Bioconductor SimpleSingleCell

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DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling

updated 4.9 years ago by Aaron Lun ★ 29k • written 6.0 years ago by C T ▴ 140

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1.8k

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simpleSingleCell

updated 6.1 years ago by Aaron Lun ★ 29k • written 6.1 years ago by Angelos Armen • 0

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967

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simpleSingleCell

updated 6.1 years ago by Aaron Lun ★ 29k • written 6.1 years ago by Angelos Armen • 0

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DropletUtils EmptyDrops simpleSingleCell

updated 3.1 years ago by Stefano Mangiola ▴ 40 • written 6.1 years ago by shbrief ▴ 20

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2.3k

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scran simpleSingleCell

updated 6.1 years ago by Aaron Lun ★ 29k • written 6.1 years ago by Angelos Armen • 0

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limma edgeR simplesingleCell scran scater

updated 6.1 years ago by Aaron Lun ★ 29k • written 6.1 years ago by Bogdan ▴ 670

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2.2k

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SingleCellExperiment scran limma simpleSingleCell

updated 6.3 years ago by Aaron Lun ★ 29k • written 6.3 years ago by Matt Mulé • 0

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DropletUtils SingleCellExperiement DelayedArray simpleSingleCell

updated 6.3 years ago by Aaron Lun ★ 29k • written 6.3 years ago by Steve Pederson ▴ 170

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3.5k

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singlecellexperiment dropletutils simplesinglecell

updated 6.9 years ago by Aaron Lun ★ 29k • written 6.9 years ago by Peter Hickey ▴ 760

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1.2k

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workflows simplesinglecell

updated 7.0 years ago by Aaron Lun ★ 29k • written 7.0 years ago by es.azadian • 0

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simplesinglecell

updated 7.5 years ago by Aaron Lun ★ 29k • written 7.5 years ago by Xingyu • 0

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scater singlecellexperiment simplesinglecell

updated 7.6 years ago by Aaron Lun ★ 29k • written 7.6 years ago by Xingyu • 0

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scater simpleSingleCell workflows

updated 8.2 years ago by Aaron Lun ★ 29k • written 8.2 years ago by sandmann.t ▴ 70

13 results • Page 1 of 1

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Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …

Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k

> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…

Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k

The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…

Comment: voomLmFit fitted log-CPM values by Lina ▴ 10

Is the output from fitted(v) in the log2 CPM scale? or CPM scale?

Answer: voomLmFit fitted log-CPM values by Gordon Smyth 53k

Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```

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A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea

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