Bioconductor EmptyDrops

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4.4k

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DropletUtils EmptyDrops simpleSingleCell

updated 20 months ago by Stefano Mangiola ▴ 10 • written 4.7 years ago by shbrief ▴ 20

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2.3k

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DropletUtils emptyDrops scRNA scRNAseq 10x

21 months ago • updated 20 months ago Peter Hickey ▴ 740

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2.0k

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DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling

updated 3.5 years ago by Aaron Lun ★ 28k • written 4.7 years ago by C T ▴ 140

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1.0k

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DropletUtils emptyDrops 10x

updated 3.3 years ago by Aaron Lun ★ 28k • written 3.3 years ago by Peter Hickey ▴ 740

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1.0k

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dropletutils emptydrops

updated 4.9 years ago by Aaron Lun ★ 28k • written 4.9 years ago by rosano • 0

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653

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SingleCell emptyDrops 10X

updated 11 months ago by Peter Hickey ▴ 740 • written 11 months ago by sandra.garces.19 • 0

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195

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CellRanger emptyDrops scRNAseq 10X

5 weeks ago rocanja ▴ 60

7 results • Page 1 of 1

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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k

Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0

Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…

Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k

IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…

Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0

I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…

Votes

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Answer: Interpret plot from DiffBind

Answer: How to retrieve gene ontology GO class from gene list?

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Supporter to JKim • 0