Bioconductor Sushi

Showing : Sushi • reset

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sushi bed

7.3 years ago maltethodberg ▴ 180

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989

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sushi plotGenes

8.0 years ago portia.mcghan • 0

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sushi

9.3 years ago snamjoshi87 ▴ 40

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sushi plotBed data.frame

9.8 years ago waqasnayab • 0

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sushi plotBed

updated 9.8 years ago by dphansti ▴ 10 • written 10.0 years ago by Dimitris Polychronopoulos ▴ 80

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Sushi

updated 9.8 years ago by dphansti ▴ 10 • written 9.8 years ago by Till ▴ 30

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R sushi

updated 10.0 years ago by dphansti ▴ 10 • written 10.0 years ago by javier.mendoza • 0

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sushi

updated 10.4 years ago by Steve Lianoglou ★ 13k • written 10.4 years ago by Bogdan ▴ 670

8 results • Page 1 of 1

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Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0

Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew

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

Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…

Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k

Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…

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…

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A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen

Comment: limpa analysis advice

Answer: When to use edgeR or limma

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