User: PR

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PR10
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Posts by PR

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Comment: C: ATAC-seq: differential peaks using macs2 bdgdiff yields strange results
... Hi ATpoint, > If you have no replicates, thresholding the log2-fold change at say > 1.5x may give you a rough idea in which regions things are changing upon treatment. I face the same situation, and so I'll be very grateful if you could please elaborate a bit on your suggestion above. That ...
written 3 months ago by PR10
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Input genes for GSVA
... Hello All, I would like to know what exactly should be the set of genes that go as input in the expression matrix to GSVA. I am working particularly within the context of single-cell data, and have marker genes for two groups. I would like to find out the differential pathways between these two g ...
gene expression gsva written 5 months ago by PR10 • updated 5 months ago by Kevin Blighe28k
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Comment: C: Single-cell cluster : up- vs down-regulated marker genes
... Thanks a lot for your response, Igor. That helps! ...
written 6 months ago by PR10
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Single-cell cluster : up- vs down-regulated marker genes
... Hello All, I would like to know what the experts feel about defining single-cell clusters using up-regulated versus down-regulated marker genes. There is this general view that down-regulated marker genes are ambiguous (and justifiably so), and hence clusters are much better defined by considering ...
single-cell cluster marker genes rna-seq seurat written 6 months ago by PR10 • updated 6 months ago by igor6.6k
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Answer: A: Clustering Cells using known marker genes (Single cell RNAseq)
... Not sure if my answer will still be useful to you, as the post is pretty old. I just bumped onto your question now. I'm guessing you are using the FindMarkers function in Seurat to call DE. You can make this function call differential expression between any two subgroups of cells by first assigni ...
written 7 months ago by PR10
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GSVA for single-cell marker genes
... Hello Bio Stars, I am trying to do a GSVA analysis to determine differential pathways between two genotypes in single-cell data. I think I have an overall understanding of how GSVA works, but some parts of the method are still vague to me. So, I thought I will post what I think makes sense to me, ...
single-cell R gsva rna-seq written 7 months ago by PR10 • updated 6 months ago by Biostar ♦♦ 20
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Comment: C: Recent Ngs Paper
... Sorry, just wanted to share this paper. Maybe I picked the wrong tags. Apologize! ...
written 4.7 years ago by PR10
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News: (Closed) Recent Ngs Paper
... http://www.biomedcentral.com/1753-6561/7/S7/S7 ...
reads ngs news sequencing written 4.7 years ago by PR10

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