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Recent Replies
Comment: Should matched samples (not paired) be included in the DESeq2 design model?
by
marieke
•
0
Ah yes, looking at the PCA makes sense, thanks!
I'm not sure I understand your last paragraph, though. With 'running tests', do you mean r…
Comment: Trouble Using GEO Files with Seurat
by
Jamie
•
0
Thank you so much @antonioggsousa! You've helped me a lot!
Comment: Trajectory Analysis scRNA-seq with one cell type and two developmental stages
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Bastien Hervé
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It makes sense to me to give it a try like this, however along the way depending on your batch effect correction or your pseudotime sanity …
Comment: Insert size is zero
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It is possible, if your have libraries that failed and are just adapter dimers.
You could also try `bbmerge.sh` from BBMap suite to get a…
Comment: Trouble Using GEO Files with Seurat
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1769mkc
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merge and the scanpy anndata.concat are they doing exactly same?
Comment: Trajectory Analysis scRNA-seq with one cell type and two developmental stages
by
npont
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10
Hello, Thank you for your reply
Indeed visium HD goes down to 2um resolution but I applied a nuclei segmentation which worked pretty nicel…
Answer: Should matched samples (not paired) be included in the DESeq2 design model?
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i.sudbery
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You add an extra covariate to the design matrix when you expect that it will explain some of the variance in gene expression. In general, i…
Comment: Trajectory Analysis scRNA-seq with one cell type and two developmental stages
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Bastien Hervé
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I am not sure if there is a "best" approach to do what you want.
Some comments :
> let's consider them as scRNA-seq data
The visium HD g…
Comment: Is this the correct DESeq2 design for model with interaction terms and batch eff
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marieke
•
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Sorry for my late answer!
This was more of a theoretical question. I'm analyzing multiple projects, and some of them need a batch effect co…
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lessismore
★
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Dear, thanks for your answer. There's indeed a double interest, one is purely exploratory and and one more specific and that's why I'd like…
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npont
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Hello,
I was interested by the same topic. Did you follow this procedure at the end?
I wonder if you should have filter for neutrophil…
Comment: Distribution of assayed SNPs per sample
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I don't think it will be possible for you discern "not on chip" from "on chip but failed" without more information about the chip design, o…
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Your suggestion sounds good to me. There's no need to integrate all the cells if you're only interested in TNK cells - provided you can ide…
Answer: Trouble Using GEO Files with Seurat
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Hi,
Yes, if you have three patient samples that you aim to integrate, you need to merge them first. If the three patient samples are `S…
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