Process Nanopore EPI2ME Output for Use in R


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Documentation for package ‘epi2me2r’ version 0.1.0

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