Bioconductor Cell calling

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DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling

updated 4.5 years ago by Aaron Lun ★ 28k • written 5.6 years ago by C T ▴ 140

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single-cell 10X Cell calling DropletUtils cellranger

updated 6.1 years ago by Aaron Lun ★ 28k • written 6.1 years ago by xingxd16 ▴ 20

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Answer: fast apply on RleList by story.benjamin ▴ 20

solved with viewApply (code is simplified below) test.split <- split(test.gr,seqnames(test.gr)) final.stats <- mclapply(uniqu…

Comment: fast apply on RleList by story.benjamin ▴ 20

Hi James, thanks for the reply. I ultimately figured it out ... viewApply showed a massive speed increase for me (see other answer) - I was…

Answer: fast apply on RleList by James W. MacDonald 68k

There is already a 'mean' function that will dispatch on an `RleList` that you can use. I don't have a long `RleList` in hand to test it on…

Answer: Custom CDF creation for HTA 2.0 array using GTF annotation by James W. MacDonald 68k

It doesn't appear that Manhong Dai is working at UM any longer, and the webpage appears to have fallen into disrepair (for example, the lin…

Comment: how to use `arrayWeightsQuick()`? by matthew • 0

In the specific use-case I have in mind, `expression` is a simple `matrix` of log2 gene expression per sample, no missing values.

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Answer: BiocParallel_1.40.1.tar.gz not available

Comment: BiocParallel_1.40.1.tar.gz not available

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