Bioconductor Biotype

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ssgsea GSVA biotype proteincoding msigdb

updated 16 months ago by tifaGis • 0 • written 2.2 years ago by snijesh ▴ 200

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2.2k

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grch37 transcripts biotype biomaRt ncrna

updated 7.4 years ago by James W. MacDonald 68k • written 7.4 years ago by sergio.martinezcuesta ▴ 10

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2.5k

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DESeq2 PCA rlog transformation biotype

7.8 years ago JoannaF ▴ 10

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1.4k

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scater sce biotype R

updated 7.9 years ago by Aaron Lun ★ 29k • written 7.9 years ago by thebadpenny • 0

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1.9k

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biomart TF biotype ensembl mus musculus

updated 8.0 years ago by Mike Smith ★ 6.6k • written 8.0 years ago by rbronste ▴ 60

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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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Comment: limpa analysis advice

Answer: When to use edgeR or limma

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