZJU-UoE-CCW-LAB / scCDC

single-cell Contamination Detection and Correction
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Using cellbender with scCDC? #5

Closed yimwy closed 3 days ago

yimwy commented 5 months ago

Hi, I have a quick question. I am wondering if it is rationale to perform empty droplet based methods such as cellbender, then further perform decontamination using scCDC after clustering?

ChaochenWang commented 5 months ago

We recommend to perform DecontX and then scCDC. We have not tested combining cellbender and scCDC.

发件人: @. @.> 代表 yimwy 发送时间: 2024年5月31日 12:57 收件人: ZJU-UoE-CCW-LAB/scCDC @.> 抄送: Subscribed @.> 主题: [SPAM] [ZJU-UoE-CCW-LAB/scCDC] Using cellbender with scCDC? (Issue #5)

Hi, I have a quick question. I am wondering if it is rationale to perform empty droplet based methods such as cellbender, then further perform decontamination using scCDC after clustering?

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wuliRothschild commented 2 months ago

Hello, I wonder if this step of scCDC decontamination should be performed after filtering low-quality cells and removing doublets or before?

ChaochenWang commented 2 months ago

Yes. It is suggested to perform scCDC after these quality control steps.

发件人: @. @.> 代表 wuliRothschild 发送时间: 2024年8月27日 18:30 收件人: ZJU-UoE-CCW-LAB/scCDC @.> 抄送: ChaochenWang @.>; Comment @.***> 主题: Re: [ZJU-UoE-CCW-LAB/scCDC] Using cellbender with scCDC? (Issue #5)

Hello, I wonder if this step of scCDC decontamination should be performed after filtering low-quality cells and removing doublets or before?

— Reply to this email directly, view it on GitHub https://github.com/ZJU-UoE-CCW-LAB/scCDC/issues/5#issuecomment-2312150881 , or unsubscribe https://github.com/notifications/unsubscribe-auth/A2ETL3JHM7UCEHJNR2UTWSDZTRIJXAVCNFSM6AAAAABISDMHJ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJSGE2TAOBYGE . You are receiving this because you commented.Message ID: @.***>