flowPhyto: Methods for Continuous Flow Cytometry

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Automated Analysis of Continuous Flow Cytometry Data.

Author
Francois Ribalet <ribalet@u.washington.edu>
Date of publication
None
Maintainer
Chris Berthiaume <chrisbee@uw.edu>
License
Artistic-2.0
Version
1.16.0
URLs

View on Bioconductor

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

Files in this package

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