User: andres.firrincieli

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Posts by andres.firrincieli

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Comment: C: Network analysis: where to start?
... This is old but it is good start: [link][1] Have fun! [1]: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-328 ...
written 29 minutes ago by andres.firrincieli960
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Answer: A: Attempt to set 'rownames' on an object with no dimensions
... Try this: rownames(SpiecEasi.matrix$refit$stars) <- colnames(amgut1.filt) ...
written 1 day ago by andres.firrincieli960
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Comment: C: Network analysis: where to start?
... > I would like to understand how to study likely correlation between > genes differentially expressed, if that makes any sense to you? just a thought but my understanding is that a correlation network built with differentially expressed gene is less informative than a simple heatmap with hier ...
written 2 days ago by andres.firrincieli960
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Comment: C: Picrust2 and EC description
... Hi Claire, upload your EC numbers as `txt` file: 1.1.1.116 1.1.1.137 ... And then run KEGG mapper in Reference mode ...
written 4 days ago by andres.firrincieli960
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Answer: A: Picrust2 and EC description
... Hi Claire, for the pathways use this link: https://www.genome.jp/kegg/tool/map_pathway1.html ...
written 5 days ago by andres.firrincieli960
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Answer: A: Metabolomics / Transcriptomics dataset?
... Hello Federico, I would try with this one: [link][1], but with microarray data... More studies in human can be found here: [metaboLight][2], but unfortunately the database does not have a search function which allows you to check for studies with metabolomic and transcriptomic data. I hope this h ...
written 7 days ago by andres.firrincieli960
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Answer: A: SparCC repository gone
... fast_sparCC was extremely painful to install. So if someone is having problems with fast_sparCC installation you can try with fastspar: https://github.com/scwatts/fastspar ...
written 9 days ago by andres.firrincieli960
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Comment: C: SparCC repository gone
... The fast version is just perfect. Thank you! ...
written 9 days ago by andres.firrincieli960
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SparCC repository gone
... It seems that the SparCC repository does not work anymore: https://bitbucket.org/yonatanf/sparcc/downloads/ Does anyone have a link with the SparCC python sricpts? Thanks! ...
sparcc co-occurence network written 10 days ago by andres.firrincieli960
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Comment: C: 16S amplicon sequencing unequal read lengths
... Hi, I do not recall why the Illumina add one base at the end of the read but you could use the Force-trim modulo (`ftm`) of bbduk to remove the very last base. Here is an explanation of how this works: > The right end so that the read’s length is equal to zero modulo 5 > (ftm=5). The reason ...
written 16 days ago by andres.firrincieli960

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