User: chitsazanalex

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Posts by chitsazanalex

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Comment: C: DistanceToNearest Not giving nearest Range
... Thank you very much! ...
written 10 weeks ago by chitsazanalex0
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Comment: C: DistanceToNearest Not giving nearest Range
... I'm doing more than that. It's a function I have that can map any set of ranges to another, not just annotate peaks as it is in this function. Sometimes it's peaks. Sometimes it's an ENCODE dataset, a bed file, etc. I'd more would like to figure out why DistanceToNearest doesn't chose the nearest ra ...
written 10 weeks ago by chitsazanalex0
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DistanceToNearest Not giving nearest Range
... I'm having trouble why the order of my subject is calling two different nearest cordinates. One is obviously closer, but for some reason it's chosing the first one rather than the actual nearest one. How can I fix this?  Thanks!   Here is my code and a session_info() printout. > ALL_merge ...
granges distancetonearest written 10 weeks ago by chitsazanalex0 • updated 10 weeks ago by Julie Zhu3.8k
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Comment: C: Split Genome into 2kb bins GenomicRanges
... Oh man, that is EXACTLY what I was looking for. Thank you ...
written 4 months ago by chitsazanalex0
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Split Genome into 2kb bins GenomicRanges
... Is there a way to split the entire genome into a genomicRanges of 2kb bins? Im thinking something along that line that uses `seqlengths()` to get chromosome length and then some function to split into 2kb bins, with a GRange for each bin. It's that 'some function' i can't seem to find.    ...
genomicranges written 4 months ago by chitsazanalex0 • updated 4 months ago by Hervé Pagès ♦♦ 13k
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Error with DESeq2 installation
... Im getting the error when trying to install DESeq. I'm installing this on a university cluster interactive node.   > biocLite("DESeq2") BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.2 ...
deseq2 installation rccparmadillo written 11 months ago by chitsazanalex0 • updated 11 months ago by JunLVI40
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Comment: C: GenomicFeatures makeTxDbFromBiomart fails with "unkown species" error
... This solved the problem, thank you ...
written 12 months ago by chitsazanalex0
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Comment: C: GenomicFeatures makeTxDbFromBiomart fails with "unkown species" error
... I'm getting the same error? Weirdly, it works if I use an archived 'host'="jul2016.archive.ensembl.org" > CanFam.txdb <- makeTxDbFromBiomart(biomart = "ENSEMBL_MART_ENSEMBL", + dataset = "cfamiliaris_gene_ensembl", + hos ...
written 12 months ago by chitsazanalex0
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Comment: C: rtracklayer - export.bw bug
... Is there a way to download version 1.35.1? and or a work around hack to get this to work under current framework? I'm having a similar problem that is affecting pipelines but the latest update of rtracklayer is 1.34.0 ...
written 15 months ago by chitsazanalex0

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