Bioconductor SimplesingleCell

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DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling

updated 4.1 years ago by Aaron Lun ★ 28k • written 5.2 years ago by C T ▴ 140

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1.4k

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simpleSingleCell

updated 5.3 years ago by Aaron Lun ★ 28k • written 5.3 years ago by Angelos Armen • 0

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822

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simpleSingleCell

updated 5.3 years ago by Aaron Lun ★ 28k • written 5.3 years ago by Angelos Armen • 0

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DropletUtils EmptyDrops simpleSingleCell

updated 2.3 years ago by Stefano Mangiola ▴ 20 • written 5.3 years ago by shbrief ▴ 20

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scran simpleSingleCell

updated 5.3 years ago by Aaron Lun ★ 28k • written 5.3 years ago by Angelos Armen • 0

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limma edgeR simplesingleCell scran scater

updated 5.3 years ago by Aaron Lun ★ 28k • written 5.3 years ago by Bogdan ▴ 670

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1.9k

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SingleCellExperiment scran limma simpleSingleCell

updated 5.5 years ago by Aaron Lun ★ 28k • written 5.5 years ago by Matt Mulé • 0

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1.9k

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DropletUtils SingleCellExperiement DelayedArray simpleSingleCell

updated 5.5 years ago by Aaron Lun ★ 28k • written 5.5 years ago by Steve Pederson ▴ 170

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2.8k

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singlecellexperiment dropletutils simplesinglecell

updated 6.1 years ago by Aaron Lun ★ 28k • written 6.1 years ago by Peter Hickey ▴ 740

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1.0k

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workflows simplesinglecell

updated 6.2 years ago by Aaron Lun ★ 28k • written 6.2 years ago by es.azadian • 0

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simplesinglecell

updated 6.7 years ago by Aaron Lun ★ 28k • written 6.7 years ago by Xingyu • 0

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scater singlecellexperiment simplesinglecell

updated 6.8 years ago by Aaron Lun ★ 28k • written 6.8 years ago by Xingyu • 0

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scater simpleSingleCell workflows

updated 7.4 years ago by Aaron Lun ★ 28k • written 7.4 years ago by sandmann.t ▴ 70

13 results • Page 1 of 1

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Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by Paul • 0

Unfortunately I've updated my code with the newest GRCm39 genome, and yet I am still getting the same error.... Is there anything else I ca…

Comment: WGCNA with TPM tables by ATpoint ★ 4.5k

WGCNA is not a Bioconductor package, but generally: If you want to do serious analysis then find the raw data. There is no guarantee what …

Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by James W. MacDonald 67k

The `EnsDb.Mmusculus.v79` package is mm38, not mm39. If you want a current `EnsDb`, use `AnnotationHub` ``` > library(AnnotationHub) >…

Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…

Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

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Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (

Comment: does anyone how to create rarefaction curves from a phyloseq object?

Answer: ANOVA like approach of edgeR

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

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