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I have been making extensive use of ggtree in my work (its wonderful). I are about to release an R package for microbiome data analysis as we submit for publication. In our package I currently have im…
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Hi all,
In the [tutorial](http://benjjneb.github.io/dada2/tutorial.html) you input taxa and seqtab.nochim to phyloseq without prior normalization/subsampling. Does that mean that we don't need to nor…
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Hi
So ive tried to search through the old posts in the forum to find answers to my problem. I am quite new in R, and I am not sure how to approach this.
Im working on 16s sequence data. Im looki…
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"Bioconductor (http://www.bioconductor.org/) is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based prima…
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Hi All,
There were files called BIOM files for every case study where the data was stored @ QIITA. I was about to download the data but now i see that the site itself has been changed and there are no…
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Hi yours,
My data have two batches. I used DESeq2 to normalize the count data and model the batch effect with “Design=~Batch+Treatment”. Then, I used rlog function the same as Shiny-phyloseq except I…
pl618 updated
8 years ago
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--microbiome --skipPreliminary
those 2 options does not work properly
input for microbiome is fastq but supposed to be fasta
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Using the following PDF as reference....
http://www.nature.com/nature/journal/v486/n7402/pdf/nature11234.pdf
Selecting the abstract text and doing a copy paste into a text editor results in a string…
dwhly updated
8 years ago
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I've been going through the phyloseq tutorials, trying to implement the negative binomial variance stabilization by way of DESeq, (as in the 'Waste not, want not' paper) and I'm running into a bit of …
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P. J. Turnbaugh, V. K. Ridaura, J. J. Faith, F. E. Rey, R. Knight, J. I. Gordon, The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice. Sci. Transl. Med.…