Man pages for joelewis101/blantyreESBL
Data and Code Repository For a Study Describing Antimicrobial Resistance in Blantyre, Malawi
| btESBL_amrgenes | Data: AMR genes identified in sequenced isolates (excluding... |
| btESBL_AST | Data: Antimicrobial sensitivity testing for a suvet of... |
| btESBL_CARD_qrdr_mutations | Data: CARD described QRDR mutations |
| btESBL_contigclusters | Data: Contig cluster membership |
| btESBL_contigclusters_msa_alignments | Data: Contig cluster multiple sequence alignments as... |
| btESBL_contigclusters_msa_blastoutput | Data: Contig clusters BLASTed against ISFinder,... |
| btESBL_contigclusters_msa_paf_files | Data: Contig cluster multiple sequence alignment .paf files |
| btESBL_contigclusters_sensax | Data: Contig cluster assignment in sensitivity analyses |
| btESBL_coregene_tree_esco | Data: E. coli core gene tree |
| btESBL_coregene_tree_kleb | Data: K. pneumoniae complex core gene tree |
| btESBL_ecoli_global_popPUNK_clusters | Data: popPUNK cluster assignment of study E. coli isolates... |
| btESBL_ecoli_globalst131_tree | Data: E. coli ST131 global phylogeny |
| btESBL_ecoli_globalst167_tree | Data: E. coli ST167 global phylogeny |
| btESBL_ecoli_globalst410_tree | Data: E. coli ST410 global phylogeny |
| btESBL_ecoli_globaltree | Data: E.coli global context tree |
| btESBL_ecoli_horesh_metadata | Data: metadata of 10,146 global E. coli genomes from Horesh... |
| btESBL_ecoli_musicha_metadata | Data: Accession numbers and metadata of 97 E. coli genomes... |
| btESBL_ecoli_st131_amr | Data: AMR genes identified in global ST131 isolates |
| btESBL_ecoli_st131_metadata | Data: metadata of global E. coli ST131 isolates |
| btESBL_ecoli_st131_plasmids | Data: Plasmid replicons identified in global ST131 isolates |
| btESBL_ecoli_st167_amr | Data: AMR genes identified in global ST167 isolates |
| btESBL_ecoli_st167_metadata | Data: metadata of global E. coli ST167 isolates |
| btESBL_ecoli_st167_plasmids | Data: Plasmid replicons identified in global ST167 isolates |
| btESBL_ecoli_st410_amr | Data: AMR genes identified in global ST410 isolates |
| btESBL_ecoli_st410_metadata | Data: metadata of global E. coli ST410 isolates |
| btESBL_ecoli_st410_plasmids | Data: Plasmid replicons identified in global ST410 isolates |
| btESBL_exposures | Data: Exposures of included participants |
| btESBL_kleb_global_metadata | Data: Accession numbers and metadata of 682 global K.... |
| btESBL_kleb_globaltree | Data: K. pneumoniae complex global context phylogeny |
| btESBL_kleb_malawi_allisolate_core_gene_tree | Data: K. pneumoniae complex core gene tree of Malawian... |
| btESBL_model1posterior | Data: Posterior of fitted carriage model (constant... |
| btESBL_model2posterior | Data: Posterior of fitted carriage model (decaying... |
| btESBL_model2simulations | Data: Results of simulations from the model posterior |
| btESBL_model2simulations_2 | Data: Summary of results of simulations from model2 posterior... |
| btESBL_model3posterior | Data: Posterior of fitted carriage model (seperate... |
| btESBL_modeldata | Data: Covariate data to pass to Stan longitudinal carriage... |
| btESBL_NCBI_phenotypic_bl | Data: NCBI phenotypic beta-lactamase classifications |
| btESBL_participants | Data: Characteristics of study participants. |
| btESBL_plasmidreplicons | Data: Plasmid replicons identified in sequenced isolates |
| btESBL_qrdr_mutations | Data: Identified QRDR mutations |
| btESBL_sequence_sample_metadata | Data: Accession numbers and metadata of isolates sequenced... |
| btESBL_snpdists_esco | Data: Pairwise SNP-distance matrix for all E. coli genomes |
| btESBL_snpdists_kleb | Data: Pairwise SNP-distance matrix for all K. pneumoniae... |
| btESBL_stanmodeldata | Data: Covariate data to pass to Stan longitudinal carriage... |
| btESBL_stoolESBL | Data: Results of stool culture for ESBL |
| btESBL_stoolorgs | Data: Species of bacteria isolated from stool culture for... |
