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_enterotypes_to_metadata Source code
add_interpro_to_featuredata Man page Source code
adjust_phenotable Man page Source code
agglomerate_features 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_samples Man page Source code
compare_ucobias Man page Source code
compose_metadata Man page Source code
compute_readcounts Man page Source code
compute_signature_numbases Man page
consolidate_tables 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
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
fix_interproscanoutput Man page Source code
fix_kraken Man page Source code
fix_qiime2_taxonomy Man page Source code
gather_run_info 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_accession_table_parallel 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
infer_LKT Man page Source code
install_biocon_deps 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
load_qiime2_data Man page Source code
log2PPMtoPct Man page Source code
make_SummarizedExperiments Man page Source code
make_alpha_report Man page Source code
make_antibiogram_experiment Man page Source code
make_colour_dictionary Man page Source code
make_heatmap_report Man page Source code
make_jams_file Man page Source code
make_metadata_from_taxtable Man page Source code
make_metagenomeSeq_experiments Man page Source code
make_ordination_report Man page Source code
make_readdata Man page Source code
make_sequences_caps Man page Source code
name_samples Man page Source code
pareto_abundance Man page Source code
plot_Ordination Man page Source code
plot_Venn Man page
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_duet_heatmap Man page Source code
plot_feature_relabund Man page Source code
plot_readdata Man page Source code
plot_readscatter Man page Source code
plot_relabund_heatmap Man page Source code
plot_relabund_heatmap_mgseq Man page Source code
plot_wordcloud_sample 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
randomize_experiment Man page
rename_sequences_consecutively Man page Source code
sample_by_category Man page Source code
shrink_perbasecoverage Man page Source code
spew_heatmap_report Man page Source code
trim_reads Man page Source code
trim_whitespace_from_df Man page Source code
whoopsieplot Man page Source code
johnmcculloch/JAMS_BW documentation built on Feb. 11, 2020, 9:22 p.m.