Bioconductor DES

Showing : DES • reset

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342

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des DESeq2

written 5 months ago by fedor.bezrukov ▴ 10

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678

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DESeq2 des

updated 18 months ago by James W. MacDonald 68k • written 18 months ago by Atul K. • 0

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1.9k

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DESeq2 RUVSeq RUVseq BatchEffect DES

updated 21 months ago by James W. MacDonald 68k • written 21 months ago by Alexandre • 0

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655

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Des DESeq2

updated 21 months ago by hemantcnaik • 0 • written 21 months ago by Sahar • 0

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828

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DESeq2 DEs

22 months ago feather-W • 0

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941

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DESeq2 des

updated 3.2 years ago by Michael Love 43k • written 3.2 years ago by Devin • 0

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1.0k

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DES DESIGN

updated 3.3 years ago by Michael Love 43k • written 3.4 years ago by mike • 0

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1.3k

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DESeq2 DES

updated 5.1 years ago by Michael Love 43k • written 5.1 years ago by heikki.sarin ▴ 10

8 results • Page 1 of 1

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

Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…

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.

Votes

A: DESeq2: Is it possible to convert read counts to expression values via TPM and r

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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