PathoStat: PathoStat Statistical Microbiome Analysis Package

The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.

Author
Solaiappan Manimaran <manimaran_1975@hotmail.com>, Matthew Bendall <bendall@gwmail.gwu.edu>, Sandro Valenzuela Diaz <sandrolvalenzuelad@gmail.com>, Eduardo Castro <castronallar@gmail.com>, Tyler Faits <tfaits@gmail.com>, W. Evan Johnson <wej@bu.edu>
Date of publication
None
Maintainer
Solaiappan Manimaran <manimaran_1975@hotmail.com>
License
GPL (>= 2)
Version
1.0.0
URLs

View on Bioconductor

Man pages

coreOTUModule
Server function for Core OTU Module
coreOTUModuleUI
UI function for Core OTU Module
createPathoStat
Generates a PathoStat object from the PathoScope reports for...
findRAfromCount
Return the Relative Abundance (RA) data for the given count...
findTaxonLevel
Find the taxonomy for the given taxon id
findTaxonLevelData
Find the taxonomy level data for the given taxon level
findTaxonMat
Find the Taxonomy Information Matrix
findTaxonomy
Find the taxonomy for each taxon ids
formatTaxTable
Format taxonomy table for rendering
get_core
Select rows of OTU matrix that meet given detection and...
get_coremat
Create core OTU matrix containing number of OTUs detected at...
get_coremat_lineplot
Create line plot from core OTU matrix
getShinyInput
Getter function to get the shinyInput option
getShinyInputCombat
Getter function to get the shinyInputCombat option
getShinyInputOrig
Getter function to get the shinyInputOrig option
grepTid
Greps the tid from the given identifier string
loadPathoscopeReports
Loads all data from a set of PathoID reports. For each column...
loadPstat
Load the R data(.rda) file with pathostat object
log2CPM
Compute log2(counts per mil reads) and library size for each...
pathostat
Build PathoStat-class object from its phyloseq component.
PathoStat-class
PathoStat class to store PathoStat input data including...
plotConfRegion
Compute the confidence region for the given proportions
pstat_data
pathostat object generated from example pathoscope report...
readPathoscopeData
Reads the data from PathoScope reports and returns a list of...
runPathoStat
Statistical Microbiome Analysis on the pathostat input and...
savePstat
Save the pathostat object to R data(.rda) file
setShinyInput
Setter function to set the shinyInput option
setShinyInputCombat
Setter function to set the shinyInputCombat option
setShinyInputOrig
Setter function to set the shinyInputOrig option

Files in this package

PathoStat/DESCRIPTION
PathoStat/NAMESPACE
PathoStat/R
PathoStat/R/allClasses.R
PathoStat/R/confRegion.R
PathoStat/R/coreOTUModule.R
PathoStat/R/pathoStat.R
PathoStat/R/taxonomy.R
PathoStat/R/utils.R
PathoStat/README.md
PathoStat/build
PathoStat/build/vignette.rds
PathoStat/data
PathoStat/data/pstat_data.rda
PathoStat/data/pstat_data_2_L1.rda
PathoStat/data/pstat_data_2_L2.rda
PathoStat/inst
PathoStat/inst/NEWS.Rd
PathoStat/inst/doc
PathoStat/inst/doc/PathoStatAdvanced.R
PathoStat/inst/doc/PathoStatAdvanced.Rmd
PathoStat/inst/doc/PathoStatAdvanced.html
PathoStat/inst/doc/PathoStatIntro.Rmd
PathoStat/inst/doc/PathoStatIntro.html
PathoStat/inst/doc/PathoStatUserManual.R
PathoStat/inst/doc/PathoStatUserManual.Rmd
PathoStat/inst/doc/PathoStatUserManual.pdf
PathoStat/inst/example
PathoStat/inst/example/data
PathoStat/inst/example/data/Sample_01_1-sam-report.tsv
PathoStat/inst/example/data/Sample_01_2-sam-report.tsv
PathoStat/inst/example/data/Sample_01_3-sam-report.tsv
PathoStat/inst/example/data/Sample_02_1-sam-report.tsv
PathoStat/inst/example/data/Sample_02_2-sam-report.tsv
PathoStat/inst/example/data/Sample_02_3-sam-report.tsv
PathoStat/inst/example/data/Sample_03_1-sam-report.tsv
PathoStat/inst/example/data/Sample_03_2-sam-report.tsv
PathoStat/inst/example/data/Sample_03_3-sam-report.tsv
PathoStat/inst/example/data/sample_data.tsv
PathoStat/inst/example/pathostat_pipeline.R
PathoStat/inst/reports
PathoStat/inst/reports/PathoStat.html
PathoStat/inst/reports/libs
PathoStat/inst/reports/libs/bootstrap
PathoStat/inst/reports/libs/bootstrap/css
PathoStat/inst/reports/libs/bootstrap/css/bootstrap-responsive.min.css
PathoStat/inst/reports/libs/bootstrap/css/bootstrap.min.css
PathoStat/inst/reports/libs/bootstrap/css/user.css
PathoStat/inst/reports/libs/bootstrap/javascript
PathoStat/inst/reports/libs/bootstrap/javascript/bootstrap.min.js
PathoStat/inst/reports/libs/bootstrap/javascript/jquery-1.10.1.min.js
PathoStat/inst/reports/libs/bootstrap/javascript/user.js
PathoStat/inst/reports/pathostat_report.Rmd
PathoStat/inst/shiny
PathoStat/inst/shiny/PathoStat
PathoStat/inst/shiny/PathoStat/server.R
PathoStat/inst/shiny/PathoStat/ui.R
PathoStat/man
PathoStat/man/PathoStat-class.Rd
PathoStat/man/coreOTUModule.Rd
PathoStat/man/coreOTUModuleUI.Rd
PathoStat/man/createPathoStat.Rd
PathoStat/man/findRAfromCount.Rd
PathoStat/man/findTaxonLevel.Rd
PathoStat/man/findTaxonLevelData.Rd
PathoStat/man/findTaxonMat.Rd
PathoStat/man/findTaxonomy.Rd
PathoStat/man/formatTaxTable.Rd
PathoStat/man/getShinyInput.Rd
PathoStat/man/getShinyInputCombat.Rd
PathoStat/man/getShinyInputOrig.Rd
PathoStat/man/get_core.Rd
PathoStat/man/get_coremat.Rd
PathoStat/man/get_coremat_lineplot.Rd
PathoStat/man/grepTid.Rd
PathoStat/man/loadPathoscopeReports.Rd
PathoStat/man/loadPstat.Rd
PathoStat/man/log2CPM.Rd
PathoStat/man/pathostat.Rd
PathoStat/man/plotConfRegion.Rd
PathoStat/man/pstat_data.Rd
PathoStat/man/readPathoscopeData.Rd
PathoStat/man/runPathoStat.Rd
PathoStat/man/savePstat.Rd
PathoStat/man/setShinyInput.Rd
PathoStat/man/setShinyInputCombat.Rd
PathoStat/man/setShinyInputOrig.Rd
PathoStat/tests
PathoStat/tests/testthat
PathoStat/tests/testthat.R
PathoStat/tests/testthat/test_PathoStat.R
PathoStat/vignettes
PathoStat/vignettes/PathoStatAdvanced.Rmd
PathoStat/vignettes/PathoStatIntro.Rmd
PathoStat/vignettes/PathoStatUserManual.Rmd
PathoStat/vignettes/img
PathoStat/vignettes/img/cr.png
PathoStat/vignettes/img/cu.png
PathoStat/vignettes/img/de_limma.png
PathoStat/vignettes/img/de_rp.png
PathoStat/vignettes/img/de_table.png
PathoStat/vignettes/img/di_ad.png
PathoStat/vignettes/img/di_bd.png
PathoStat/vignettes/img/di_bip.png
PathoStat/vignettes/img/di_coo.png
PathoStat/vignettes/img/di_et.png
PathoStat/vignettes/img/pca_ev.png
PathoStat/vignettes/img/pca_pca.png
PathoStat/vignettes/img/ra_ct.png
PathoStat/vignettes/img/ra_heat.png
PathoStat/vignettes/img/ra_ra.png
PathoStat/vignettes/img/ra_summary.png
PathoStat/vignettes/img/ra_taxlevel.png
PathoStat/vignettes/img/ts.png