Files in fbreitwieser/pavian
Visualize and analyze metagenomics classification results
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md
R/alignment-get_pileup.R
R/alignment-module.R
R/alignment-plot_pileup.R
R/comparison-merge_reports.R
R/comparison-module.R
R/datainput-module.R
R/datainput-read_report.R
R/datainput-read_reports.R
R/datainput-read_sample_data.R
R/datainput-read_server_directory.R
R/helper-contaminants.R
R/helper-functions.R
R/helper-ggtheme.R
R/helper-humanreadable.R
R/helper-load_or_create.R
R/overview-formatSummaryDT.R
R/overview-module.R
R/overview-summarize_report.R
R/runApp.R
R/sample-build_sankey_network.R
R/sample-module.R
R/shinyapp-server.R
R/shinyapp-ui.R
README.md
inst/docker/Dockerfile
inst/docker/Makefile
inst/docker/README.md
inst/docker/shiny-server.conf
inst/docker/shiny-server.sh
inst/pavian-report-style.css
inst/pavian-report.Rmd
inst/shinyapp/app.R
inst/shinyapp/example-data/PT5-JC_polyomavirus.bam
inst/shinyapp/example-data/PT5-JC_polyomavirus.bam.bai
inst/shinyapp/example-data/brain-biopsies/PT1-DNA.report
inst/shinyapp/example-data/brain-biopsies/PT10-DNA.report
inst/shinyapp/example-data/brain-biopsies/PT2-DNA.report
inst/shinyapp/example-data/brain-biopsies/PT3-RNA.report
inst/shinyapp/example-data/brain-biopsies/PT4-RNA.report
inst/shinyapp/example-data/brain-biopsies/PT5-RNA.report
inst/shinyapp/example-data/brain-biopsies/PT6-RNA.report
inst/shinyapp/example-data/brain-biopsies/PT7-DNA.report
inst/shinyapp/example-data/brain-biopsies/PT8-DNA-S1.report
inst/shinyapp/example-data/brain-biopsies/PT8-DNA-S2.report
inst/shinyapp/example-data/brain-biopsies/PT9-DNA.report
inst/shinyapp/example-data/brain-biopsies/sample_data.csv
inst/shinyapp/example-data/hmp/SRS011061.profile
inst/shinyapp/example-data/hmp/SRS011084.profile
inst/shinyapp/example-data/hmp/SRS011086.profile
inst/shinyapp/example-data/hmp/SRS011090.profile
inst/shinyapp/example-data/hmp/SRS011098.profile
inst/shinyapp/example-data/hmp/SRS011105.profile
inst/shinyapp/example-data/hmp/SRS011111.profile
inst/shinyapp/example-data/hmp/SRS011115.profile
inst/shinyapp/example-data/hmp/SRS011126.profile
inst/shinyapp/example-data/hmp/SRS011132.profile
inst/shinyapp/example-data/hmp/SRS011134.profile
inst/shinyapp/example-data/hmp/SRS011140.profile
inst/shinyapp/example-data/hmp/SRS011144.profile
inst/shinyapp/example-data/hmp/SRS011152.profile
inst/shinyapp/style.css
inst/shinyapp/www/baboon-outline.png
inst/shinyapp/www/favicon.ico
inst/shinyapp/www/loading.gif
man/alignmentModule.Rd
man/alignmentModuleUI.Rd
man/beautify_colnames.Rd
man/comparisonModule.Rd
man/comparisonModuleUI.Rd
man/dashboardUI.Rd
man/dataInputModule.Rd
man/dataInputModuleUI.Rd
man/filter_cladeReads.Rd
man/filter_taxa.Rd
man/filter_taxon.Rd
man/get_nreads.Rd
man/get_pileup.Rd
man/get_seqlengths.Rd
man/humanreadable.Rd
man/load_or_create.Rd
man/merge_reports.Rd
man/merge_reports2.Rd
man/normalize.Rd
man/pavianServer.Rd
man/plot_pileup.Rd
man/read_report.Rd
man/read_report2.Rd
man/read_reports.Rd
man/read_sample_data.Rd
man/read_server_directory1.Rd
man/reportOverviewModule.Rd
man/reportOverviewModuleUI.Rd
man/robust_zscore.Rd
man/runApp.Rd
man/sampleModule.Rd
man/sampleModuleUI.Rd
man/summarize_report.Rd
man/summarize_reports.Rd
man/zero_if_na.Rd
pavian.Rproj
tests/testthat.R
tests/testthat/read_report/input/k2uniq-report.txt
tests/testthat/read_report/input/kraken-report.txt
tests/testthat/read_report/input/krakenuniq-report.txt
tests/testthat/read_report/input/metaphlan2-report.txt
tests/testthat/read_report/input/metaphlan3-report.txt
tests/testthat/read_report/input/metaphlan4-report.txt
tests/testthat/read_report/ref_output/k2uniq-report-res.rds
tests/testthat/read_report/ref_output/kraken-report-res.rds
tests/testthat/read_report/ref_output/krakenuniq-report-res.rds
tests/testthat/read_report/ref_output/metaphlan2-report-res.rds
tests/testthat/read_report/ref_output/metaphlan3-report-res.rds
tests/testthat/read_report/ref_output/metaphlan4-report-res.rds
tests/testthat/test-read_report.R
vignettes/MANUAL.md
vignettes/alignment-viewer-pt5.png
vignettes/download-genome-jcv.png
vignettes/flow-pt5-2.png
vignettes/flow-pt5.png
vignettes/load-data-set.png
vignettes/menu-comp.png
vignettes/menu-comp2.png
vignettes/pavian-bibliography.bib
vignettes/pavian-vignette.Rmd
vignettes/pavian-vignette.html
vignettes/pavian-walkthrough.Rmd
vignettes/pavian-walkthrough.pdf
vignettes/pavian-walkthrough.tex
vignettes/results-overview.png
vignettes/shoot_pavian_screenshots.R
