Files in fbreitwieser/pavian
Visualize and analyze metagenomics classification results

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
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
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/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
fbreitwieser/pavian documentation built on Oct. 15, 2018, 11:06 a.m.