User: Lucy

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Lucy40
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40
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New User
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1 week, 5 days ago
Joined:
1 year, 2 months ago
Email:
l**********@merton.ox.ac.uk

Posts by Lucy

<prev • 39 results • page 1 of 4 • next >
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Comment: C: Seurat sctransform return.only.var.genes = FALSE
... Thank you - that makes sense with the data that I have been getting. Do you know where in the code this is specified? ...
written 12 days ago by Lucy40
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Comment: C: Seurat sctransform return.only.var.genes = FALSE
... Thanks - that's really helpful. However, I am a bit confused as my UMAP seems to look they same whether I set return.var.only.genes = TRUE or return.var.only.genes = FALSE. ...
written 12 days ago by Lucy40
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Seurat sctransform return.only.var.genes = FALSE
... Hi, If I set return.only.var.genes = FALSE for sctransform in Seurat, will RunPCA use all genes by default or only variable genes (as it would with return.only.var.genes = TRUE)? I am struggling to find the relevant code on their GitHub. If anyone could point me in the direction of that code, tha ...
scrna-seq sctransform seurat written 12 days ago by Lucy40 • updated 12 days ago by jared.andrews073.9k
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Comment: C: RNA velocity on 5' 10x data?
... The Single Cell Gene Expression kits are 3', but the Single Cell Immune Profiling gene expression data is 5'. ...
written 14 days ago by Lucy40
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Comment: C: RNA velocity on 5' 10x data?
... Great thanks. I thought it would be because it also uses poly(T) priming but I hadn't seen anyone mention it, so I just wanted to check before I tried. ...
written 15 days ago by Lucy40
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RNA velocity on 5' 10x data?
... Hi, I was wondering whether RNA velocity (https://www.nature.com/articles/s41586-018-0414-6) can be used on 5' 10x scRNA-seq data and whether the results are similar to that achieved with 3' 10x data? Many thanks, Lucy ...
scrna-seq rna velocity rna-seq written 15 days ago by Lucy40 • updated 15 days ago by jared.andrews073.9k
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Comment: C: Differential-expression analysis using logistic regression in Seurat - glm.fit w
... Ah great, thank you. ...
written 26 days ago by Lucy40
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Differential-expression analysis using logistic regression in Seurat - glm.fit warning message
... Hi, I am performing differential-expression analysis in Seurat using the logistic regression test with "donor" as a latent variable. While it does give me an output, I am getting the following warning message. Warning message: glm.fit: fitted probabilities numerically 0 or 1 occurred Wha ...
scrna-seq differential-expression analysis seurat written 26 days ago by Lucy40 • updated 26 days ago by jared.andrews073.9k
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Answer: A: Does Harmony batch correction for scRNA-seq require the same populations to be p
... Thanks, this shows cell types that are present in two out of the three datasets. Does this work equally well if one of your populations is only present in a single dataset? ...
written 4 weeks ago by Lucy40
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Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
... Hi, I would like to use Harmony to remove batch effects from my 10x Genomics scRNA-seq data combined from three donors. However, I am wondering whether Harmony requires the same cell populations to be present in all samples, or how it deals with a population that is e.g. unique to one donor? Ma ...
scrna-seq single-cell batch correction harmony written 4 weeks ago by Lucy40

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Popular Question 7 months ago, created a question with more than 1,000 views. For FRIP score ATAC-seq

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