| add_blast_results_to_featuredata | add_blast_results_to_featuredata |
| add_interpro_to_featuredata | add_interpro_to_featuredata |
| add_shape_to_plot_safely | add_shape_to_plot_safely(p = NULL, shapevec = NULL, shapeby =... |
| adjust_phenotable | adjust_phenotable(opt = NULL, list.data = NULL,... |
| agglomerate_features | agglomerate_features(ExpObj = NULL, glomby = NULL) |
| analyze_fastq_filename | analyze_fastq_filename(fn = NULL, maintain_Illumina_format =... |
| annotate_contigs | annotate_contigs |
| assemble_contigs | assemble_contigs |
| bank_reads | bank_reads |
| blast_databases | blast_databases |
| calculate_matrix_stats | calculate_matrix_stats(countmatrix = NULL, uselog = NULL,... |
| can_be_made_numeric | can_be_made_numeric(x, cats_to_ignore = NULL) Returns logical... |
| check_resources | check_resources(opt = opt, application = "WGS") |
| classify_16S_from_contigs | classify_16S_from_contigs(opt=opt) |
| compare_ucobias | compare_ucobias |
| compute_readcounts | compute_readcounts(opt=opt) |
| compute_signature_numbases | compute_signature_numbases |
| compute_x_font | compute_x_font(nx = 1, upper_n = 400, upper_fs = 0.1, lower_n... |
| consolidate_tables | consolidate_tables(opt=opt) |
| constrain_JAMS_SEobj_to_wanted_taxa | Constrains a functional (non-taxonomic) JAMS-style... |
| convert_matrix_log2 | convert_matrix_log2(mat = NULL, transformation = NULL) |
| convert_matrix_PA | convert_matrix_PA(mat = NULL, threshPA = 0) |
| countfastq | countfastq(fastqfile) Wrapper for counting number of reads... |
| countfastq_files | countfastq_files(fastqfiles = NULL, threads = NULL) Wrapper... |
| declare_filtering_presets | declare_filtering_presets(analysis = NULL, applyfilters =... |
| deconvolute_contaminated_isolates | deconvolute_contaminated_isolates This function is... |
| define_kinds_of_variables | define_kinds_of_variables(metadataXL = NULL, phenolabels =... |
| detectHardwareResources | detectHardwareResources() Generic function for getting number... |
| evaluate_assembly | evaluate_assembly(opt=NULL) |
| evaluate_metaBAT_bin | evaluate_metaBAT_bin(opt=NULL) |
| evaluate_metaBAT_bin_CheckM | evaluate_metaBAT_bin_CheckM(opt=NULL) |
| ExpObjVetting | ExpObjVetting(ExpObj = NULL) |
| export_expvec_to_XL | Exports counts and featuredata in a SummarizedExperiment... |
| export_from_list | export_from_list |
| exporttabletsv | exporttabletsv(dataobj = NULL, project = NULL, basename =... |
| filetype | filetype(path) Wrapper for returning class of system file. |
| filter_correlations | filter_correlations(corrmat = NULL, mincorrelcoeff = NULL)... |
| filter_experiment | filter_experiment(ExpObj = NULL, featmaxatleastPPM = 0,... |
| filter_host | filter_host |
| filter_sample_by_class_to_ignore | filter_sample_by_class_to_ignore(SEobj = NULL, variables =... |
| filter_sequence_by_length | filter_sequence_by_length(sequence=NULL, minlength=0,... |
| filter_sequence_by_name | filter_sequence_by_name(input_sequences = NULL, sequencenames... |
| find_accession_from_keyterm | find_accession_from_keyterm(ExpObj = NULL, keyterm = NULL) |
| find_clusters_in_matrix | find_clusters_in_matrix(input_matrix = NULL, kmeans_split =... |
| fix_interproscanoutput | fix_interproscanoutput(opt = NULL, check_ipro_jobs_status =... |
| fixrelpath | fixrelpath(JAMSpath = NULL) |
| gather_run_info | gather_run_info |
| generate_filename | generate_filename(title = "ABC_look_at_me", add_date = TRUE,... |
| get_contig_coverage | get_contig_coverage(opt = NULL, markduplicates = FALSE,... |
| get_contigs | get_contigs |
| get_feature_stats | get_feature_stats |
| get_feature_to_accession_table | get_feature_to_accession_table |
| get_feature_to_blast_result_table | get_feature_to_blast_result_table |
| get_genome_completeness | get_genome_completeness<-function(pheno=pheno,... |
| get_genomes_NCBI | get_genomes_NCBI(organisms="bacteria", assembly_summary=NULL,... |
| getOrdinalNumber1 | Author: Phillip Burger Date: Sept 3, 2014 Purpose: Get the... |
| get_reads | get_reads |
| get_sequence_stats | get_sequence_stats |
| harvest_functions | harvest_functions |
| hm_fontsize_computer | hm_fontsize_computer(mat_rownames = NULL, mat_colnames =... |
| infer_column_type | infer_column_type(phenotable = NULL, colm = NULL,... |
| infer_LKT | infer_LKT |
| infer_LKT_pr2 | infer_LKT_pr2 |
| install_biocon_deps | install_biocon_deps() |
| IO_jams_workspace_image | IO_jams_workspace_image(opt = NULL, workspaceimage = NULL,... |
| is.redundant | is.redundant(vec) |
| is.useful | is.useful(vec) |
| kraken_classify_taxonomy | kraken_classify_taxonomy |
| launch_interpro | launch_interpro |
| load_jamsfiles_from_system | load_jamsfiles_from_system(path = ".", recursive = TRUE,... |
| load_metadata_from_file | load_metadata_from_file(xlsxFile = NULL, phenotable_tsv =... |
| log2PPMtoPct | log2PPMtoPct(log2PPM) |
| make_antibiogram_experiment | make_antibiogram_experiment(mgseqresfinder = NULL,... |
| make_colour_dictionary | make_colour_dictionary(variable_list = NULL, pheno = NULL,... |
| make_featuredata_from_bedfile | make_featuredata_from_bedfile |
| make_jams_file | make_jams_file |
| make_metadata_from_taxtable | make_metadata_from_taxtable(taxlvlinterest = NULL,... |
| make_phenolabels_from_phenotable | make_phenolabels_from_phenotable(phenotable = NULL) |
| make_readdata | make_readdata(Samples=NULL, list.data=NULL) |
| make_sequences_caps | make_sequences_caps(sequence = NULL) |
| make_SummarizedExperiment_from_tables | make_SummarizedExperiment_from_tables(pheno = NULL, pheno_fn=... |
| make_SummarizedExperiments | make_SummarizedExperiments(pheno = NULL, onlysamples = NULL,... |
| merge_JAMS_SEobj | Safely merges two compatible JAMS-style SummarizedExperiment... |
| merge_sparse_matrix | Safely merges two sparse matrices. This function was written... |
| name_samples | name_samples(list.data = NULL) |
| pareto_abundance | pareto_abundance(LKTdose=NULL, samplename=NULL,... |
| Pct2log2PPM | Pct2log2PPM(Pct) |
| plot_alpha_diversity | Generates relative abundance plots per feature annotated by... |
| plot_bar_graph | Creates bar graph of relative taxonomic abundance from... |
| plot_bias | plot_bias(bias, method = c("pca", tSNE"), frac = 0.25)) |
| plot_correlation_heatmap | plot_correlation_heatmap(ExpObj = NULL, glomby = NULL,... |
| plot_genome_taxonomy_donut | plot_genome_taxonomy_donut(opt = opt, contigsdata = NULL) |
| plot_Ordination | Creates ordination plots based on PCA, tSNE or tUMAP |
| plot_readdata | plot_readdata(readdata=NULL) |
| plot_readscatter | plot_readscatter(opt = NULL) |
| plot_relabund_features | plot_relabund_features(ExpObj = NULL, glomby = NULL,... |
| plot_relabund_heatmap | Plots relative abundance heatmaps annotated by the metadata... |
| plot_wordcloud_sample | plot_wordcloud_sample(opt=opt, elements=NULL) |
| prepare_contigs_for_JAMS | prepare_contigs_for_JAMS |
| print_jams_report | print_jams_report(opt=opt) |
| print_table | print_table(tb=NULL, tabletitle=NULL, fontsize=6, numrows=20) |
| quiet | quiet(function(x)) Suppresses output messages By Hadley... |
| RAMbytes_status | RAMbytes_status(RAMbytesavail = NULL) Reports how much RAM... |
| rename_sequences_consecutively | rename_sequences_consecutively(sequence=NULL, sequence=NULL,... |
| replace_NAs_with_character | replace_NAs_with_character(df) Replaces NAs with a specific... |
| replace_Sample_names_in_SEobj | replace_Sample_names_in_SEobj(curr_SEobj = NULL,... |
| retrieve_features_by_taxa | retrieve_features_by_taxa(FuncExpObj = NULL, assay_for_matrix... |
| sample_by_category | sample_by_category |
| shrink_perbasecoverage | shrink_perbasecoverage(perbasecoverage=NULL, percentage=2) |
| spew_heatmap_report | spew_heatmap_report(c("analysis", "report")) Wrapper for... |
| split_featname | split_featname(featname = NULL, thresh_featname_split = 40) |
| SraRunTable_to_metadata | SraRunTable_to_metadata(SraRunTable=NULL, Sample=NULL,... |
| trim_reads | trim_reads |
| trim_whitespace_from_df | trim_whitespace_from_df(df) Trims leading and trailing... |
| update_ExpObj_metadata | update_ExpObj_metadata(ExpObj = NULL, phenotable = NULL) |
| whoopsieplot | whoopsieplot(msg = NULL) Shuts down the device and gives a... |
