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Hi, very cool repo!
I had a small question regarding the last few bullet points in the readme workflow, as I have been thinking of implementing something similar to address the fact that most MAGs ge…
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Hi all,
I have a phyloseq object ps containing ID for over 200 samples and 10 sampling sties. Before plotting anything, I normalized the sampling depth by following the DEseq approach as shown bel…
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We should repeat the analysis after filtering the data removing potentially poor quality features. Potential criteria could be:
- RSD in QC samples > 30%
- *weights*/detected calls
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Goal: write a script/method that transforms the `x` vector returned by [MinDivLP.py ](https://github.com/KoslickiLab/DiversityOptimization/blob/master/PythonCode/src/MinDivLP.py) into a format used by…
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Hi DADA2 help,
We used DADA2 to process our PacBio HiFi reads from two machines: SeqII and Revio. We completed the DADA2 pipeline for both, but encountered an issue with the Revio samples—only abou…
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Hi
I'm sorry, but could you please help me on this, so I have determined the relative abundance for each bin, but I wanted to normalize the values according to the overall metagenome, but I really no…
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Hi,
I have been running simper without problems
simper(fourth_root_sqrt_OTU_abundances_relative, AGDX_samples$Fjord, permutations=1000)
However, when I tried to repeat the analysis with simper.…
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The max relative abundance for samples are 1, but when I plot bar plot for case vs control is greater than one. What do you suggest?
physeq11 = transform_sample_counts(physeq1 , function(OTU) OTU/su…
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Some microbiome studies are starting to report measures of absolute abundance in addition to sequencing read counts and relative abundances. The `MicrobiomeExperiment` could/should support incorporati…
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Hi
I have ran a microbiome modeling data with 95 samples and about 200 taxons.
But it's about 3weeks that is performing FVA with CPLEX 128 (fvatype=1) on 1 sample without any changing. Matlab shows …