Bioconductor Slingshot

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monocle slingshot

19 months ago EspressoKris ▴ 10

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tradeSeq slingshot

2.8 years ago manduchi ▴ 10

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slingshot plot3d.SlingshotDataSet

updated 11 months ago by Kelly Street • 0 • written 2.9 years ago by manduchi ▴ 10

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Slingshot

updated 5.1 years ago by Martin Morgan 25k • written 5.1 years ago by Adrian Johnson ▴ 330

4 results • Page 1 of 1

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Comment: How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignm by Charles • 0

I am trying this but it is slow. ``` aln2mismatches <- function (gal) { gr <- GRanges(gal) irl <- cigarRangesAlongReferenceSpace(cigar…

Answer: DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change by James W. MacDonald 68k

Yes, you can simply flip the sign of the logFC to reverse the direction of the comparison.

Comment: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k

The argument for annotation_col is meant to be a `data.frame`, not a vector. The hint in the error is that it has the wrong number of dimen…

Comment: Heatmap of a transformed deseq object with pheatmap by caroline.zanchi • 0

I used this argument in the second paragraph of code forthe heatmap, this is wehre I got the message Error in `[.default`(annotation_col, c…

Answer: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k

Ah, yes. The non-ASCII character error. My favorite! Please note that `pheatmap` is not a Bioconductor package, so you should be asking …

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Comment: Heatmap of a transformed deseq object with pheatmap

DESeq2: Question about the alpha in summary() and results()

Comment: How to load scRNA-seq data from GEO

limma correction for tumor purity

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