API for johnmcculloch/JAMS_BW
Just A Microbiology System
| Global functions | |
|---|---|
| ExpObjVetting | Man page Source code |
| IO_jams_workspace_image | Man page Source code |
| Pct2log2PPM | Man page Source code |
| RAMbytes_status | Man page Source code |
| SraRunTable_to_metadata | Man page Source code |
| add_blast_results_to_featuredata | Man page Source code |
| add_interpro_to_featuredata | Man page Source code |
| add_shape_to_plot_safely | Man page |
| adjust_phenotable | Man page Source code |
| agglomerate_features | Man page Source code |
| analyze_fastq_filename | Man page Source code |
| annotate_contigs | Man page Source code |
| assemble_contigs | Man page Source code |
| bank_reads | Man page Source code |
| blast_databases | Man page Source code |
| calculate_matrix_stats | Man page Source code |
| can_be_made_numeric | Man page Source code |
| check_resources | Man page Source code |
| classify_16S_from_contigs | Man page Source code |
| compare_ucobias | Man page Source code |
| compute_readcounts | Man page Source code |
| compute_signature_numbases | Man page |
| compute_x_font | Man page Source code |
| consolidate_tables | Man page Source code |
| constrain_JAMS_SEobj_to_wanted_taxa | Man page Source code |
| convert_matrix_PA | Man page Source code |
| convert_matrix_log2 | Man page Source code |
| countfastq | Man page Source code |
| countfastq_files | Man page Source code |
| declare_filtering_presets | Man page Source code |
| deconvolute_contaminated_isolates | Man page Source code |
| define_kinds_of_variables | Man page Source code |
| detectHardwareResources | Man page Source code |
| evaluate_assembly | Man page Source code |
| evaluate_metaBAT_bin | Man page Source code |
| evaluate_metaBAT_bin_CheckM | Man page Source code |
| export_expvec_to_XL | Man page Source code |
| export_from_list | Man page Source code |
| exporttabletsv | Man page Source code |
| filetype | Man page Source code |
| filter_correlations | Man page Source code |
| filter_experiment | Man page Source code |
| filter_host | Man page Source code |
| filter_sample_by_class_to_ignore | Man page Source code |
| filter_sequence_by_length | Man page Source code |
| filter_sequence_by_name | Man page Source code |
| find_accession_from_keyterm | Man page Source code |
| find_clusters_in_matrix | Man page Source code |
| fix_interproscanoutput | Man page Source code |
| fixrelpath | Man page Source code |
| gather_run_info | Man page Source code |
| generate_filename | Man page Source code |
| getOrdinalNumber1 | Man page Source code |
| get_contig_coverage | Man page Source code |
| get_contigs | Man page Source code |
| get_feature_stats | Man page Source code |
| get_feature_to_accession_table | Man page Source code |
| get_feature_to_blast_result_table | Man page Source code |
| get_genome_completeness | Man page Source code |
| get_genomes_NCBI | Man page Source code |
| get_reads | Man page Source code |
| get_sequence_stats | Man page Source code |
| harvest_functions | Man page Source code |
| hm_fontsize_computer | Man page Source code |
| infer_LKT | Man page Source code |
| infer_LKT_pr2 | Man page Source code |
| infer_column_type | Man page Source code |
| install_biocon_deps | Man page Source code |
| is.redundant | Man page Source code |
| is.useful | Man page Source code |
| kraken_classify_taxonomy | Man page Source code |
| launch_interpro | Man page Source code |
| load_jamsfiles_from_system | Man page Source code |
| load_metadata_from_file | Man page Source code |
| log2PPMtoPct | Man page Source code |
| make_SummarizedExperiment_from_tables | Man page Source code |
| make_SummarizedExperiments | Man page Source code |
| make_antibiogram_experiment | Man page Source code |
| make_classes_df | Man page Source code |
| make_colour_dictionary | Man page Source code |
| make_featuredata_from_bedfile | Man page Source code |
| make_jams_file | Man page Source code |
| make_metadata_from_taxtable | Man page Source code |
| make_phenolabels_from_phenotable | Man page |
| make_readdata | Man page Source code |
| make_sequences_caps | Man page Source code |
| merge_JAMS_SEobj | Man page Source code |
| merge_sparse_matrix | Man page Source code |
| name_samples | Man page Source code |
| pareto_abundance | Man page Source code |
| plot_Ordination | Man page Source code |
| plot_alpha_diversity | Man page Source code |
| plot_bar_graph | Man page Source code |
| plot_bias | Man page Source code |
| plot_correlation_heatmap | Man page Source code |
| plot_genome_taxonomy_donut | Man page Source code |
| plot_readdata | Man page Source code |
| plot_readscatter | Man page Source code |
| plot_relabund_features | Man page Source code |
| plot_relabund_heatmap | Man page Source code |
| plot_wordcloud_sample | Man page Source code |
| post_message | Man page Source code |
| prepare_contigs_for_JAMS | Man page Source code |
| print_jams_report | Man page Source code |
| print_table | Man page Source code |
| quiet | Man page Source code |
| rename_sequences_consecutively | Man page Source code |
| replace_NAs_with_character | Man page Source code |
| replace_Sample_names_in_SEobj | Man page Source code |
| retrieve_features_by_taxa | Man page Source code |
| sample_by_category | Man page Source code |
| shrink_perbasecoverage | Man page Source code |
| spew_heatmap_report | Man page Source code |
| split_featname | Man page Source code |
| trim_reads | Man page Source code |
| trim_whitespace_from_df | Man page Source code |
| update_ExpObj_metadata | Man page Source code |
| whoopsieplot | Man page Source code |
