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> packageVersion("phyloseq")
> [1] ‘1.4.4’
This is my phyloseq object :
> run1
> phyloseq-class experiment-level object
> otu_table() OTU Table: [ 1388 taxa and 24 samples ]
> sample_data…
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Assess similarities between different time trajectories across body-sites or even across individuals.
The idea here is to be able to find _signals_, where the `x-axis` is time and the `y/z-axes` are …
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Add mouseover definitions for technical terms:
- [x] OTU
- [x] beta diversity
- [x] alpha diversity
- [x] ordination
@gregcaporaso will add definitions here, and @jrrideout will add the mouseover fu…
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1). Split each OTU into sample and control tables to determine which negative control otus to substract
a). echo "split_otu_table.py -i /home/gifl2111/scratch/SMP/split_otu_table_by_body_site/Fore…
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Jonathan suggested using the best-understood microbial ecosystem for the paper. We could analyze enterotypes, and at the very least should analyze the HMP mock communities. HMP mock community data is …
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Depending on the question we wish to ask to our knowledge-base after we have trained our dataset, the problem can be either categorized as a _Classification_ or a _Regression_ problem.
For example. A…
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The species abundance table is the expected data source for this. Some code has been contributed to include some additional analysis and possible simulations for comparison and possibly testing. This …