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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(ExpObjVetting)
export(IO_jams_workspace_image)
export(Pct2log2PPM)
export(RAMbytes_status)
export(SraRunTable_to_metadata)
export(add_blast_results_to_featuredata)
export(add_interpro_to_featuredata)
export(add_shape_to_plot_safely)
export(adjust_phenotable)
export(agglomerate_features)
export(analyze_fastq_filename)
export(annotate_contigs)
export(assemble_contigs)
export(bank_reads)
export(blast_databases)
export(calculate_matrix_stats)
export(can_be_made_numeric)
export(check_resources)
export(classify_16S_from_contigs)
export(compare_ucobias)
export(compute_readcounts)
export(compute_signature_numbases)
export(compute_x_font)
export(consolidate_tables)
export(constrain_JAMS_SEobj_to_wanted_taxa)
export(convert_matrix_PA)
export(convert_matrix_log2)
export(countfastq)
export(countfastq_files)
export(declare_filtering_presets)
export(deconvolute_contaminated_isolates)
export(define_kinds_of_variables)
export(detectHardwareResources)
export(evaluate_assembly)
export(evaluate_metaBAT_bin)
export(evaluate_metaBAT_bin_CheckM)
export(export_expvec_to_XL)
export(export_from_list)
export(exporttabletsv)
export(filetype)
export(filter_correlations)
export(filter_experiment)
export(filter_host)
export(filter_sample_by_class_to_ignore)
export(filter_sequence_by_length)
export(filter_sequence_by_name)
export(find_accession_from_keyterm)
export(find_clusters_in_matrix)
export(fix_interproscanoutput)
export(fixrelpath)
export(gather_run_info)
export(generate_filename)
export(getOrdinalNumber1)
export(get_contig_coverage)
export(get_contigs)
export(get_feature_stats)
export(get_feature_to_accession_table)
export(get_feature_to_blast_result_table)
export(get_genome_completeness)
export(get_genomes_NCBI)
export(get_reads)
export(get_sequence_stats)
export(harvest_functions)
export(hm_fontsize_computer)
export(infer_LKT)
export(infer_LKT_pr2)
export(infer_column_type)
export(install_biocon_deps)
export(is.redundant)
export(is.useful)
export(kraken_classify_taxonomy)
export(launch_interpro)
export(load_jamsfiles_from_system)
export(load_metadata_from_file)
export(log2PPMtoPct)
export(make_SummarizedExperiment_from_tables)
export(make_SummarizedExperiments)
export(make_antibiogram_experiment)
export(make_classes_df)
export(make_colour_dictionary)
export(make_featuredata_from_bedfile)
export(make_jams_file)
export(make_metadata_from_taxtable)
export(make_phenolabels_from_phenotable)
export(make_readdata)
export(make_sequences_caps)
export(merge_JAMS_SEobj)
export(merge_sparse_matrix)
export(name_samples)
export(pareto_abundance)
export(plot_Ordination)
export(plot_alpha_diversity)
export(plot_bar_graph)
export(plot_bias)
export(plot_correlation_heatmap)
export(plot_genome_taxonomy_donut)
export(plot_readdata)
export(plot_readscatter)
export(plot_relabund_features)
export(plot_relabund_heatmap)
export(plot_wordcloud_sample)
export(post_message)
export(prepare_contigs_for_JAMS)
export(print_jams_report)
export(print_table)
export(quiet)
export(rename_sequences_consecutively)
export(replace_NAs_with_character)
export(replace_Sample_names_in_SEobj)
export(retrieve_features_by_taxa)
export(sample_by_category)
export(shrink_perbasecoverage)
export(spew_heatmap_report)
export(split_featname)
export(trim_reads)
export(trim_whitespace_from_df)
export(update_ExpObj_metadata)
export(whoopsieplot)