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SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
3.2 years ago
georgia.katsoula
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Comment: Struggle with the replicates of epic array data
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edubaievisa.online
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Comment: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
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Aaron Lun
★ 28k
IIRC loading ~million cells into memory took about 3-5 minutes, but that was with a rather slow filesystem (HDD on a HPC), so YMMV dependin…
Comment: Differential Expression Genes as Independent Variables
by
Gordon Smyth
52k
Does not allow mixed models. And is for a different purpose to what your aims seem to be: it's purely for prediction rather than for testin…
Comment: Differential Expression Genes as Independent Variables
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abadgerw
• 0
Thanks! I was thinking about this but do not believe glmnet allows for regularized mixed models unless I am mistaken?
Comment: lfcShrink and alpha value
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cropero
• 0
Thank you for your fast answer, I have everything clear now
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A: How to bin a GRanges to small bins
C: How to bin a GRanges to small bins
C: How to bin a GRanges to small bins
A: deseq2 filter the low counts
A: deseq2 filter the low counts
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