Showing : macs • reset
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MeDIP seq data analysis
medip_seq Macs
5.8 years ago Mar Mar ▴ 20
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1
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1.4k
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How to find sites with H3K27me3 loss?
Chip Seq Histone H3K27me3 macs diffbind
6.4 years ago researcher • 0
2
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3
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11k
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DiffBind for ATAC-seq
atac-seq diffbind macs2 macs peak finding
updated 8.8 years ago by ▴ 70 • written 9.4 years ago by ▴ 50
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2.8k
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MEDIPS vs MACS: why does MEDIPS generate more conservative p-values
p-value medips MACS
updated 10.6 years ago by ▴ 570 • written 10.6 years ago by • 0
4 results • Page 1 of 1
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Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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