Function reference
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CARD_taxonomy - CARD 3.1.4 and 1.1.3 aro_index hand curated and combine
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amr_raw_to_metagenomeseq - Raw AMR files plus metadata to phyloseq object
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amr_raw_to_phyloseq - Raw AMR files plus metadata to phyloseq object
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amr_read_taxonomy - assign taxonomy for phylogenetic and AMR for each read
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epi2me2r - epi2me2r.
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generate_amr_taxonomy - Generates a taxonomy file for AMR count table
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generate_wimp_taxonomy() - Generates a taxonomy file for WIMP court table using taxonomizr
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read_in_amr_files - Convert raw AMR CSV files to data table
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read_in_wimp_files() - Convert raw WIMP CSV files to data table
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wimp_raw_to_metagenomeseq() - Raw WIMP files plus metadata to metagenomeseq object
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wimp_raw_to_phyloseq() - Raw WIMP files plus metadata to phyloseq object