Files in johnmcculloch/JAMS_BW
Just A Microbiology System

BWlibexec/bankit
BWlibexec/bootstrapswarm
BWlibexec/install_brew_dependencies.sh
DESCRIPTION
JAMSinstaller_BW
LICENSE
NAMESPACE
R/SraRunTable_to_metadata.R R/add_blast_results_to_featuredata.R R/add_enterotypes_to_metadata.R R/add_interpro_to_featuredata.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_samples.R R/compare_ucobias.R R/compose_metadata.R R/compute_readcounts.R R/compute_signature_numbases.R R/consolidate_tables.R R/deconvolute_contaminated_isolates.R R/define_kinds_of_variables.R R/evaluate_assembly.R R/export_expvec_to_XL.R R/export_from_list.R R/filter_experiment.R R/filter_host.R R/filter_sample_by_class_to_ignore.R R/filter_sequence_by_length.R R/filter_sequence_by_name.R R/find_accession_from_keyterm.R R/fix_interproscanoutput.R R/fix_kraken.R R/fix_qiime_taxonomy.R R/gather_run_info.R R/getOrdinalNumber1.R R/get_contig_coverage.R R/get_contigs.R R/get_feature_stats.R R/get_feature_to_accession_table.R R/get_feature_to_accession_table_parallel.R R/get_feature_to_blast_result_table.R R/get_genome_completeness.R R/get_genomes_NCBI.R R/get_reads.R R/get_sequence_stats.R R/harvest_functions.R R/infer_LKT.R R/installbioconductordependencies.R R/kraken_classify_taxonomy.R R/launch_interpro.R R/load_jamsfiles_from_system.R R/load_metadata_from_file.R R/load_qiime2_data.R R/make_SummarizedExperiments.R R/make_alpha_report.R R/make_antibiogram_experiment.R R/make_colour_dictionary.R R/make_heatmap_report.R R/make_jams_file.R R/make_metadata_from_taxtable.R R/make_metagenomeSeq_experiments.R R/make_ordination_report.R R/make_readdata.R R/make_sequences_caps.R R/mpa2JAMS.R R/name_samples.R R/pareto_abundance.R R/plot_Ordination.R R/plot_Venn.R R/plot_alpha_diversity.R R/plot_bar_graph.R R/plot_bias.R R/plot_correlation_heatmap.R R/plot_duet_heatmap.R R/plot_feature_relabund.R R/plot_readdata.R R/plot_readscatter.R R/plot_relabund_features.R R/plot_relabund_heatmap.R R/plot_relabund_heatmap_mgseq.R R/plot_wordcloud_sample.R R/prepare_contigs_for_JAMS.R R/print_jams_report.R R/print_table.R R/randomize_experiment.R R/rename_sequences_consecutively.R R/sample_by_category.R R/shrink_perbasecoverage.R R/trim_reads.R R/useful_functions.R README.md
data/ECdescmap.rda
data/GOtermdict.rda
data/Gram.rda
data/JAMSMedian_Genome_Sizes.rda
data/JAMStaxtable.rda
data/resfinderlookup.rda
data/seqadapters.rda
data/taxlevels.rda
libexec/JAMSalpha
libexec/JAMSbankit
libexec/JAMSbeta
libexec/JAMSbuildk2db
libexec/JAMSfastqprefixrenamer
libexec/JAMSjoinlanes
libexec/JAMSmakeswarm
libexec/dointerproBW.sh
libexec/fasta2length.sh
libexec/fastannotate_JAMS.sh
libexec/fastq2fasta4kraken.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_enterotypes_to_metadata.Rd man/add_interpro_to_featuredata.Rd man/adjust_phenotable.Rd man/agglomerate_features.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_samples.Rd man/compare_ucobias.Rd man/compose_metadata.Rd man/compute_readcounts.Rd man/compute_signature_numbases.Rd man/consolidate_tables.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/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/fix_interproscanoutput.Rd man/fix_kraken.Rd man/fix_qiime2_taxonomy.Rd man/fixrelpath.Rd man/gather_run_info.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_accession_table_parallel.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/infer_LKT.Rd man/kraken_classify_taxonomy.Rd man/launch_interpro.Rd man/load_jamsfiles_from_system.Rd man/load_metadata_from_file.Rd man/load_qiime2_data.Rd man/log2PPMtoPct.Rd man/make_SummarizedExperiments.Rd man/make_alpha_report.Rd man/make_antibiogram_experiment.Rd man/make_colour_dictionary.Rd man/make_heatmap_report.Rd man/make_jams_file.Rd man/make_metadata_from_taxtable.Rd man/make_metagenomeSeq_experiments.Rd man/make_ordination_report.Rd man/make_readdata.Rd man/make_sequences_caps.Rd man/mpa2JAMS.Rd man/name_samples.Rd man/pareto_abundance.Rd man/plot_Ordination.Rd man/plot_Venn.Rd man/plot_alpha_diversity.Rd man/plot_bar_graph.Rd man/plot_bias.Rd man/plot_correlation_heatmap.Rd man/plot_duet_heatmap.Rd man/plot_feature_relabund.Rd man/plot_readdata.Rd man/plot_readscatter.Rd man/plot_relabund_features.Rd man/plot_relabund_heatmap.Rd man/plot_relabund_heatmap_mgseq.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/randomize_experiment.Rd man/rename_sequences_consecutively.Rd man/sample_by_category.Rd man/shrink_perbasecoverage.Rd man/spew_heatmap_report.Rd man/trim_reads.Rd man/trim_whitespace_from_df.Rd man/update_ExpObj_metadata.Rd man/whoopsieplot.Rd
johnmcculloch/JAMS_BW documentation built on Feb. 26, 2020, 2:11 a.m.