Bioconductor Parameters

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xcms adjustRtime parameters scantime error biocparallel error

6.4 years ago abrsoule ▴ 30

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1.7k

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MAST AIC calcuation Parameters single cell hurdle model

updated 22 months ago by rproendo ▴ 30 • written 7.0 years ago by mcalgaro93 • 0

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1.7k

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rtracklayer liftOver parameters minMatch

updated 7.8 years ago by Michael Lawrence ★ 11k • written 7.8 years ago by Nik dAK ▴ 10

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2.0k

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Volcano plot Parameters

updated 8.3 years ago by Gordon Smyth 53k • written 8.3 years ago by Sanches • 0

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1.4k

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lpsymphony R parameters control warm start

updated 9.6 years ago by Wolfgang Huber ★ 13k • written 9.6 years ago by chiel • 0

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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k

You just need the mouse identifier (controls baseline) and the group specific allelic effect.

Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0

Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k

You may want to speak with a local statistician, because you don't just want to find the first full rank matrix and run with that if it doe…

Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k

It is fine for your mass spec facility to include blank samples as part of their internal QC, but such samples should not in my opinion be …

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0

Hm, okay, in building a fake model by hand I think I'm realizing the problem: `mouse` and its variants are ideally acting as basically a ra…

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Comment: limpa analysis advice

Answer: When to use edgeR or limma

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