User: Vang Le

gravatar for Vang Le
Vang Le70
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70
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Denmark
Last seen:
8 months ago
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3 years, 3 months ago
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v**@rn.dk

Posts by Vang Le

<prev • 14 results • page 1 of 2 • next >
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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 8 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 10 months ago by Vang Le70 • updated 10 months ago by Michael Lawrence9.8k
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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 11 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 19 months ago by Vang Le70 • updated 19 months ago by Martin Morgan ♦♦ 20k
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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 21 months 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 21 months ago by Vang Le70 • updated 21 months ago by Michael Lawrence9.8k
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count overlapping reads for CpG islands and annotate with gene names?
... I am using Ensembl gene model for rat. I want to count reads that are mapped to CpG islands which overlaps with the regions flanked by  geneStart-2kbase and geneStop + 2kbase. I want to avoid false read count by reads mapped to non-methylated areas,  therefore I want count reads overlapping CpG isla ...
annotation rattus norvegicus chippeakanno medip-seq written 21 months ago by Vang Le70
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Comment: C: edgeR, very big lib.size makes CPM very small
... Thank you for the confirmation, Gordon. Even though it might be a small thing, but very assuring for me to know. Best regards Vang On 15 Aug 2014, at 03:04, Gordon K Smyth > wrote: Date: Wed, 13 Aug 2014 13:37:23 +0000 From: Vang Quy Le / Region Nordjylland > To: "bioconductor at r-project. ...
written 3.3 years ago by Vang Le70
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edgeR, very big lib.size makes CPM very small
... Hello, I am working with count table that has very big lib.size: > dge at .Data[[2]]$lib.size [1] 3.2e+08 4.2e+08 4.5e+08 3.8e+08 2.3e+08 2.1e+08 3.3e+08 2.8e+08 This causes CPM very small, and consequently very negative logCPM. This is 'head' of my cpm(counts): C1 C2 C3 ...
written 3.3 years ago by Vang Le70 • updated 3.3 years ago by Gordon Smyth32k
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Comment: C: edgeR: Analyze mini-time-series MeDIP data of pooled DNAs without replicates
... That?s it! Thanks for the clarification, Gordon. I was looking at ?estimateGLMCommonDisp and ?voom to see input/output compatibility. Thanks again for your help. Best wishes to you too. Vang On 13 Aug 2014, at 07:00, Gordon K Smyth > wrote: Dear Vang, There is still a misunderstanding. You ca ...
written 3.3 years ago by Vang Le70

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