User: grp2009

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grp20090
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Posts by grp2009

<prev • 6 results • page 1 of 1 • next >
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What does SNPRelate::snpgdsDiss calculate?
... The documentation for the `snpgdsDiss` function in the `SNPRelate` package says: > The details will be described in future. The description of the function is > Calculate the individual dissimilarities for each pair of individuals. What exactly does this function calculate and where can I ...
snprelate written 9 weeks ago by grp20090 • updated 9 weeks ago by zhengx30
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Comment: C: Metaphlan2 marker database used by curatedMetagenomicData
... Excellent, thanks! ...
written 11 months ago by grp20090
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Comment: C: Metaphlan2 marker database used by curatedMetagenomicData
... Thanks Levi. A few questions: - Are viruses not included in the output of getMetaphlanTree? If I run it (with simplify=F to show full taxonomy) I see Archaea and Bacteria but no Viruses - Is it possible to distinguish an organism that was not found in a sample from an organism that was not looked ...
written 11 months ago by grp20090
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Metaphlan2 marker database used by curatedMetagenomicData
... Which version of the Metaphlan2 marker database was used to generate the marker and bug abundance data in curatedMetagenomicData? I am looking for some species that are represented in v20 of the Metaphlan2 marker database, but can't find them in the curatedMetagenomicData package. If an earlier mark ...
curatedmetagenomicdata written 11 months ago by grp20090 • updated 11 months ago by Levi Waldron950
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In ggbio, plot transcripts from a TxDb with gene labels
... I am trying to change the labels in ggbio's autoplot output (specifically, when the input is a TxDb) so that the transcripts are labelled with the corresponding gene symbol. What I'm starting with is the following code: library(ggbio) library(GenomicRanges) wh <- GRanges(seqnames='chr18', ...
ggbio written 2.5 years ago by grp20090 • updated 2.5 years ago by Michael Lawrence11k
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Writing a biom (JSON) file using biomformat package
... I am unable to create a biom (JSON, aka BIOM 1.0.0) format file using the biomformat package. Here is my attempt to make a simple biom (JSON) file: library(biomformat) otu <- as.data.frame( matrix(rpois(9,10),nrow=3) ) rownames(otu) <- c('OTU1','OTU2','OTU3') colnames(otu) <- c('Sampl ...
json biomformat written 2.5 years ago by grp20090

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