Bioconductor Vranges

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somaticsignatures vranges readvcfasvranges

7.4 years ago guillaume.dachy • 0

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variantannotation vcf readvcf vranges

updated 7.6 years ago by Michael Lawrence ★ 11k • written 7.6 years ago by david.mas • 0

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variantannotation VRanges R Rle

updated 7.6 years ago by Valerie Obenchain ★ 6.8k • written 7.6 years ago by Jayendra Shinde • 0

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somaticsignatures somaticsignatures package readvcfasvranges vranges

8.5 years ago • updated 8.4 years ago guillaume.dachy • 0

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vranges vcf to vranges

9.0 years ago Bogdan ▴ 670

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somaticsignatures vranges

updated 9.6 years ago by Julian Gehring ★ 1.3k • written 9.6 years ago by arsala521 ▴ 10

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granges vranges readvcfasvranges somaticsignatures

updated 9.8 years ago by Michael Lawrence ★ 11k • written 9.8 years ago by jpluta26 • 0

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SomaticSignatures mutationContext VRanges

updated 10.4 years ago by Julian Gehring ★ 1.3k • written 10.4 years ago by tesa.severson ▴ 10

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variantannotation vranges readvcf readvcfasvranges metadata

10.9 years ago summerela • 0

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variantannotation granges DNAStringSetList findoverlaps Vranges

10.9 years ago summerela • 0

10 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

I think that some historical context will help here. Aaron Lun was a PhD student in my Lab back in 2015, and the analysis approach that he …

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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