Files in mani2012/PathoStat
PathoStat Statistical Microbiome Analysis Package
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/allClasses.R
R/biomarker.R
R/differentialAnalysis.R
R/pathoStat.R
R/taxonomy.R
R/utils.R
R/visualization.R
README.md
data/asthma_pstat_data.rda
data/pstat_data.rda
data/pstat_data_2_L1.rda
data/pstat_data_2_L2.rda
inst/example/data/Sample_01_1-sam-report.tsv
inst/example/data/Sample_01_2-sam-report.tsv
inst/example/data/Sample_01_3-sam-report.tsv
inst/example/data/Sample_02_1-sam-report.tsv
inst/example/data/Sample_02_2-sam-report.tsv
inst/example/data/Sample_02_3-sam-report.tsv
inst/example/data/count_example/annotation_example.csv
inst/example/data/count_example/count_example.csv
inst/example/data/count_example/taxonomy_table.csv
inst/example/data/pathoscope_example/Sample_01_1-sam-report.tsv
inst/example/data/pathoscope_example/Sample_01_2-sam-report.tsv
inst/example/data/pathoscope_example/Sample_01_3-sam-report.tsv
inst/example/data/pathoscope_example/Sample_02_1-sam-report.tsv
inst/example/data/pathoscope_example/Sample_02_2-sam-report.tsv
inst/example/data/pathoscope_example/Sample_02_3-sam-report.tsv
inst/example/data/pathoscope_example/sample_data.tsv
inst/example/data/sample_data.tsv
inst/example/pathostat_pipeline.R
inst/shiny/PathoStat/app.R
inst/shiny/PathoStat/server/server_01_upload.R
inst/shiny/PathoStat/server/server_02_filter.R
inst/shiny/PathoStat/server/server_03_ra.R
inst/shiny/PathoStat/server/server_04_diversity.R
inst/shiny/PathoStat/server/server_05_dimreduction.R
inst/shiny/PathoStat/server/server_06_differential.R
inst/shiny/PathoStat/server/server_07_biomarker.R
inst/shiny/PathoStat/ui/ui_01_upload.R
inst/shiny/PathoStat/ui/ui_02_filter.R
inst/shiny/PathoStat/ui/ui_03_ra.R
inst/shiny/PathoStat/ui/ui_04_diversity.R
inst/shiny/PathoStat/ui/ui_05_dimreduction.R
inst/shiny/PathoStat/ui/ui_06_differential.R
inst/shiny/PathoStat/ui/ui_07_biomarker.R
inst/shiny/PathoStat/utils/helpers.R
inst/shiny/PathoStat/utils/old_server_stuff.R
inst/shiny/PathoStat/utils/old_ui_stuff.R
inst/shiny/PathoStat/www/ajax-loader-bar.gif
inst/shiny/PathoStat/www/bootstrap.min.css
inst/shiny/PathoStat/www/bu_bioinfo_logo.png
inst/shiny/PathoStat/www/bu_logo.png
inst/shiny/PathoStat/www/cbm_logo.jpeg
inst/shiny/PathoStat/www/cbm_logo.png
inst/shiny/PathoStat/www/count_table_example.png
man/Bootstrap_LOOCV_LR_AUC.Rd
man/Chisq_Test_Pam.Rd
man/Fisher_Test_Pam.Rd
man/GET_PAM.Rd
man/LOOAUC_simple_multiple_noplot_one_df.Rd
man/LOOAUC_simple_multiple_one_df.Rd
man/PathoStat-class.Rd
man/TranslateIdToTaxLevel.Rd
man/Wilcox_Test_df.Rd
man/findRAfromCount.Rd
man/findTaxonMat.Rd
man/findTaxonomy.Rd
man/findTaxonomy300.Rd
man/formatTaxTable.Rd
man/getShinyInput.Rd
man/getShinyInputCombat.Rd
man/getShinyInputOrig.Rd
man/getSignatureFromMultipleGlmnet.Rd
man/grepTid.Rd
man/loadPathoscopeReports.Rd
man/loadPstat.Rd
man/log2CPM.Rd
man/percent.Rd
man/phyloseq_to_edgeR.Rd
man/plotPCAPlotly.Rd
man/plotPCoAPlotly.Rd
man/pstat_data.Rd
man/readPathoscopeData.Rd
man/runPathoStat.Rd
man/savePstat.Rd
man/setShinyInput.Rd
man/setShinyInputCombat.Rd
man/setShinyInputOrig.Rd
man/summarizeTable.Rd
tests/testthat.R
tests/testthat/test_try.R
vignettes/PathoStat-vignette.Rmd
