User: muad.abdelhay

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Posts by muad.abdelhay

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Comment: C: Differential expressiong with two groups in BASiCS
... I ran it as you suggested. The results have similarities to what I get from DESeq2.   Is there something I need to take into account if I used the WithSpikes = FALSE option (as my data lacks spike-ins)? ...
written 10 days ago by muad.abdelhay10
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Differential expressiong with two groups in BASiCS
... I have two groups of cells with two predefined phenotypes. There are 30 in each group (60 in total) and I wanted to use BASiCS to perform differential expression between the two groups. How do I go about it?   The vignette suggests providing two chains into the DE-function of BASiCS. Does that mea ...
bayesian differential expression single-cell basics written 12 days ago by muad.abdelhay10 • updated 7 days ago by CataVallejos10
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Batch effect removal before SC3?
... I wanted to run SC3 on normalized (scran/scater) logcounts that were then sent through limma's removeBatchEffect using the follwing script: library(scater) library(scran) library(SC3) txi.bbsplit <- readRDS("txi-bbsplit.rds") counts.annotated <- txi.bbsplit$counts ### Removes genes that h ...
batch effect removebatcheffect sc3 written 10 weeks ago by muad.abdelhay10 • updated 10 weeks ago by Vladimir Kiselev130

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