Files in LANL-Bioinformatics/MetaComp

EDGE Taxonomy Assignments Visualization

.Rbuildignore

.gitignore

.lintr

.travis.yml

DESCRIPTION

MetaComp.Rproj

NAMESPACE

NEWS.md R/load_edge_assignment.R R/load_edge_assignments.R R/merge_edge_assignments.R R/merge_edge_counts.R R/plot_edge_assignment.R R/plot_merged_assignment.R README.md cran-comments.md

inst/extdata/HMP_even/allReads-bwa.list.txt

inst/extdata/HMP_even/allReads-diamond.list.txt

inst/extdata/HMP_even/allReads-gottcha-genDB-b.list.txt

inst/extdata/HMP_even/allReads-gottcha-genDB-v.list.txt

inst/extdata/HMP_even/allReads-gottcha-speDB-b.list.txt

inst/extdata/HMP_even/allReads-gottcha-speDB-v.list.txt

inst/extdata/HMP_even/allReads-gottcha-strDB-v.list.txt

inst/extdata/HMP_even/allReads-gottcha2-speDB-b.list.txt

inst/extdata/HMP_even/allReads-kraken_mini.list.txt

inst/extdata/HMP_even/allReads-metaphlan.list.txt

inst/extdata/HMP_even/allReads-pangia.list.txt

inst/extdata/HMP_stagger/allReads-bwa.list.txt

inst/extdata/HMP_stagger/allReads-diamond.list.txt

inst/extdata/HMP_stagger/allReads-gottcha-genDB-b.list.txt

inst/extdata/HMP_stagger/allReads-gottcha-genDB-v.list.txt

inst/extdata/HMP_stagger/allReads-gottcha-speDB-b.list.txt

inst/extdata/HMP_stagger/allReads-gottcha-speDB-v.list.txt

inst/extdata/HMP_stagger/allReads-gottcha-strDB-v.list.txt

inst/extdata/HMP_stagger/allReads-gottcha2-speDB-b.list.txt

inst/extdata/HMP_stagger/allReads-kraken_mini.list.txt

inst/extdata/HMP_stagger/allReads-metaphlan.list.txt

inst/extdata/HMP_stagger/allReads-pangia.list.txt

inst/site/.gitignore

inst/site/assignments_table_bwa.txt

inst/site/assignments_table_bwa_single_file.txt

inst/site/assignments_table_diamond.txt

inst/site/assignments_table_diamond_single_file.txt

inst/site/assignments_table_gottcha.txt

inst/site/assignments_table_gottcha2.txt

inst/site/assignments_table_gottcha2_single_file.txt

inst/site/assignments_table_gottcha_single_file.txt

inst/site/assignments_table_kraken.txt

inst/site/assignments_table_kraken_single_file.txt

inst/site/assignments_table_metaphlan.txt

inst/site/assignments_table_metaphlan_single_file.txt

inst/site/assignments_table_pangia.txt

inst/site/assignments_table_pangia_single_file.txt

inst/site/create_table.R inst/site/merge_and_plot_bwa_assignments.R inst/site/merge_and_plot_diamond_assignments.R inst/site/merge_and_plot_edge_assignments.R inst/site/merge_and_plot_gottcha2_assignments.R inst/site/merge_and_plot_gottcha_assignments.R inst/site/merge_and_plot_kraken_assignments.R inst/site/merge_and_plot_metaphlan_assignments.R inst/site/merge_and_plot_pangia_assignments.R inst/site/merge_bwa_test.pdf

inst/site/merge_bwa_test.svg

inst/site/merge_gottcha_assignments.R inst/site/merge_gottcha_test.pdf

inst/site/merge_gottcha_test.svg

inst/site/merge_kraken_test.pdf

inst/site/merge_kraken_test.svg

inst/site/merge_metaphlan_test.pdf

inst/site/merge_metaphlan_test.svg

inst/site/merge_test.pdf

inst/site/merge_test.svg

inst/site/merged_assignments.txt

inst/site/merged_assignments_bwa.txt

inst/site/merged_assignments_bwa_s.txt

inst/site/merged_assignments_gottcha.txt

inst/site/merged_assignments_kraken.txt

inst/site/merged_assignments_metaphlan.txt

inst/site/test1.png

inst/site/test2.png

man/load_edge_assignment.Rd man/load_edge_assignments.Rd man/merge_edge_assignments.Rd man/merge_edge_counts.Rd man/plot_edge_assignment.Rd man/plot_merged_assignment.Rd

tests/test_data/100187/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt

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/100197/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/100198/gottcha-genDB-b/allReads-gottcha-genDB-b.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/100204/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt

tests/test_data/100218/gottcha-genDB-b/allReads-gottcha-genDB-b.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/100236/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt

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/100237/gottcha-genDB-b/allReads-gottcha-genDB-b.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/100301/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt

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/100400/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/100404/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/100455/gottcha-genDB-b/allReads-gottcha-genDB-b.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/100456/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt

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/100477/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt

tests/test_data/248/allReads-bwa.list.txt

tests/test_data/248/allReads-gottcha-genDB-b.list.txt

tests/test_data/248/allReads-gottcha-genDB-v.list.txt

tests/test_data/248/allReads-gottcha-speDB-b.list.txt

tests/test_data/248/allReads-gottcha-speDB-v.list.txt

tests/test_data/248/allReads-gottcha-strDB-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/allReads-metaphlan.list.txt

tests/test_data/248/retrieve.sh

tests/test_data/HMP_even/allReads-bwa.list.txt

tests/test_data/HMP_even/allReads-diamond.list.txt

tests/test_data/HMP_even/allReads-gottcha-genDB-b.list.txt

tests/test_data/HMP_even/allReads-gottcha-genDB-v.list.txt

tests/test_data/HMP_even/allReads-gottcha-speDB-b.list.txt

tests/test_data/HMP_even/allReads-gottcha-speDB-v.list.txt

tests/test_data/HMP_even/allReads-gottcha-strDB-v.list.txt

tests/test_data/HMP_even/allReads-gottcha2-speDB-b.list.txt

tests/test_data/HMP_even/allReads-kraken_mini.list.txt

tests/test_data/HMP_even/allReads-metaphlan.list.txt

tests/test_data/HMP_even/allReads-pangia.list.txt

tests/test_data/HMP_stagger/allReads-bwa.list.txt

tests/test_data/HMP_stagger/allReads-diamond.list.txt

tests/test_data/HMP_stagger/allReads-gottcha-genDB-b.list.txt

tests/test_data/HMP_stagger/allReads-gottcha-genDB-v.list.txt

tests/test_data/HMP_stagger/allReads-gottcha-speDB-b.list.txt

tests/test_data/HMP_stagger/allReads-gottcha-speDB-v.list.txt

tests/test_data/HMP_stagger/allReads-gottcha-strDB-v.list.txt

tests/test_data/HMP_stagger/allReads-gottcha2-speDB-b.list.txt

tests/test_data/HMP_stagger/allReads-kraken_mini.list.txt

tests/test_data/HMP_stagger/allReads-metaphlan.list.txt

tests/test_data/HMP_stagger/allReads-pangia.list.txt

tests/test_data/SRR059928/SRR059928_gottcha2-speDB-refseq/allReads.summary.tsv

tests/test_data/SRR061287/SRR061287_gottcha2-speDB-refseq/allReads.summary.tsv

tests/test_data/SRR062284/SRR062284_gottcha2-speDB-refseq/allReads.summary.tsv

tests/test_data/SRR062419/SRR062419_gottcha2-speDB-refseq/allReads.summary.tsv

tests/test_data/SRR353621/SRR353621_gottcha2-speDB-refseq/allReads.summary.tsv

tests/test_data/SSputum-DNase-RAB/bwa/allReads-bwa.list.txt

tests/test_data/SSputum-DNase-RAB/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt

tests/test_data/SSputum-DNase-RAB/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt

tests/test_data/SSputum-DNase-RAB/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt

tests/test_data/SSputum-DNase-RAB/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt

tests/test_data/SSputum-DNase-RAB/gottcha-strDB-b/allReads-gottcha-strDB-b.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/metaphlan/allReads-metaphlan.list.txt

tests/test_data/SSputum-DNase-cDNA/bwa/allReads-bwa.list.txt

tests/test_data/SSputum-DNase-cDNA/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt

tests/test_data/SSputum-DNase-cDNA/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt

tests/test_data/SSputum-DNase-cDNA/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt

tests/test_data/SSputum-DNase-cDNA/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt

tests/test_data/SSputum-DNase-cDNA/gottcha-strDB-b/allReads-gottcha-strDB-b.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/metaphlan/allReads-metaphlan.list.txt

tests/test_data/SSputum-dil-DNase-RAB/bwa/allReads-bwa.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/gottcha-genDB-v/allReads-gottcha-genDB-v.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-speDB-v/allReads-gottcha-speDB-v.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-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/metaphlan/allReads-metaphlan.list.txt

tests/test_data/SSputum-dil-DNase-cDNA/bwa/allReads-bwa.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/gottcha-genDB-v/allReads-gottcha-genDB-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-speDB-v/allReads-gottcha-speDB-v.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-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/metaphlan/allReads-metaphlan.list.txt

tests/test_data/SSputum-dil-no-RAB/bwa/allReads-bwa.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/gottcha-genDB-v/allReads-gottcha-genDB-v.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-speDB-v/allReads-gottcha-speDB-v.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-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/metaphlan/allReads-metaphlan.list.txt

tests/test_data/SSputum-dil-no-cDNA/bwa/allReads-bwa.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/gottcha-genDB-v/allReads-gottcha-genDB-v.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-speDB-v/allReads-gottcha-speDB-v.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-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/metaphlan/allReads-metaphlan.list.txt

tests/test_data/SSputum-no-RAB/bwa/allReads-bwa.list.txt

tests/test_data/SSputum-no-RAB/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt

tests/test_data/SSputum-no-RAB/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt

tests/test_data/SSputum-no-RAB/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt

tests/test_data/SSputum-no-RAB/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt

tests/test_data/SSputum-no-RAB/gottcha-strDB-b/allReads-gottcha-strDB-b.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/metaphlan/allReads-metaphlan.list.txt

tests/test_data/SSputum-no-cDNA/bwa/allReads-bwa.list.txt

tests/test_data/SSputum-no-cDNA/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt

tests/test_data/SSputum-no-cDNA/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt

tests/test_data/SSputum-no-cDNA/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt

tests/test_data/SSputum-no-cDNA/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt

tests/test_data/SSputum-no-cDNA/gottcha-strDB-b/allReads-gottcha-strDB-b.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/metaphlan/allReads-metaphlan.list.txt

tests/test_data/an_empty_file.tsv

tests/test_data/bwa_emtpy_list.txt

tests/test_data/merged_table.tsv

tests/test_data/mock_metadata.tsv

tests/test_data/test_all_taxa/allReads-bwa.list.txt

tests/test_data/test_all_taxa/allReads-diamond.list.txt

tests/test_data/test_all_taxa/allReads-gottcha-genDB-b.list.txt

tests/test_data/test_all_taxa/allReads-gottcha-genDB-v.list.txt

tests/test_data/test_all_taxa/allReads-gottcha-speDB-b.list.txt

tests/test_data/test_all_taxa/allReads-gottcha-speDB-v.list.txt

tests/test_data/test_all_taxa/allReads-gottcha-strDB-v.list.txt

tests/test_data/test_all_taxa/allReads-gottcha2-speDB-b.list.txt

tests/test_data/test_all_taxa/allReads-kraken_mini.list.txt

tests/test_data/test_all_taxa/allReads-metaphlan.list.txt

tests/test_data/test_all_taxa/allReads-pangia.list.txt

tests/test_data/test_table_bwa.txt

tests/test_data/test_table_diamond.txt

tests/test_data/test_table_gottcha.txt

tests/test_data/test_table_gottcha2.txt

tests/test_data/test_table_kraken.txt

tests/test_data/test_table_metaphlan.txt

tests/test_data/test_table_pangia.txt

tests/testthat.R

tests/testthat/.gitignore

tests/testthat/test_load_bwa_assignment.R tests/testthat/test_load_bwa_assignments.R tests/testthat/test_load_diamond_assignment.R tests/testthat/test_load_diamond_assignments.R tests/testthat/test_load_gottcha2_assignment.R tests/testthat/test_load_gottcha2_assignments.R tests/testthat/test_load_gottcha_assignment.R tests/testthat/test_load_gottcha_assignments.R tests/testthat/test_load_kraken_assignment.R tests/testthat/test_load_kraken_assignments.R tests/testthat/test_load_metaphlan_assignment.R tests/testthat/test_load_metaphlan_assignments.R tests/testthat/test_load_pangia_assignment.R tests/testthat/test_load_pangia_assignments.R tests/testthat/test_merge_bwa_assignments.R tests/testthat/test_merge_bwa_count_assignments.R tests/testthat/test_merge_diamond_assignments.R tests/testthat/test_merge_gottcha2_assignments.R tests/testthat/test_merge_gottcha2_count_assignments.R tests/testthat/test_merge_gottcha_assignments.R tests/testthat/test_merge_kraken_assignments.R tests/testthat/test_merge_metaphlan_assignments.R tests/testthat/test_merge_pangia_assignments.R tests/testthat/test_pipeline.R tests/testthat/test_plot_bwa_assignment.R tests/testthat/test_plot_diamond_assignment.R tests/testthat/test_plot_gottcha_assignment.R tests/testthat/test_plot_kraken_assignment.R tests/testthat/test_plot_merged_assignment_b.R tests/testthat/test_plot_merged_assignment_d.R tests/testthat/test_plot_merged_assignment_g.R tests/testthat/test_plot_merged_assignment_g2.R tests/testthat/test_plot_merged_assignment_k.R tests/testthat/test_plot_merged_assignment_m.R tests/testthat/test_plot_merged_assignment_p.R tests/testthat/test_plot_metaphlan_assignment.R tests/testthat/test_plot_pangia_assignment.R

LANL-Bioinformatics/MetaComp documentation built on May 8, 2019, 4:51 p.m.