Bioconductor SequencingData

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sequencing Sequencing SequencingData

21 months ago communication • 0

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edgeR SequencingData miRNA TMM Normalization

updated 3.0 years ago by Gordon Smyth 53k • written 3.0 years ago by tleona3 • 0

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Transcriptomics SequencingData

3.2 years ago Rom • 0

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SequencingData

4.3 years ago • updated 4.2 years ago adR ▴ 40

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1.8k

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SequencingData ATACSeq ATACseqQC

updated 3.4 years ago by Rory Stark ★ 5.2k • written 4.3 years ago by adR ▴ 40

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SequencingData STR MutationalPatterns pedigree HapMap

4.5 years ago Negar • 0

6 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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