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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.…
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Hi everyone,
I'm trying to apply FDR-adjusted test on UniFrac distances...does anyone know how to perform it?
I imagine that at first I should perfom _distance(data,"wunifrac") _ but then? Have a ni…
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Hi all,
I am trying to compare alpha diversities for my dataset and was able to plot the data as follows:
``` rsplus
plot_richness(mydata, x="condition", measures=c("Shannon"))
```
I have four cond…
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Hi Kevin,
I'm trying to run kwip on metgenomic datasets. These are Illumina 2 X 150 paired end reads. I have a total of 90 samples with an average number of 1.5 million read pairs.
Unfortunately I'…
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Hi,
I would like to request your help in creating a phyloseq object for further analysis. This is the first time am getting to use phyloseq and am eager to see some plots and perform some analysis.
My…
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Have you, the snpr core, thought about adding support for importing data from ubiome? I thought about making an "opensnp for ubiome" but realized it's probably better to just add ubiome support to snp…
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Hi,
## not exactly an issue but request fro help
I am unable to get a output file which can be used by Tax4Fun post Dada2 processing. I tried the otu_table and write_biom options to get a table cont…