Bioconductor BigWig

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2.6k

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DESeq2 edgeR bigwig limma

3.3 years ago • updated 3.0 years ago Bogdan ▴ 670

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2.9k

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bedgraph wiggleplotr bigwig wig

updated 3.4 years ago by complaintguide • 0 • written 3.4 years ago by Bogdan ▴ 670

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2.2k

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bigWig RNASeqData

4.0 years ago bas_work ▴ 30

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2.8k

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software error BigWig import windows

5.8 years ago lsilva.m • 0

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2.8k

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wiggleplotr bigwig coverage ngs

updated 8.3 years ago by kaur.alasoo ▴ 30 • written 8.3 years ago by borgmichael • 0

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4.3k

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bigwig rtracklayer import granges grangeslist

updated 8.5 years ago by Michael Lawrence ★ 11k • written 8.5 years ago by Assa Yeroslaviz ★ 1.5k

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1.6k

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rtracklayer bigwig import

updated 9.2 years ago by Michael Lawrence ★ 11k • written 9.2 years ago by zx8754 ▴ 10

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1.9k

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bigwig rtracklayer export.bw

updated 9.2 years ago by Michael Lawrence ★ 11k • written 9.2 years ago by story.benjamin ▴ 20

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3.2k

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rtracklayer bigwig

updated 10.0 years ago by laurent.lacroix ▴ 30 • written 10.0 years ago by koneill ▴ 30

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1.6k

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rtracklayer BigWig

updated 10.2 years ago by Michael Lawrence ★ 11k • written 10.2 years ago by dborgesrmit • 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

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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