Bioconductor Rna seq

Showing : rna seq • reset

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4.3k

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deseq2 mahattan plot RNA Seq

updated 5.3 years ago by bernatgel ▴ 150 • written 6.3 years ago by adeler001 • 0

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5.3k

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batch effect limma rna seq DE

updated 5.8 years ago by Steve Lianoglou ★ 13k • written 5.8 years ago by svlachavas ▴ 840

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1.6k

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RNA seq cpm

updated 5.8 years ago by Kevin Blighe ★ 4.0k • written 5.8 years ago by isabel.pieterse • 0

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sgseq alternative splicing rna seq

updated 17 months ago by Sara • 0 • written 6.2 years ago by 116100016 • 0

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1.4k

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edger RNA Seq

updated 6.2 years ago by James W. MacDonald 68k • written 6.2 years ago by abf ▴ 30

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848

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rna seq

6.2 years ago adeler001 • 0

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1.4k

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rna seq SGSeq Alternative splicing

updated 6.3 years ago by Leonard Goldstein ▴ 260 • written 6.3 years ago by 116100016 • 0

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871

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deseq2 likelihood ratio rna seq wald test

updated 6.4 years ago by Michael Love 43k • written 6.4 years ago by adeler001 • 0

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1.6k

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volcano plot rna seq

updated 6.4 years ago by Michael Love 43k • written 6.4 years ago by adeler001 • 0

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2.0k

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limma voom RNA Seq Time-course experiments

updated 6.6 years ago by Aaron Lun ★ 29k • written 6.6 years ago by mahes.muniandy • 0

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1.8k

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RNA seq wgcna

updated 6.6 years ago by Peter Langfelder ★ 3.0k • written 6.6 years ago by agustin.gonvi ▴ 20

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rna seq trimmomatic trimming adapter trimming paired analysis

6.7 years ago Mozart ▴ 30

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2.2k

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heatmap.2 hierarchical clustering microarray RNA seq DEG

7.9 years ago lawarde.ankita1 ▴ 30

13 results • Page 1 of 1

Recent ...

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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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