Bioconductor Recount2

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TCGAbiolinks RECOUNT2 DESeq2

updated 3.8 years ago by Michael Love 43k • written 3.8 years ago by xiaofeiwang18266 ▴ 50

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R TCGA recount2 recount

updated 4.8 years ago by Leonardo Collado Torres ★ 1.1k • written 4.9 years ago by alex.v.nesta • 0

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recount recount2 RangedSummarizedExperiment

updated 5.4 years ago by Leonardo Collado Torres ★ 1.1k • written 6.2 years ago by k.vitting.seerup ▴ 120

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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…

Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0

It was due to the comma. Thank you!

Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k

Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…

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Teacher to Axel Klenk ★ 1.1k