User: Kyle Johnsen

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Posts by Kyle Johnsen

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Comment: C: Can I create a GmapGenome with a relative file path?
... Great, thank you! ...
written 6 months ago by Kyle Johnsen0
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Comment: C: Can I create a GmapGenome with a relative file path?
... Yes it does ...
written 7 months ago by Kyle Johnsen0
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Can I create a GmapGenome with a relative file path?
... I'm developing a package which uses a GmapGenome in calling variants, and therefore am trying to create a small GmapGenome (out of a fasta file for just one chromosome) in my unit tests. The problem I run into, however, is that GmapGenome seems not to work for relative file paths. I confirmed this ...
gmapr gmapgenome fastafile written 7 months ago by Kyle Johnsen0 • updated 7 months ago by Michael Lawrence9.8k
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Using GRanges and IRanges to simply get all chromosome data
... Hi! I have basically two questions. I'm trying to analyze RNA-seq data, contained in BAM files, using applyPileups. The ApplyPileupsParam, however, needs the 'which' paremeter, which needs a GRanges object. Is there an easy way to, say, get all chromosomes from a file (not contigs)? And since it ...
iranges granges written 15 months ago by Kyle Johnsen0 • updated 15 months ago by Martin Morgan ♦♦ 21k

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