23 lines
591 B
R
23 lines
591 B
R
if (!requireNamespace("easy16S", quietly = TRUE)) {
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# install.packages("remotes")
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remotes::install_gitlab(
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repo = "migale/easy16S@main",
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host = "forgemia.inra.fr"
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)
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}
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library(easy16S)
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library(MicroBioMap)
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library(phyloseq)
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library(mia)
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cpd <- getCompendium()
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cpd_phyloseq <- convertToPhyloseq(x = cpd)
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sample_data(cpd_phyloseq)$geo_loc_name |> grepl(pattern = "europe")
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rm(cpd)
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gc()
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sample_data(cpd_phyloseq)
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cpd_phyloseq_europe <- subset_samples(cpd_phyloseq, grepl("europe", geo_loc_name))
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rm(cpd_phyloseq)
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gc()
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easy16S::run_app(physeq = cpd_phyloseq_europe)
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