Bioconductor 10x

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scrn 10x scRNAseq emptyDrops DropletUtils

6 months ago Peter Hickey ▴ 760

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labels PBMC SingleCellMultiModal 10X

updated 10 months ago by ATpoint ★ 5.0k • written 10 months ago by javier.ruizramirez • 0

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CellRanger emptyDrops scRNAseq 10X

23 months ago rocanja ▴ 60

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SingleCell emptyDrops 10X

updated 2.8 years ago by Peter Hickey ▴ 760 • written 2.8 years ago by sandra.garces.19 • 0

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RNAseq 10X

2.9 years ago wt215 • 0

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5.1k

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DropletUtils emptyDrops scRNA scRNAseq 10x

3.5 years ago Peter Hickey ▴ 760

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DropletUtils emptyDrops 10x

updated 5.1 years ago by Aaron Lun ★ 29k • written 5.1 years ago by Peter Hickey ▴ 760

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deseq2 zinbwave 10X scRNA-seq Differential expression

updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by vincent.croset ▴ 20

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10x scrna-seq

updated 6.8 years ago by Aaron Lun ★ 29k • written 6.8 years ago by jma1991 ▴ 70

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10k

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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

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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: Which preprocessing steps are needed before running limpa?

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?

Answer: Which preprocessing steps are needed before running limpa?

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?

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Popular Question to Peter Hickey ▴ 760