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Right now, I'm realizing its rather difficult to use the quantities feature at all, unless your farmOS server already has an extensive list of units available. From the Drupal application, it's pretty…
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The current `Dataset` has type and subtype which is slightly problematic. `Type` is really indicating the row format used in the DwC-A and causes problems since a checklist can have occurrences, and a…
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Notes from my Jan. 31, 2014 email:
I know that today we were leaning away from the idea of possibly using OGC Domain Features for taxa (discussion threads on Taxonomic Classifiers in #4 & #15), how…
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Simple premise: use merge_samples to do exactly that but on different "merging" functions. Specifically: mean (the default), sd, and sum. In R terms:
md1 = merge_samples(OTU,"descriptor",fun=mean)
…
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2020/01/26 TODOs and suggestions from @smroecker
## Core R data manipulation functional themes:
- loading/fetching data
- filtering
- transforming
- aggregating
- iterating
### TOD…
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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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Hi-
Within DESeq you normally apply some sort of contrast with the results function i.e. (from: https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-mixture-model…
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Hi Chi
Firstly thank you very much for microeco package.
I try to run the relative abundance for dominant functions using the package's dataset using the following script.
library(microeco)
fun_16…
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It is possible to get the classification for some interesting functional genes:
I want to know both the abundance and the classification for AOA, AOB, nirK/S and nosZ; wonder how can I do this usin…
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Create a taxonomic database from the existent species table. Once established, a post-processing workflow will be created to recognize when new taxa have been added to the synthesized species table an…