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.

AuthorSolaiappan 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 publicationNone
MaintainerSolaiappan Manimaran <manimaran_1975@hotmail.com>
LicenseGPL (>= 2)
Version1.0.0
https://github.com/mani2012/PathoStat

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

Functions

coreOTUModule Man page
coreOTUModuleUI Man page
createPathoStat Man page
findRAfromCount Man page
findTaxonLevel Man page
findTaxonLevelData Man page
findTaxonMat Man page
findTaxonomy Man page
formatTaxTable Man page
get_core Man page
get_coremat Man page
get_coremat_lineplot Man page
getShinyInput Man page
getShinyInputCombat Man page
getShinyInputOrig Man page
grepTid Man page
loadPathoscopeReports Man page
loadPstat Man page
log2CPM Man page
pathostat Man page
pathostat1 Man page
PathoStat-class Man page
plotConfRegion Man page
pstat Man page
pstat_data Man page
readPathoscopeData Man page
runPathoStat Man page
savePstat Man page
setShinyInput Man page
setShinyInputCombat Man page
setShinyInputOrig Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.