User: Vang Le

gravatar for Vang Le
Vang Le70
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70
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Location:
Denmark
Last seen:
5 days ago
Joined:
3 years, 11 months ago
Email:
v**@rn.dk

Posts by Vang Le

<prev • 18 results • page 1 of 2 • next >
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Comment: C: AnnotationHub, force update snapshot date?
... Not possible to upgrade to R 3.5 now, but I believe it will solve the problem as you suggested. Thanks   ...
written 5 days ago by Vang Le70
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AnnotationHub, force update snapshot date?
... Somehow I can't get the latest date: > library(AnnotationHub) > ah <- AnnotationHub() snapshotDate(): 2017-10-27 > query(ah, c("norvegicus", "release-92")) AnnotationHub with 0 records # snapshotDate(): 2017-10-27 Is there cache data somewhere that I need to delete? > sessionInf ...
annotationhub written 5 days ago by Vang Le70 • updated 5 days ago by shepherl ♦♦ 650
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Comment: C: 'downstream' disappeared from GenomicRanges package?
... Thank you Martin. I will look into that function but I am hesitated to use it before finding some better solution. This is because I don't work anything with variants for this data. Can follow or precede do the job? ...
written 7 days ago by Vang Le70
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'downstream' disappeared from GenomicRanges package?
... I have a legacy script using `downstream` function which I believe it is from GenomicRanges package. I may be wrong, then I would like to know the correct package to use. I found out about this after updating to bioconductor version 3.6 (see full sessioninfo below). > sessionInfo() R version 3. ...
genomicranges written 8 days ago by Vang Le70
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Job: Bioinformatician in Aalborg University Hospital, Denmark
... Aalborg University Hospital Section of Molecular Diagnostics We are looking for a motivated bioinformatician to strengthen and expand bioinformatic work force in response to increasing needs of a molecular diagnostic group utilizing big data. Application deadline: 19th of April 2017 Core tasks D ...
job bioinformatician job written 16 months ago by Vang Le70
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count coverage for exact matches to sequence pattern
... I have BSgenome hg19, a GTF file containing gene coordinates, and a BAM file. This is what I want to do: 1. Search for all occurrences of my sequence, and save the coordinates in a range objects. Following is the current implementation, but the output found coordinates are based on the first bases ...
genomicfeatures rsamtools written 18 months ago by Vang Le70 • updated 18 months ago by Michael Lawrence10k
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Comment: C: resize (shrink/expand) GenomicRanges
... I want to do the same thing, like to include promoter regions (2kb upstream) to my genes. I wonder what is the reasons for not having this feature in GenomicRanges package until now? I was also trying to use `resize` function for this purpose. Luckily I found this thread. ...
written 19 months ago by Vang Le70
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extract chromosomes and read-starts from a BAM file to a data.frame?
... like the title says, I am looking for a concise and high-performance way to extract only the chromosome name and read start position from a BAM file. It can be easily done from outside R like this: samtools view my.bam |cut -f 3,4 but I want to try it within R code. Calling command via `system` i ...
rsamtools genomicalignments bam samtools written 2.2 years ago by Vang Le70 • updated 2.2 years ago by Martin Morgan ♦♦ 22k
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Answer: A: rtracklayer /GRange object to BED format?
... Well. as.data.frame(cpgcano) give almost what I want. I bit of more adjustment will do. Consider case close.   ...
written 2.4 years ago by Vang Le70
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rtracklayer /GRange object to BED format?
... What is a quick way to convert the `cpgcano` object below to a data.frame that is BED6 format? I need to write out this BED6 format to work with tools outside R. Thanks   library(rtracklayer) session <- browserSession() genome(session) <- "rn6" cpg <- session[["CpG Islands"]] methods(cla ...
rtracklayer granges written 2.4 years ago by Vang Le70 • updated 2.4 years ago by Michael Lawrence10k

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