Package: cyanoFilter 1.21.0

Oluwafemi Olusoji

cyanoFilter: Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

An approach to filter out and/or identify phytoplankton cells from all particles measured via flow cytometry pigment and cell complexity information. It does this using a sequence of one-dimensional gates on pre-defined channels measuring certain pigmentation and complexity. The package is especially tuned for cyanobacteria, but will work fine for phytoplankton communities where there is at least one cell characteristic that differentiates every phytoplankton in the community.

Authors:Oluwafemi Olusoji [cre, aut], Aerts Marc [ctb], Delaender Frederik [ctb], Neyens Thomas [ctb], Spaak jurg [aut]

cyanoFilter_1.21.0.tar.gz
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cyanoFilter_1.21.0.tgz(r-4.6-any)cyanoFilter_1.21.0.tgz(r-4.5-any)
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cyanoFilter_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cyanoFilter/json (API)

# Install 'cyanoFilter' in R:

install.packages('cyanoFilter', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fomotis/cyanofilter/issues

On BioConductor:cyanoFilter-1.21.0(bioc 3.24)cyanoFilter-1.20.0(bioc 3.23)

flowcytometry clustering onechannel

4.30 score 4 scripts 34 exports 117 dependencies

Last updated from:68460c0fe0. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	195
linux-devel-x86_64	OK	290
source / vignettes	OK	295
linux-release-x86_64	OK	284
macos-release-arm64	OK	139
macos-oldrel-arm64	OK	123
windows-devel	OK	164
windows-release	OK	115
windows-oldrel	OK	172
wasm-release	OK	196

Exports:accTest accuracy cellMargin clusterExtract clusterExtractp DebrisFilter debrisNc fullFlowframe gateFunc getChannel ggpairsDens ggplotDens ggplotDens2 goodFcs is.DebrisFilter is.flowFrame is.flowSet is.MarginEvents is.PhytopFilter lnTrans MarginEvents newFlowframe noNA noNeg oneDgate pairsPlot phytoFilter PhytopFilter pigmentGate plot reducedFlowframe retain rowNumbers summaries

Dependencies:abind backports BH Biobase BiocGenerics biocmake bitops boot broom car carData caTools cli colorspace cowplot cpp11 crayon cytolib cytometree deldir Deriv dir.expiry doBy dplyr farver filelock flowClust flowCore flowDensity flowViz forcats forecast Formula fracdiff generics geometry GGally ggplot2 ggstats glue GoFKernel gplots graph gtable gtools hexbin hms IDPmisc igraph interp isoband jpeg KernSmooth labeling lattice latticeExtra lifecycle linprog lme4 lmtest lpSolve magic magrittr MASS Matrix MatrixModels matrixStats mclust mgcv minqa modelr mrfDepth nlme nloptr nnet numDeriv patchwork pbkrtest pillar pkgconfig plyr png polyclip prettyunits progress purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppProgress Rdpack reformulas reshape2 Rhdf5lib rlang RProtoBufLib S4Vectors S7 scales SparseM stringi stringr survival tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite withr zoo

cyanoFilter

Rendered fromcyanoFilter.Rmdusingknitr::rmarkdown

Last update: 2021-03-08
Started: 2020-09-30

Help page	Topics
tests the accuracy of several automated gating functions on monoculture flow cytometry experiments.	accTest
samples two rows in a matrix and check if the samples are similar or different based on their cluster labels	accuracy
Removes or assign indicators to margin events.	cellMargin
extract clusters based on supplied cluster indicator	clusterExtract
takes a flowframe, name of cluster column and extracts part of flowframe that makes up proportion.	clusterExtractp
cyanoFilter: A package to identify and cluster phytoplankton cells contained in flow cytometry data.	cyanoFilter
the Debris class	DebrisFilter
gates out or assign indicators to debris particle based on their chlorophyll expression.	debrisNc
generic function for extracting the full flowframe	fullFlowframe
accesor method for reduced flowframe (DebrisFilter class)	fullFlowframe,DebrisFilter-method
accesor method for the fullflowframe (MarginEvent class)	fullFlowframe,MarginEvents-method
accesor method for full flowframe(PhytoFilter class)	fullFlowframe,PhytopFilter-method
tests the accuracy of several automated gating functions on monoculture flow cytometry experiments.	gateFunc
returns the channel with more than one peak present. It returns NA if there is only one peak present.	getChannel
produces a scatter plot of the expression matrix of the flowframe. If a cluster variable is given, it assigns different colors to the clusters.	ggpairsDens
plots two channels of a flowframe.	ggplotDens
plots two channels of a flowframe with different colors for clusters identified.	ggplotDens2
indicates if measurement from a flowfile is good or bad.	goodFcs
function to check if object is of class cyanoFilter(DebrisFilter)	is.DebrisFilter
function to check if object is a flowFrame	is.flowFrame
function to check if object is a flowSet	is.flowSet
function to check if object is of class cyanoFilter(MarginEvents)	is.MarginEvents
function to check if object is of class cyanoFilter(PhytoFilter)	is.PhytopFilter
log transforms the expression matrix of a flowframe	lnTrans
the marginEvent class	MarginEvents
takes a flowframe, a group indicator and formulates another flowframe with group indicator as part of the expression matrix of the new flowframe.	newFlowframe
Removes NA values from the expression matrix of a flow cytometer file.	noNA
Removes negative values from the expression matrix	noNeg
returns the labels stating the cluster of each row in a flowfile.	oneDgate
produces a scatter plot of the expression matrix of a flowframe. Note that, it takes some time to display the plot.	pairsPlot
gates out and assign indicators to phytoplankton cells based on the expression of measured cell complexity channels.	phytoFilter
the phytofilter class	PhytopFilter
gates out or assign indicators to phytoplankton cells based on the expression of the measured pigments.	pigmentGate
plot method for DebrisFilter objects	plot,DebrisFilter,ANY-method
plot method for MarginEvents objects	plot,MarginEvents,ANY-method
plot method for PhytoFilter objects	plot,PhytopFilter,ANY-method
generic function for extracting the full flowframe	reducedFlowframe
accesor method for reduced flowframe (DebrisFilter class)	reducedFlowframe,DebrisFilter-method
accesor method for reduced flowframe (MarginEvent class)	reducedFlowframe,MarginEvents-method
accesor method for reduced flowframe(PhytoFilter class)	reducedFlowframe,PhytopFilter-method
Decides if a file should be retiained or removed based on its status.	retain
returns the position of the cells below, above or between estimated gates	rowNumbers
takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster	summaries
takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster	summaries,DebrisFilter-method
takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster	summaries,MarginEvents-method
takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster	summaries,PhytopFilter-method

Package: cyanoFilter 1.21.0

cyanoFilter: Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

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