Files in LANL-Bioinformatics/MetaComp
EDGE Taxonomy Assignments Visualization

.Rbuildignore
.gitignore
.lintr
.travis.yml
DESCRIPTION
MetaComp.Rproj
NAMESPACE
NEWS.md R/load_bwa_assignment.R R/load_bwa_assignments.R R/load_gottcha2_assignment.R R/load_gottcha2_assignments.R R/load_gottcha_assignment.R R/load_gottcha_assignments.R R/load_kraken_assignment.R R/load_kraken_assignments.R R/load_metaphlan_assignment.R R/load_metaphlan_assignments.R R/merge_bwa_assignments.R R/merge_bwa_assignments_counts.R R/merge_gottcha_assignments.R R/merge_gottcha_assignments_count.R R/merge_kraken_assignments.R R/merge_metaphlan_assignments.R R/plot_bwa_assignment.R R/plot_gottcha_assignment.R R/plot_kraken_assignment.R R/plot_merged_assignment.R R/plot_metaphlan_assignment.R README.md cran-comments.md
inst/site/.gitignore
inst/site/assignments_table_bwa.txt
inst/site/assignments_table_bwa_single_file.txt
inst/site/assignments_table_gottcha.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/create_table.R inst/site/merge_and_plot_bwa_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_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/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_bwa_assignment.Rd man/load_bwa_assignments.Rd man/load_gottcha2_assignment.Rd man/load_gottcha2_assignments.Rd man/load_gottcha_assignment.Rd man/load_gottcha_assignments.Rd man/load_kraken_assignment.Rd man/load_kraken_assignments.Rd man/load_metaphlan_assignment.Rd man/load_metaphlan_assignments.Rd man/merge_bwa_assignments.Rd man/merge_bwa_counts.Rd man/merge_gottcha_assignments.Rd man/merge_gottcha_counts.Rd man/merge_kraken_assignments.Rd man/merge_metaphlan_assignments.Rd man/plot_bwa_assignment.Rd man/plot_gottcha_assignment.Rd man/plot_kraken_assignment.Rd man/plot_merged_assignment.Rd man/plot_metaphlan_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/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/merged_table.tsv
tests/test_data/mock_metadata.tsv
tests/test_data/test_table_bwa.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/testthat.R
tests/testthat/.gitignore
tests/testthat/test_load_bwa_assignment.R tests/testthat/test_load_bwa_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_merge_bwa_assignments.R tests/testthat/test_merge_bwa_count_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_pipeline.R tests/testthat/test_plot_bwa_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_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_metaphlan_assignment.R
LANL-Bioinformatics/MetaComp documentation built on June 3, 2017, 1:37 a.m.