Files in MetaComp
EDGE Taxonomy Assignments Visualization
MD5
DESCRIPTION
README.md
NAMESPACE
inst/extdata/HMP_stagger/allReads-gottcha-genDB-b.list.txt
inst/extdata/HMP_stagger/allReads-gottcha-speDB-v.list.txt
inst/extdata/HMP_stagger/allReads-diamond.list.txt
inst/extdata/HMP_stagger/allReads-gottcha-speDB-b.list.txt
inst/extdata/HMP_stagger/allReads-gottcha-strDB-v.list.txt
inst/extdata/HMP_stagger/allReads-kraken_mini.list.txt
inst/extdata/HMP_stagger/allReads-pangia.list.txt
inst/extdata/HMP_stagger/allReads-gottcha2-speDB-b.list.txt
inst/extdata/HMP_stagger/allReads-bwa.list.txt
inst/extdata/HMP_stagger/allReads-gottcha-genDB-v.list.txt
inst/extdata/HMP_stagger/allReads-metaphlan.list.txt
inst/extdata/HMP_even/allReads-gottcha-genDB-b.list.txt
inst/extdata/HMP_even/allReads-gottcha-speDB-v.list.txt
inst/extdata/HMP_even/allReads-diamond.list.txt
inst/extdata/HMP_even/allReads-gottcha-speDB-b.list.txt
inst/extdata/HMP_even/allReads-gottcha-strDB-v.list.txt
inst/extdata/HMP_even/allReads-kraken_mini.list.txt
inst/extdata/HMP_even/allReads-pangia.list.txt
inst/extdata/HMP_even/allReads-gottcha2-speDB-b.list.txt
inst/extdata/HMP_even/allReads-bwa.list.txt
inst/extdata/HMP_even/allReads-gottcha-genDB-v.list.txt
inst/extdata/HMP_even/allReads-metaphlan.list.txt
R/plot_merged_assignment.R
R/load_edge_assignment.R
R/merge_edge_assignments.R
R/load_edge_assignments.R
R/merge_edge_counts.R
R/plot_edge_assignment.R
man/load_edge_assignment.Rd
man/plot_edge_assignment.Rd
man/merge_edge_assignments.Rd
man/load_edge_assignments.Rd
man/merge_edge_counts.Rd
man/plot_merged_assignment.Rd
tests/testthat.R
tests/test_data/test_table_metaphlan.txt
tests/test_data/merged_table.tsv
tests/test_data/test_table_diamond.txt
tests/test_data/test_table_gottcha.txt
tests/test_data/mock_metadata.tsv
tests/test_data/test_table_bwa.txt
tests/test_data/an_empty_file.tsv
tests/test_data/test_table_pangia.txt
tests/test_data/bwa_emtpy_list.txt
tests/test_data/test_table_gottcha2.txt
tests/test_data/test_table_kraken.txt
tests/test_data/248/allReads-gottcha-genDB-b.list.txt
tests/test_data/248/allReads-gottcha-speDB-v.list.txt
tests/test_data/248/allReads-gottcha-speDB-b.list.txt
tests/test_data/248/allReads-gottcha-strDB-v.list.txt
tests/test_data/248/allReads-kraken_mini.list.txt
tests/test_data/248/retrieve.sh
tests/test_data/248/allReads-bwa.list.txt
tests/test_data/248/allReads-gottcha-strDB-b.list.txt
tests/test_data/248/allReads-gottcha-genDB-v.list.txt
tests/test_data/248/allReads-metaphlan.list.txt
tests/test_data/SRR061287/SRR061287_gottcha2-speDB-refseq/allReads.summary.tsv
tests/test_data/100187/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/100187/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/100187/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/100404/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/100404/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/100404/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/100477/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-DNase-RAB/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/SSputum-DNase-RAB/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/SSputum-DNase-RAB/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
tests/test_data/SSputum-DNase-RAB/metaphlan/allReads-metaphlan.list.txt
tests/test_data/SSputum-DNase-RAB/gottcha-strDB-v/allReads-gottcha-strDB-v.list.txt
tests/test_data/SSputum-DNase-RAB/kraken_mini/allReads-kraken_mini.list.txt
tests/test_data/SSputum-DNase-RAB/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-DNase-RAB/bwa/allReads-bwa.list.txt
tests/test_data/SSputum-DNase-RAB/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt
tests/test_data/HMP_stagger/allReads-gottcha-genDB-b.list.txt
tests/test_data/HMP_stagger/allReads-gottcha-speDB-v.list.txt
tests/test_data/HMP_stagger/allReads-diamond.list.txt
tests/test_data/HMP_stagger/allReads-gottcha-speDB-b.list.txt
tests/test_data/HMP_stagger/allReads-gottcha-strDB-v.list.txt
tests/test_data/HMP_stagger/allReads-kraken_mini.list.txt
tests/test_data/HMP_stagger/allReads-pangia.list.txt
tests/test_data/HMP_stagger/allReads-gottcha2-speDB-b.list.txt
tests/test_data/HMP_stagger/allReads-bwa.list.txt
tests/test_data/HMP_stagger/allReads-gottcha-genDB-v.list.txt
tests/test_data/HMP_stagger/allReads-metaphlan.list.txt
tests/test_data/SSputum-no-RAB/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/SSputum-no-RAB/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/SSputum-no-RAB/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
tests/test_data/SSputum-no-RAB/metaphlan/allReads-metaphlan.list.txt
tests/test_data/SSputum-no-RAB/gottcha-strDB-v/allReads-gottcha-strDB-v.list.txt
tests/test_data/SSputum-no-RAB/kraken_mini/allReads-kraken_mini.list.txt
tests/test_data/SSputum-no-RAB/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-no-RAB/bwa/allReads-bwa.list.txt
tests/test_data/SSputum-no-RAB/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt
tests/test_data/SRR062284/SRR062284_gottcha2-speDB-refseq/allReads.summary.tsv
tests/test_data/100456/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/100456/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/100456/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-dil-no-RAB/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/SSputum-dil-no-RAB/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/SSputum-dil-no-RAB/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
tests/test_data/SSputum-dil-no-RAB/metaphlan/allReads-metaphlan.list.txt
tests/test_data/SSputum-dil-no-RAB/gottcha-strDB-v/allReads-gottcha-strDB-v.list.txt
tests/test_data/SSputum-dil-no-RAB/kraken_mini/allReads-kraken_mini.list.txt
tests/test_data/SSputum-dil-no-RAB/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-dil-no-RAB/bwa/allReads-bwa.list.txt
tests/test_data/SSputum-dil-no-RAB/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt
tests/test_data/100198/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/100198/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/100198/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/100197/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/100197/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/100197/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/HMP_even/allReads-gottcha-genDB-b.list.txt
tests/test_data/HMP_even/allReads-gottcha-speDB-v.list.txt
tests/test_data/HMP_even/allReads-diamond.list.txt
tests/test_data/HMP_even/allReads-gottcha-speDB-b.list.txt
tests/test_data/HMP_even/allReads-gottcha-strDB-v.list.txt
tests/test_data/HMP_even/allReads-kraken_mini.list.txt
tests/test_data/HMP_even/allReads-pangia.list.txt
tests/test_data/HMP_even/allReads-gottcha2-speDB-b.list.txt
tests/test_data/HMP_even/allReads-bwa.list.txt
tests/test_data/HMP_even/allReads-gottcha-genDB-v.list.txt
tests/test_data/HMP_even/allReads-metaphlan.list.txt
tests/test_data/100218/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/100218/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/100218/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-dil-DNase-RAB/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/SSputum-dil-DNase-RAB/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/SSputum-dil-DNase-RAB/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
tests/test_data/SSputum-dil-DNase-RAB/metaphlan/allReads-metaphlan.list.txt
tests/test_data/SSputum-dil-DNase-RAB/gottcha-strDB-v/allReads-gottcha-strDB-v.list.txt
tests/test_data/SSputum-dil-DNase-RAB/kraken_mini/allReads-kraken_mini.list.txt
tests/test_data/SSputum-dil-DNase-RAB/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-dil-DNase-RAB/bwa/allReads-bwa.list.txt
tests/test_data/SSputum-dil-DNase-RAB/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt
tests/test_data/SRR062419/SRR062419_gottcha2-speDB-refseq/allReads.summary.tsv
tests/test_data/100301/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/100301/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/100301/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SRR059928/SRR059928_gottcha2-speDB-refseq/allReads.summary.tsv
tests/test_data/100204/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/100400/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/100400/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/100400/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-dil-no-cDNA/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/SSputum-dil-no-cDNA/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/SSputum-dil-no-cDNA/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
tests/test_data/SSputum-dil-no-cDNA/metaphlan/allReads-metaphlan.list.txt
tests/test_data/SSputum-dil-no-cDNA/gottcha-strDB-v/allReads-gottcha-strDB-v.list.txt
tests/test_data/SSputum-dil-no-cDNA/kraken_mini/allReads-kraken_mini.list.txt
tests/test_data/SSputum-dil-no-cDNA/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-dil-no-cDNA/bwa/allReads-bwa.list.txt
tests/test_data/SSputum-dil-no-cDNA/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt
tests/test_data/100237/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/100237/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/100237/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-DNase-cDNA/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/SSputum-DNase-cDNA/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/SSputum-DNase-cDNA/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
tests/test_data/SSputum-DNase-cDNA/metaphlan/allReads-metaphlan.list.txt
tests/test_data/SSputum-DNase-cDNA/gottcha-strDB-v/allReads-gottcha-strDB-v.list.txt
tests/test_data/SSputum-DNase-cDNA/kraken_mini/allReads-kraken_mini.list.txt
tests/test_data/SSputum-DNase-cDNA/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-DNase-cDNA/bwa/allReads-bwa.list.txt
tests/test_data/SSputum-DNase-cDNA/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt
tests/test_data/SSputum-dil-DNase-cDNA/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/SSputum-dil-DNase-cDNA/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/SSputum-dil-DNase-cDNA/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
tests/test_data/SSputum-dil-DNase-cDNA/metaphlan/allReads-metaphlan.list.txt
tests/test_data/SSputum-dil-DNase-cDNA/gottcha-strDB-v/allReads-gottcha-strDB-v.list.txt
tests/test_data/SSputum-dil-DNase-cDNA/kraken_mini/allReads-kraken_mini.list.txt
tests/test_data/SSputum-dil-DNase-cDNA/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-dil-DNase-cDNA/bwa/allReads-bwa.list.txt
tests/test_data/SSputum-dil-DNase-cDNA/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt
tests/test_data/100455/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/100455/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/100455/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/test_all_taxa/allReads-gottcha-genDB-b.list.txt
tests/test_data/test_all_taxa/allReads-gottcha-speDB-v.list.txt
tests/test_data/test_all_taxa/allReads-diamond.list.txt
tests/test_data/test_all_taxa/allReads-gottcha-speDB-b.list.txt
tests/test_data/test_all_taxa/allReads-gottcha-strDB-v.list.txt
tests/test_data/test_all_taxa/allReads-kraken_mini.list.txt
tests/test_data/test_all_taxa/allReads-pangia.list.txt
tests/test_data/test_all_taxa/allReads-gottcha2-speDB-b.list.txt
tests/test_data/test_all_taxa/allReads-bwa.list.txt
tests/test_data/test_all_taxa/allReads-gottcha-genDB-v.list.txt
tests/test_data/test_all_taxa/allReads-metaphlan.list.txt
tests/test_data/SSputum-no-cDNA/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/SSputum-no-cDNA/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/SSputum-no-cDNA/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
tests/test_data/SSputum-no-cDNA/metaphlan/allReads-metaphlan.list.txt
tests/test_data/SSputum-no-cDNA/gottcha-strDB-v/allReads-gottcha-strDB-v.list.txt
tests/test_data/SSputum-no-cDNA/kraken_mini/allReads-kraken_mini.list.txt
tests/test_data/SSputum-no-cDNA/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/test_data/SSputum-no-cDNA/bwa/allReads-bwa.list.txt
tests/test_data/SSputum-no-cDNA/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt
tests/test_data/SRR353621/SRR353621_gottcha2-speDB-refseq/allReads.summary.tsv
tests/test_data/100236/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
tests/test_data/100236/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
tests/test_data/100236/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
tests/testthat/test_plot_merged_assignment_d.R
tests/testthat/test_load_diamond_assignment.R
tests/testthat/test_merge_gottcha2_count_assignments.R
tests/testthat/test_plot_merged_assignment_g2.R
tests/testthat/test_merge_metaphlan_assignments.R
tests/testthat/test_load_gottcha_assignments.R
tests/testthat/test_merge_gottcha_assignments.R
tests/testthat/test_merge_kraken_assignments.R
tests/testthat/test_load_kraken_assignments.R
tests/testthat/Rplots.pdf
tests/testthat/test_load_pangia_assignments.R
tests/testthat/test_load_kraken_assignment.R
tests/testthat/test_load_metaphlan_assignment.R
tests/testthat/test_plot_kraken_assignment.R
tests/testthat/test_plot_bwa_assignment.R
tests/testthat/test_plot_merged_assignment_p.R
tests/testthat/test_load_gottcha_assignment.R
tests/testthat/test_pipeline.R
tests/testthat/test_load_gottcha2_assignment.R
tests/testthat/test_plot_metaphlan_assignment.R
tests/testthat/test_plot_diamond_assignment.R
tests/testthat/test_load_gottcha2_assignments.R
tests/testthat/test_merge_pangia_assignments.R
tests/testthat/test_merge_gottcha2_assignments.R
tests/testthat/test_merge_bwa_assignments.R
tests/testthat/test_plot_merged_assignment_k.R
tests/testthat/test_load_diamond_assignments.R
tests/testthat/test_plot_merged_assignment_m.R
tests/testthat/test_load_bwa_assignment.R
tests/testthat/test_plot_gottcha_assignment.R
tests/testthat/test_load_metaphlan_assignments.R
tests/testthat/test_load_pangia_assignment.R
tests/testthat/test_load_bwa_assignments.R
tests/testthat/test_merge_bwa_count_assignments.R
tests/testthat/test_plot_merged_assignment_g.R
tests/testthat/test_plot_pangia_assignment.R
tests/testthat/test_merge_diamond_assignments.R
tests/testthat/test_plot_merged_assignment_b.R
