Bioconductor Cellranger

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CellRanger emptyDrops scRNAseq 10X

10 months ago rocanja ▴ 60

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ReadInR Cellranger GEX+Features+VDJ

3.0 years ago gregoire.destreel • 0

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CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq

updated 2.8 years ago by rohitsatyam102 ▴ 20 • written 3.0 years ago by gregoire.destreel • 0

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single-cell 10X Cell calling DropletUtils cellranger

updated 5.9 years ago by Aaron Lun ★ 28k • written 5.9 years ago by xingxd16 ▴ 20

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Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by jodan • 0

Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…

Answer: Unused arguments error without used arguments in GSVA? by jodan • 0

It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and max…

Answer: Using genomicRanges / plyranges to calculate score of peaks within intervals by Michael Love 43k

This should be possible with plyranges using `join_overlap` and `group_by` on the metadata from the tile. E.g. create `tile.id` as a variab…

Answer: Reducing and aggregating GRanges with gaps using plyranges by Michael Love 43k

I added `min.gapwidth` to `reduce_ranges()` in recent plyranges releases: https://github.com/tidyomics/plyranges/pull/105

Answer: Find exact GRanges match keeping metadata columns by Michael Love 43k

You could use `minoverlap` but that requires an integer, not a fraction: ``` gr1 |> join_overlap_left(gr2, minoverlap=6) ``` Plyranges do…

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Answer: Unused arguments error without used arguments in GSVA?

Unused arguments error without used arguments in GSVA?

Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte

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Teacher to Axel Klenk ★ 1.1k