User: lee.s

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lee.s70
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Posts by lee.s

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Understanding group_by, reduce_ranges,
... it seems like the support site code editor doesn't show the bracket - how strange! What do you mean by the second part? ...
written 4 weeks ago by lee.s70
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Comment: C: Understanding group_by, reduce_ranges,
... could you try running the example in a clean session? ...
written 5 weeks ago by lee.s70
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Comment: C: Understanding group_by, reduce_ranges,
... how odd I can't seem to reproduce this on my end ``` r suppressPackageStartupMessages(library(plyranges)) set.seed(42) pos <- sample(1:10000, size = 100) size <- sample(10:50, size = 100, replace = TRUE) strand <- sample(c("+","-"), size = 100, replace = TRUE) rep1 <- data.frame(seqname ...
written 5 weeks ago by lee.s70
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Comment: C: Understanding group_by, reduce_ranges,
... what version of plyranges are you using? could you post your sessionInfo or provide a reprex? ...
written 5 weeks ago by lee.s70
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Answer: A: Understanding group_by, reduce_ranges,
... Hi Konstantinos, > r1 and r4 are identical, as r2, r3, r5. Although we start from 500 ranges with grouping by strand and replicate it keeps 457 ranges. In my specific case, I have the information about the strand and using whichever of the "r2,r3,r5" ways to collapse the Granges probably it does ...
written 5 weeks ago by lee.s70
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Comment: C: Annotating GRanges with TxDb gene models using plyranges
... Hi Aditya, I've fixed the left overlap join modifying the seqinfo in the current and devel versions of plyranges. I'm currently working on a big overhaul of how plyranges does grouping so will chime back in to give you a proper answer to your query soon! ...
written 5 weeks ago by lee.s70
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Comment: C: extracting gene names, gene id and transcript id
... Yes you're right, thanks! - the backend of the readers use import so read_gff() should still work. I should update plyranges to explicitly include gtf. ...
written 15 months ago by lee.s70
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Comment: C: the closest gene to a breakpoint
... Another option is to use join_nearest() or pair_nearest() from plyranges ...
written 15 months ago by lee.s70
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Answer: A: extracting gene names, gene id and transcript id
... Another option with plyranges library(plyranges) gr <- read_gff("your_file.gtf") %>% select(gene_id, gene_name, transcript_id) ...
written 15 months ago by lee.s70
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Comment: C: subsetByOverlaps : comparing GRANGES and keeping all the information in the MET
... Hi Bogdan, You need R >= 3.5 so you can use Bioc 3.7. Thanks, Stuart ...
written 15 months ago by lee.s70

Latest awards to lee.s

Scholar 16 months ago, created an answer that has been accepted. For A: subsetByOverlaps : comparing GRANGES and keeping all the information in the MET
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: subsetByOverlaps : comparing GRANGES and keeping all the information in the MET

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