Bioconductor SimplesingleCell

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DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling

updated 5.3 years ago by Aaron Lun ★ 29k • written 6.5 years ago by C T ▴ 140

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simpleSingleCell

updated 6.5 years ago by Aaron Lun ★ 29k • written 6.5 years ago by Angelos Armen • 0

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simpleSingleCell

updated 6.5 years ago by Aaron Lun ★ 29k • written 6.5 years ago by Angelos Armen • 0

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DropletUtils EmptyDrops simpleSingleCell

updated 3.5 years ago by Stefano Mangiola ▴ 40 • written 6.5 years ago by shbrief ▴ 20

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scran simpleSingleCell

updated 6.5 years ago by Aaron Lun ★ 29k • written 6.5 years ago by Angelos Armen • 0

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limma edgeR simplesingleCell scran scater

updated 6.6 years ago by Aaron Lun ★ 29k • written 6.6 years ago by Bogdan ▴ 670

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SingleCellExperiment scran limma simpleSingleCell

updated 6.7 years ago by Aaron Lun ★ 29k • written 6.7 years ago by Matt Mulé • 0

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DropletUtils SingleCellExperiement DelayedArray simpleSingleCell

updated 6.7 years ago by Aaron Lun ★ 29k • written 6.7 years ago by Steve Pederson ▴ 170

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4.0k

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singlecellexperiment dropletutils simplesinglecell

updated 7.3 years ago by Aaron Lun ★ 29k • written 7.3 years ago by Peter Hickey ▴ 760

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workflows simplesinglecell

updated 7.4 years ago by Aaron Lun ★ 29k • written 7.4 years ago by es.azadian • 0

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simplesinglecell

updated 7.9 years ago by Aaron Lun ★ 29k • written 7.9 years ago by Xingyu • 0

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scater singlecellexperiment simplesinglecell

updated 8.0 years ago by Aaron Lun ★ 29k • written 8.0 years ago by Xingyu • 0

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scater simpleSingleCell workflows

updated 8.7 years ago by Aaron Lun ★ 29k • written 8.7 years ago by sandmann.t ▴ 70

13 results • Page 1 of 1

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Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k

I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…

Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k

Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…

Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0

Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…

Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0

Hello, I was also wondering about the same issue. Did you figure it out?

Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0

FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…

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Answer: Subsetting data verses contrasts [DESeq2]?

A: WGCNA differences two groups 10 replicates each group

A: WGCNA sample size minimum: why?

Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name

Answer: Can you colour dendrogram branch clusters in pheatmap?

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Popular Question to Peter Hickey ▴ 760