plethy: R framework for exploration and analysis of respirometry data

This package provides the infrastructure and tools to import, query and perform basic analysis of whole body plethysmography and metabolism data. Currently support is limited to data derived from Buxco respirometry instruments as exported by their FinePointe software.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("plethy")
AuthorDaniel Bottomly [aut, cre], Marty Ferris [ctb], Beth Wilmot [aut], Shannon McWeeney [aut]
Bioconductor views DataImport DataRepresentation Infastructure TimeCourse biocViews
Date of publicationNone
MaintainerDaniel Bottomly <bottomly@ohsu.edu>
LicenseGPL-3
Version1.12.1
https://github.com/dbottomly/plethy

View on Bioconductor

Functions

addAnnotation Man page
addAnnotation,BuxcoDB-method Man page
add.labels.by.sample Man page
adjust.labels Man page
annoCols Man page
annoCols,BuxcoDB-method Man page
annoLevels Man page
annoLevels,BuxcoDB-method Man page
annoTable Man page
annoTable,BuxcoDB-method Man page
break.type.query Man page
BuxcoDB Man page
BuxcoDB-class Man page
buxco.sample.data.path Man page
day.infer.query Man page
dbImport Man page
dbName Man page
dbName,BuxcoDB-method Man page
get.err.breaks Man page
makeBuxcoDB Man page
mvtsplot Man page
mvtsplot,BuxcoDB-method Man page
parse.buxco Man page
parse.buxco.basic Man page
plethy Man page
plethy-package Man page
proc.sanity Man page
retrieveData Man page
retrieveData,BuxcoDB-method Man page
retrieveMatrix Man page
retrieveMatrix,BuxcoDB-method Man page
sample.db.path Man page
samples Man page
samples,BuxcoDB-method Man page
summaryMeasures Man page
summaryMeasures,BuxcoDB-method Man page
tables Man page
tables,BuxcoDB-method Man page
tsplot Man page
tsplot,BuxcoDB-method Man page
variables Man page
variables,BuxcoDB-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/BuxcoDB.R R/RetList.R R/buxco_db_v2.R R/dep_parser.R R/utilities.R
README.md
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/plethy.R
inst/doc/plethy.Rnw
inst/doc/plethy.pdf
inst/extdata
inst/extdata/BuxcoR_sample.csv
inst/extdata/BuxcoR_sample.db
inst/extdata/plethy.template
inst/extdata/plethy.template/DESCRIPTION
inst/extdata/plethy.template/NAMESPACE
inst/extdata/plethy.template/R
inst/extdata/plethy.template/R/zzz.R
inst/extdata/plethy.template/man
inst/extdata/plethy.template/man/pkg.Rd
inst/unitTests
inst/unitTests/test_check_helpers.R
man
man/BuxcoDB.Rd man/add_query_funcs.Rd man/dbImport.Rd man/parsing.Rd man/plethy.Rd man/utilities.Rd
tests
tests/runTests.R
vignettes
vignettes/plethy.Rnw

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

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

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