Files in johnmcculloch/JAMS_BW
Just A Microbiology System
DESCRIPTION
JAMSinstaller_BW
LICENSE
NAMESPACE
R/SraRunTable_to_metadata.R
R/adjust_phenotable.R
R/agglomerate_features.R
R/annotate_contigs.R
R/assemble_contigs.R
R/bank_reads.R
R/blast_databases.R
R/calculate_matrix_stats.R
R/check_resources.R
R/classify_16S_from_contigs.R
R/compare_ucobias.R
R/compute_readcounts.R
R/consolidate_tables.R
R/constrain_JAMS_SEobj_to_wanted_taxa.R
R/deconvolute_contaminated_isolates.R
R/define_kinds_of_variables.R
R/evaluate_assembly.R
R/evaluate_metaBAT_bin.R
R/evaluate_metaBAT_bin_CheckM.R
R/export_expvec_to_XL.R
R/export_from_list.R
R/filter_host.R
R/filtering_functions.R
R/find_accession_from_keyterm.R
R/gather_run_info.R
R/get_contig_coverage.R
R/get_contigs.R
R/get_feature_stats.R
R/get_genome_completeness.R
R/get_genomes_NCBI.R
R/get_reads.R
R/harvesting_functions.R
R/infer_LKT.R
R/kraken_classify_taxonomy.R
R/launch_interpro.R
R/load_jamsfiles_from_system.R
R/load_metadata_from_file.R
R/make_SummarizedExperiment_from_tables.R
R/make_SummarizedExperiments.R
R/make_antibiogram_experiment.R
R/make_colour_dictionary.R
R/make_featuredata_from_bedfile.R
R/make_jams_file.R
R/make_metadata_from_taxtable.R
R/make_readdata.R
R/merge_JAMS_SEobj.R
R/merge_sparse_matrix.R
R/pareto_abundance.R
R/plot_Ordination.R
R/plot_alpha_diversity.R
R/plot_bar_graph.R
R/plot_bias.R
R/plot_correlation_heatmap.R
R/plot_genome_taxonomy_donut.R
R/plot_readdata.R
R/plot_readscatter.R
R/plot_relabund_features.R
R/plot_relabund_heatmap.R
R/plot_wordcloud_sample.R
R/prepare_contigs_for_JAMS.R
R/print_jams_report.R
R/print_table.R
R/replace_Sample_names_in_SEobj.R
R/retrieve_features_by_taxa.R
R/sequence_handling_functions.R
R/trim_reads.R
R/useful_functions.R
README.md
data/ECdescmap.rda
data/GOtermdict.rda
data/Gram.rda
data/InterproDict.rda
data/JAMSMedian_Genome_Sizes.rda
data/JAMStaxtable.rda
data/MetaCycAccession2Description.rda
data/blast_lookup.rda
data/expvec_MR50.rda
data/seqadapters.rda
data/taxlevels.rda
libexec/JAMS16
libexec/JAMSalpha
libexec/JAMSbankit
libexec/JAMSbeta
libexec/JAMSbeta_iterative
libexec/JAMSbuildk2db
libexec/JAMSfastqprefixrenamer
libexec/JAMSjoinlanes
libexec/JAMSmakeswarm
libexec/dointerproBW.sh
libexec/fasta2length.sh
libexec/fastannotate_JAMS.sh
libexec/fastq2fasta4kraken.sh
libexec/getreadsSRAonBW.sh
libexec/makelookuptable_resfinder.R
man/ExpObjVetting.Rd
man/IO_jams_workspace_image.Rd
man/Pct2log2PPM.Rd
man/RAMbytes_status.Rd
man/SraRunTable_to_metadata.Rd
man/add_blast_results_to_featuredata.Rd
man/add_interpro_to_featuredata.Rd
man/add_shape_to_plot_safely.Rd
man/adjust_phenotable.Rd
man/agglomerate_features.Rd
man/analyze_fastq_filename.Rd
man/annotate_contigs.Rd
man/assemble_contigs.Rd
man/bank_reads.Rd
man/blast_databases.Rd
man/calculate_matrix_stats.Rd
man/can_be_made_numeric.Rd
man/check_resources.Rd
man/classify_16S_from_contigs.Rd
man/compare_ucobias.Rd
man/compute_readcounts.Rd
man/compute_signature_numbases.Rd
man/compute_x_font.Rd
man/consolidate_tables.Rd
man/constrain_JAMS_SEobj_to_wanted_taxa.Rd
man/convert_matrix_PA.Rd
man/convert_matrix_log2.Rd
man/countfastq.Rd
man/countfastq_files.Rd
man/declare_filtering_presets.Rd
man/deconvolute_contaminated_isolates.Rd
man/define_kinds_of_variables.Rd
man/detectHardwareResources.Rd
man/evaluate_assembly.Rd
man/evaluate_metaBAT_bin.Rd
man/evaluate_metaBAT_bin_CheckM.Rd
man/export_expvec_to_XL.Rd
man/export_from_list.Rd
man/exporttabletsv.Rd
man/filetype.Rd
man/filter_correlations.Rd
man/filter_experiment.Rd
man/filter_host.Rd
man/filter_sample_by_class_to_ignore.Rd
man/filter_sequence_by_length.Rd
man/filter_sequence_by_name.Rd
man/find_accession_from_keyterm.Rd
man/find_clusters_in_matrix.Rd
man/fix_interproscanoutput.Rd
man/fixrelpath.Rd
man/gather_run_info.Rd
man/generate_filename.Rd
man/getOrdinalNumber1.Rd
man/get_contig_coverage.Rd
man/get_contigs.Rd
man/get_feature_stats.Rd
man/get_feature_to_accession_table.Rd
man/get_feature_to_blast_result_table.Rd
man/get_genome_completeness.Rd
man/get_genomes_NCBI.Rd
man/get_reads.Rd
man/get_sequence_stats.Rd
man/harvest_functions.Rd
man/hm_fontsize_computer.Rd
man/infer_LKT.Rd
man/infer_column_type.Rd
man/install_biocon_deps.Rd
man/is.redundant.Rd
man/is.useful.Rd
man/kraken_classify_taxonomy.Rd
man/launch_interpro.Rd
man/load_jamsfiles_from_system.Rd
man/load_metadata_from_file.Rd
man/log2PPMtoPct.Rd
man/make_SummarizedExperiment_from_tables.Rd
man/make_SummarizedExperiments.Rd
man/make_antibiogram_experiment.Rd
man/make_colour_dictionary.Rd
man/make_featuredata_from_bedfile.Rd
man/make_jams_file.Rd
man/make_metadata_from_taxtable.Rd
man/make_phenolabels_from_phenotable.Rd
man/make_readdata.Rd
man/make_sequences_caps.Rd
man/merge_JAMS_SEobj.Rd
man/merge_sparse_matrix.Rd
man/name_samples.Rd
man/pareto_abundance.Rd
man/plot_Ordination.Rd
man/plot_alpha_diversity.Rd
man/plot_bar_graph.Rd
man/plot_bias.Rd
man/plot_correlation_heatmap.Rd
man/plot_genome_taxonomy_donut.Rd
man/plot_readdata.Rd
man/plot_readscatter.Rd
man/plot_relabund_features.Rd
man/plot_relabund_heatmap.Rd
man/plot_wordcloud_sample.Rd
man/prepare_contigs_for_JAMS.Rd
man/print_jams_report.Rd
man/print_table.Rd
man/quiet.Rd
man/rename_sequences_consecutively.Rd
man/replace_NAs_with_character.Rd
man/replace_Sample_names_in_SEobj.Rd
man/retrieve_features_by_taxa.Rd
man/sample_by_category.Rd
man/shrink_perbasecoverage.Rd
man/spew_heatmap_report.Rd
man/split_featname.Rd
man/trim_reads.Rd
man/trim_whitespace_from_df.Rd
man/update_ExpObj_metadata.Rd
man/whoopsieplot.Rd
