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GenomicRanges RleList

9 months ago story.benjamin ▴ 20

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Views IRanges GRanges RleList

updated 4.3 years ago by Mike Smith ★ 6.6k • written 4.3 years ago by Assa Yeroslaviz ★ 1.5k

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iranges s4vectors rle rlelist

7.6 years ago endrebak85 ▴ 40

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bug genomicranges granges rlelist coverage

updated 7.9 years ago by Hervé Pagès 16k • written 7.9 years ago by xiaotong.yao23 ▴ 10

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delayedarray rlelist rle

updated 8.2 years ago by Peter Hickey ▴ 760 • written 8.2 years ago by davide risso ▴ 980

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genomicranges biocgenerics rlelist genomicvars iranges

updated 8.3 years ago by Hervé Pagès 16k • written 8.3 years ago by Devin King ▴ 20

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rlelist ifelse

updated 9.0 years ago by theobroma22 ▴ 10 • written 9.1 years ago by maltethodberg ▴ 180

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Views genomicalignments IRangesList coverage RleList

updated 9.5 years ago by Hervé Pagès 16k • written 9.5 years ago by ccanchaya • 0

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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