Bioconductor Cellranger

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CellRanger emptyDrops scRNAseq 10X

22 months ago rocanja ▴ 60

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ReadInR Cellranger GEX+Features+VDJ

4.0 years ago gregoire.destreel • 0

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CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq

updated 3.7 years ago by rohitsatyam102 ▴ 20 • written 4.0 years ago by gregoire.destreel • 0

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single-cell 10X Cell calling DropletUtils cellranger

updated 6.9 years ago by Aaron Lun ★ 29k • written 6.9 years ago by xingxd16 ▴ 20

4 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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