Bioconductor Reproducibility

Showing : reproducibility • reset

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rsubread alignment reproducibility

9.3 years ago Isaac Virshup • 0

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reproducibility archive source code

updated 10.3 years ago by Dan Tenenbaum ★ 8.2k • written 10.3 years ago by brucbruc • 0

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docker reproducibility

10.3 years ago anton.kratz ▴ 60

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archive reproducibility

updated 10.1 years ago by Martin Morgan 25k • written 10.1 years ago by robert.bruccoleri ▴ 10

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deseq2 new version bioconductor software error reproducibility

9.2 years ago Daniel Elsner • 0

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reproducibility versions installing base-r

updated 5.9 years ago by Mike Smith ★ 6.6k • written 5.9 years ago by Yannick Wurm ▴ 40

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bioconductor R reproducibility

9.2 years ago lwumd1400 • 0

7 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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