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After a talk with @shiraz-shah, we should investigate if we can estimate the abundance more accurately.
He recommended using msamtools with 80% query coverage, 95% id over 80 bp, and using `msamtools…
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Changes are needed for **tracegroomer** galaxy wrapper:
- [x] update citation
- [x] there is an output file named in the wrapper "corrected isotope abundances" but it is misleading because it c…
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Hi,
I am processing samples via apLCMS. I notice that the abundance/area from RAW files do not match with abundance/area from apLCMS. Area/abundance from apLCMS is always higher than abundance from…
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https://github.com/vjjan91/nilgiris-resurvey-project/blob/916ead6085b23d12d5650c17f63404c6fa7fdc95/code/xx_relative-abundance-envtChange.Rmd#L6C1-L6C10
@pratikunterwegs I have currently removed thi…
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In this manuscript DAA methods have been benchmarked and a new method was proposed: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01320-0 we should check if any of these meth…
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Additional visualization options
- [ ] Cladogram
- [x] Abundance plot (Histogram)
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Dear Dr. Sean,
I hope this message finds you well. I am writing to express my admiration for your recent publication in Current Biology titled "High viral abundance and low diversity are associated…
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Hi,
We've been trying to simulate Zymo mock communities using your "even" pre-trained model. We've consistently found *Staphylococcus aureus* to be seemingly undersimulated, while *Cryptococcus neo…
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In order to consult other translations, interpretations and commentaries, it could be useful to separate the descriptions from the logic. Given the structure of the I Ching and the Ten Wings, a machin…
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I am trying to run ggpicrust2, and am having an issue. Below is the script I'm running:
# Load necessary data: abundance data and metadata
KO_abundance_file