flowPhyto: Methods for Continuous Flow Cytometry
Version 1.16.0

Automated Analysis of Continuous Flow Cytometry Data.

Browse man pages Browse package API and functions Browse package files

AuthorFrancois Ribalet <ribalet@u.washington.edu>
Date of publicationNone
MaintainerChris Berthiaume <chrisbee@uw.edu>
LicenseArtistic-2.0
Version1.16.0
URL http://seaflow.ocean.washington.edu
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("flowPhyto")

Man pages

census: Cross tabulate a consensus vector
censusFile: Create a consensus from several classification vector files...
CHANNEL.CLMNS: Seaflow detector column names
CHANNEL.CLMNS.SM: Seaflow detector column names
classify: Cluster the different Phytoplankton Populations
classifyFile: Cluster the different Phytoplankton Populations
cleanupLogs: Remove R Batch Output Files.
clearOutputs: Clear the output files from particular flowPhyto pipeline...
cmdArgsToVariables: Create R variables from command line parameters
combineCensusFiles: Combine the Census Files.
combineSdsFiles: Combine the SDS files.
consensus: create a consensus vector from several classification vectors
consensusFile: Create a consensus from several classification vector files...
createResamplingScheme: Generate the Population Resampling scheme.
EVT.HEADERS: Seaflow File Headers
filter: Filter Optimally Positioned Particles from an EVT dataframe
filterFile: Filter an EVT file and output an Optimally Positioned...
getCruiseFiles: Get all of the files from a cruise.
getCruisePath: Get the Cruise Directory.
getFileNumber: Get the (original) integer file number of any seaflow...
joinSDS: join this dataframe to the corresponding SDS log file entry.
pipeline: Run the SeaFlow Pipeline
plotCruiseStats: Plot a seaflow cruise statistics
plotCytogram: Plot a Phytoplankton Cytogram
plotLatLongMap: plot file location on a map
plotStatMap: plot the stat.tab file on a map
POP.DEF: population definition table
readConsensusFile: Read a Consensus File.
readPopDef: Read the Population Definition File.
readSeaflow: Read a SeaFlow File
REPO.PATH: Seaflow Data directory
summarize: Summarize phytoplankon event & log parameters
summarizeFile: Compute aggregate statistics on a collection of opp or fcs...
validatePopDef: Validate a Population Definition Dataframe.
writeSeaflow: Write A SeaFlow File

Functions

Files

flowPhyto/DESCRIPTION
flowPhyto/NAMESPACE
flowPhyto/R
flowPhyto/R/Census.R
flowPhyto/R/Classify.R
flowPhyto/R/Database.R
flowPhyto/R/Define.R
flowPhyto/R/Files.R
flowPhyto/R/Filter.R
flowPhyto/R/Globals.R
flowPhyto/R/Load.R
flowPhyto/R/Pipeline.R
flowPhyto/R/Plot.R
flowPhyto/R/SDS.R
flowPhyto/R/Summarize.R
flowPhyto/R/Util.R
flowPhyto/build
flowPhyto/build/vignette.rds
flowPhyto/inst
flowPhyto/inst/CITATION
flowPhyto/inst/NEWS
flowPhyto/inst/doc
flowPhyto/inst/doc/flowPhyto.R
flowPhyto/inst/doc/flowPhyto.Rnw
flowPhyto/inst/doc/flowPhyto.pdf
flowPhyto/inst/extdata
flowPhyto/inst/extdata/database.conf.R
flowPhyto/inst/extdata/fcs_cruise
flowPhyto/inst/extdata/fcs_cruise/CD.20070615.A.0010.fcs
flowPhyto/inst/extdata/fcs_cruise/pop.def.tab
flowPhyto/inst/extdata/seaflow_cruise
flowPhyto/inst/extdata/seaflow_cruise/2010_365
flowPhyto/inst/extdata/seaflow_cruise/2010_365/439.evt
flowPhyto/inst/extdata/seaflow_cruise/2010_365/439.evt.opp
flowPhyto/inst/extdata/seaflow_cruise/2010_365/439.evt.opp.439-class.vct
flowPhyto/inst/extdata/seaflow_cruise/2010_365/440.evt
flowPhyto/inst/extdata/seaflow_cruise/2010_365/440.evt.opp
flowPhyto/inst/extdata/seaflow_cruise/2010_365/440.evt.opp.439-class.vct
flowPhyto/inst/extdata/seaflow_cruise/2010_365/440.evt.opp.440-class.vct
flowPhyto/inst/extdata/seaflow_cruise/2010_365/440.evt.opp.census.tab
flowPhyto/inst/extdata/seaflow_cruise/2010_365/440.evt.opp.consensus.vct
flowPhyto/inst/extdata/seaflow_cruise/2010_365/sds_2010_365.txt
flowPhyto/inst/extdata/seaflow_cruise/2011_001
flowPhyto/inst/extdata/seaflow_cruise/2011_001/1.evt
flowPhyto/inst/extdata/seaflow_cruise/2011_001/1.evt.opp
flowPhyto/inst/extdata/seaflow_cruise/2011_001/1.evt.opp.1-class.vct
flowPhyto/inst/extdata/seaflow_cruise/2011_001/1.evt.opp.439-class.vct
flowPhyto/inst/extdata/seaflow_cruise/2011_001/1.evt.opp.440-class.vct
flowPhyto/inst/extdata/seaflow_cruise/2011_001/1.evt.opp.census.tab
flowPhyto/inst/extdata/seaflow_cruise/2011_001/1.evt.opp.consensus.vct
flowPhyto/inst/extdata/seaflow_cruise/2011_001/2.evt
flowPhyto/inst/extdata/seaflow_cruise/2011_001/2.evt.opp
flowPhyto/inst/extdata/seaflow_cruise/2011_001/2.evt.opp.1-class.vct
flowPhyto/inst/extdata/seaflow_cruise/2011_001/2.evt.opp.2-class.vct
flowPhyto/inst/extdata/seaflow_cruise/2011_001/2.evt.opp.440-class.vct
flowPhyto/inst/extdata/seaflow_cruise/2011_001/2.evt.opp.census.tab
flowPhyto/inst/extdata/seaflow_cruise/2011_001/2.evt.opp.consensus.vct
flowPhyto/inst/extdata/seaflow_cruise/2011_001/3.evt
flowPhyto/inst/extdata/seaflow_cruise/2011_001/3.evt.opp
flowPhyto/inst/extdata/seaflow_cruise/2011_001/3.evt.opp.1-class.vct
flowPhyto/inst/extdata/seaflow_cruise/2011_001/3.evt.opp.2-class.vct
flowPhyto/inst/extdata/seaflow_cruise/2011_001/3.evt.opp.3-class.vct
flowPhyto/inst/extdata/seaflow_cruise/2011_001/3.evt.opp.census.tab
flowPhyto/inst/extdata/seaflow_cruise/2011_001/3.evt.opp.consensus.vct
flowPhyto/inst/extdata/seaflow_cruise/2011_001/sds_2011_001.txt
flowPhyto/inst/extdata/seaflow_cruise/census.tab
flowPhyto/inst/extdata/seaflow_cruise/pop.def.tab
flowPhyto/inst/extdata/seaflow_cruise/sds.tab
flowPhyto/inst/extdata/seaflow_cruise/stats.tab
flowPhyto/inst/script
flowPhyto/inst/script/Census.R
flowPhyto/inst/script/Classify.R
flowPhyto/inst/script/Filter.R
flowPhyto/inst/script/Plot.R
flowPhyto/inst/script/Summarize.R
flowPhyto/man
flowPhyto/man/CHANNEL.CLMNS.Rd
flowPhyto/man/CHANNEL.CLMNS.SM.Rd
flowPhyto/man/EVT.HEADERS.Rd
flowPhyto/man/POP.DEF.Rd
flowPhyto/man/REPO.PATH.Rd
flowPhyto/man/census.Rd
flowPhyto/man/censusFile.Rd
flowPhyto/man/classify.Rd
flowPhyto/man/classifyFile.Rd
flowPhyto/man/cleanupLogs.Rd
flowPhyto/man/clearOutputs.Rd
flowPhyto/man/cmdArgsToVariables.Rd
flowPhyto/man/combineCensusFiles.Rd
flowPhyto/man/combineSdsFiles.Rd
flowPhyto/man/consensus.Rd
flowPhyto/man/consensusFile.Rd
flowPhyto/man/createResamplingScheme.Rd
flowPhyto/man/filter.Rd
flowPhyto/man/filterFile.Rd
flowPhyto/man/getCruiseFiles.Rd
flowPhyto/man/getCruisePath.Rd
flowPhyto/man/getFileNumber.Rd
flowPhyto/man/joinSDS.Rd
flowPhyto/man/pipeline.Rd
flowPhyto/man/plotCruiseStats.Rd
flowPhyto/man/plotCytogram.Rd
flowPhyto/man/plotLatLongMap.Rd
flowPhyto/man/plotStatMap.Rd
flowPhyto/man/readConsensusFile.Rd
flowPhyto/man/readPopDef.Rd
flowPhyto/man/readSeaflow.Rd
flowPhyto/man/summarize.Rd
flowPhyto/man/summarizeFile.Rd
flowPhyto/man/validatePopDef.Rd
flowPhyto/man/writeSeaflow.Rd
flowPhyto/vignettes
flowPhyto/vignettes/flowPhyto.Rnw
flowPhyto documentation built on Sept. 12, 2016, 6:18 a.m.