Bioconductor Cellranger

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CellRanger emptyDrops scRNAseq 10X

14 months ago rocanja ▴ 60

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ReadInR Cellranger GEX+Features+VDJ

3.3 years ago gregoire.destreel • 0

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CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq

updated 3.0 years ago by rohitsatyam102 ▴ 20 • written 3.3 years ago by gregoire.destreel • 0

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single-cell 10X Cell calling DropletUtils cellranger

updated 6.2 years ago by Aaron Lun ★ 28k • written 6.2 years ago by xingxd16 ▴ 20

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Comment: parameters of filterByExpr by caroline.zanchi ▴ 10

It worked, I think I finally understand and accept that fact. Sorry and thank you again !

Comment: parameters of filterByExpr by Gordon Smyth 52k

You seem to be coming back to the same fixed (but incorrect) idea of what filterByExpr() should be doing. I have tried to explain that filt…

Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi by Gordon Smyth 52k

modelMatrixMeth() works correctly. The second replicate factor has not been lost. Please do not make ad hoc manual modifications to the de…

Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k

Probably not. Any given gene may be appended with many different GO terms, so you would end up with something that is not very useful. ``…

Comment: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k

`heatmap.2` is a CRAN package, and that's the relevant issue for this plot. It's got nothing to do with `DESeq2` or any other Bioconductor …

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Answer: LogFC values in edgeR - w/wo intercept

How to formulate 2 factor nested design in DESeq2

Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm

Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)

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