User: Marlin

gravatar for Marlin
Marlin20
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20
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New User
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Last seen:
1 month, 4 weeks ago
Joined:
2 years ago
Email:
m******@gmx.cn

"In those days spirits were brave, the stakes were high, men were real men, women were real women, and small furry creatures from Alpha Centauri were real small furry creatures from Alpha Centauri. And all dared to brave unknown terrors, to do mighty deeds, to boldly split infinitives that no man had split before."

Posts by Marlin

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Import gff from character?
... Sorry, Martin, it was my fault, I was using import.gff and thought the arguments are passed to import, your example works for me. Thanks! ...
written 14 months ago by Marlin20
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Import gff from character?
... rtracklayer::import for signature "GFFFile,ANY,ANY" has an argument text, the help page says: ## S4 method for signature 'GFFFile,ANY,ANY' import(con, format, text, version = c("", "1", "2", "3"), genome = NA, colnames = NULL, which = NULL, feature.type = NULL, se ...
rtracklayer gff import.gff3 gtf import written 14 months ago by Marlin20 • updated 14 months ago by Martin Morgan ♦♦ 22k
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Comment: C: converting fasta file into bam file
... I think fasta format and bam format represent totally different things, one is for sequence, the other is for alignment. Could you clarify it? ...
written 14 months ago by Marlin20
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Comment: C: Long elapsed time using `import.gff3` with a toy example
... Martin, always thanks for your incisive help. I installed the BSgenome and BSgenome.Hsapiens.UCSC.hg19 packages and it solved the problem. ...
written 22 months ago by Marlin20
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Long elapsed time using `import.gff3` with a toy example
... Dear all, I encountered a really long elapsed time for importing a small toy gff3 file  when using `import.gff3()`, here is what I did: > library(rtracklayer) > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > txdb = TxDb.Hsapiens.UCSC.hg19.knownGene > grl.exons = exonsBy(txdb, by = 'tx' ...
rtracklayer import.gff3 written 22 months ago by Marlin20 • updated 22 months ago by Martin Morgan ♦♦ 22k
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makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)
... For a GTF file downloaded from iGenome, say, hg19.gtf, a significant proportion of genes will be dropped without warning when use makeTxDbFromGFF to import it. As I examined those genes in the source GTF file, I believe the genes with multiple chromosome locations (e.g. chr1 and chr2) will be dropp ...
genomicfeatures gtf maketxdbfromgff igenome written 22 months ago by Marlin20 • updated 22 months ago by Martin Morgan ♦♦ 22k
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Comment: C: Gviz: Plot only exons?
... Hey, I just want to comment a convenient way to do this, for anyone who might look at it. It can be done with:  exon <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, 'tx')[42] exon_mapped <- GenomicFeatures::mapToTranscripts(exon[[1]],exon) And this is just the intended transformation of the e ...
written 2.1 years ago by Marlin20
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ggbio: untransformed coordinate when using `tracks` function with IRanges or numeric value as `xlim`
... I encountered a problem regard to coordinate transformation when using tracks function in ggbio package. An example is here: # Create a GRanges and plot it normally library(ggbio) gr = GRanges('chr2', IRanges(start = 50, end = 100)) p = ggplot(gr) + geom_rect() p   # However, when it is wrapp ...
ggbio tracks written 2.1 years ago by Marlin20 • updated 2.0 years ago by oswaldo.lorenzo10

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