Bioconductor Aucell

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RcisTarget aucell SCENIC

updated 6.8 years ago by Martin Morgan 25k • written 6.8 years ago by jka8119 ▴ 10

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AUCell SCENIC

updated 6.8 years ago by sara.aibar ▴ 10 • written 6.8 years ago by Xingyu • 0

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AUCell AUcell

20 months ago • updated 19 months ago Lucy ▴ 60

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AUCell

updated 2.4 years ago by ATpoint ★ 4.8k • written 2.4 years ago by Lucy ▴ 60

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Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k

If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…

Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k

Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …

Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k

We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…

Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k

It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…

Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20

I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…

Votes

Looking for equivalent EPIC chip v1 vs. v2 annotation variables

Properly constructing a hypergeometric test

A: Is logFC a log2 fold change or some other base in scran::findMarkers

Comment: Error in retrieving clinical data

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