Package index • AutoSpectral

All functions

AutoSpectral-package AutoSpectral: AutoSpectral: Tools for Unmixing Spectral Flow Cytometry Data
af.qc.plot(): Autofluorescence QC Plot
assign.af.fluorophores(): Assign AF Spectrum By Fluorophore Projection
assign.af.joint.cov(): Assign AF Spectrum By Joint Covariance-Weighted Error
assign.af.residuals(): Assign AF Spectrum By Residual Alignment
assign.af.scatter.match(): Assign AF Spectrum By Scatter-Matched Reference Averaging
assign.gates(): Assign Gates
assign.variants(): Assign Variant Spectrum By Fluorophore Projection
assign.variants.cosine(): Assign Variant Spectrum By Fluorophore Projection
benchmark.af.scatter.match(): Benchmark Scatter-Match Against Existing AF Assignment Methods
benchmark.af.spectra(): Benchmark AF Assignment Accuracy Against Spectral Panel Size
calculate.condition.number(): Calculate Condition Number
calculate.hotspot.matrix(): Calculate Hotspot Matrix
calculate.optimize.necessity(): Calculate Optimization Necessity Scores for Spectral Variants
calculate.ssi(): Calculate Secondary Stain Index and Spillover
calculate.weights(): Calculate Weights
check.channels(): Check Channels
check.consistency(): Check Gate Consistency
check.control.file(): Check Control File
check.gates(): Check Gates For Errors
clean.controls(): Clean Controls
compare.af(): Compare Autofluorescence Spectra Sets
compare.unmix(): Compare Unmixing Quality Across Two Spectral References
concatenateFCS(): Concatenate Multiple FCS Files
cosine.similarity(): Calculate Cosine Similarity
cosine.similarity.plot(): Cosine Similarity Plot
create.biplot(): Create Biplot
create.control.file(): Create Control File
create.directory(): Create Directory
create.heatmap(): Create Heatmap Plot
create.parallel.lapply(): Create Parallel Lapply
define.flow.control(): Define Flow Control
define.gate.density(): Define Gate by Density
define.gate.landmarks(): Define Gate by Landmarks
define.keywords(): Define Keywords
do.gate(): Do Gate
do.gate.af(): Perform Gating on Autofluorescence Parameters
.cosine.sim.rows(): dot Cosine Similarity Rows
.new_issue(): New Issue
downsample.control(): Downsample Control Data
fit.af.spline(): Fit Spline to Autofluorescence Data
fit.robust.linear.model(): Fit Robust Linear Model
gate.af.identify.plot(): Plot Autofluorescence Identification Gate
gate.af.sample.plot(): Plot Autofluorescence Gates on Samples
gate.define.plot(): Gate Definition Plot
gate.sample.plot(): Plot Pre-defined Gate on Sample
gate.scatter.match(): Gate Matching Scatter
get.af.spectra(): Get Autofluorescence Spectra
get.autospectral.param(): Get AutoSpectral Parameters
get.autospectral.param.a5se(): Get AutoSpectral Parameters for the FACSymphony A5SE Cytometer
get.autospectral.param.a8(): Get Autospectral Parameters for DiscoverA8 Cytometer
get.autospectral.param.aurora(): Get Autospectral Parameters for Aurora Cytometer
get.autospectral.param.auroraNL(): Get Autospectral Parameters for the Aurora Northern Lights Cytometer
get.autospectral.param.id7000(): Get Autospectral Parameters for ID7000 Cytometer
get.autospectral.param.minimal(): Get Minimal Autospectral Parameters
get.autospectral.param.mosaic(): Get Autospectral Parameters for Mosaic Cytometer
get.autospectral.param.opteon(): Get Autospectral Parameters for Opteon Cytometer
get.autospectral.param.s8(): Get Autospectral Parameters for DiscoverS8 Cytometer
get.autospectral.param.xenith(): Get Autospectral Parameters for Xenith Cytometer
get.density.palette(): Get Density Color Palette
get.fluor.variants(): Get Fluorophore Variants
get.fluorophore.spectra(): Get Fluorophore Spectra
get.gated.flow.expression.data(): Get Gated Flow Expression Data
get.spectra.automated(): Get Fluorophore Spectra - Automated Workflow
get.spectral.variants(): Get Spectral Variations for Fluorophores
get.top.events(): Get Top (Brightest) Events
get.universal.negative(): Get Universal Negative Control
handle.gating.error(): Handle and Plot Gating Failures
match.fluorophores(): Match Fluorophores
match.markers(): Match Markers
optimize.unmix(): Optimize Spectral Unmixing
parallel.backend(): Parallel Backend
qc.af.spectra(): QC Autofluorescence Spectra
read.bd.spectra(): Extract Spectra From BD FCS File
read.channel(): Read Channel Information
read.scatter.parameter(): Read Scatter Parameters
read.spectra(): Read In Saved Spectra
read.spectroflo.expt(): Extract Spectra From SpectroFlo Expt File
readFCS(): Read FCS File
readFCSheader(): Read FCS Header
reload.flow.control(): Reload Flow Control Information
remove.af(): Remove Autofluorescence Contamination
run.af.removal(): Run Autofluorescence Removal
run.downsample(): Run Downsample
run.universal.negative(): Run Universal Negative
sample.fcs.file(): Sample FCS File
sanitize.optimization.inputs(): Sanitize Optimization Inputs
save.unmixing.matrix(): Save Unmixing Matrix
scatter.match.plot(): Plot Scatter-Matching of Universal Negative
sim.flow.data(): Simulate Spectral Flow Cytometry Data
spectral.heatmap(): Spectral Heatmap
spectral.mismatch.plot(): Spectral Mismatch Plot
spectral.reference.plot(): Spectral Reference Plot
spectral.ribbon.plot(): Spectral Ribbon Plot
spectral.trace(): Plot Fluorophore Spectra Traces
spectral.variant.plot(): Spectral Variant Plot
spectral.variant.plot.dens(): Spectral Variant Density Plot
test.af.accuracy(): Test Autofluorescence Assignment Accuracy
tune.gate(): Define Gate by Density
unmix.autospectral(): Unmix AutoSpectral
unmix.autospectral.joint(): Joint AutoSpectral Unmixing (Pure R)
unmix.fcs(): Unmix FCS Data
unmix.folder(): Unmix All FCS Files in a Directory
unmix.ols(): Unmix OLS
unmix.ols.fast(): Unmix OLS Fast
unmix.poisson(): Unmix Using Poisson Regression
unmix.wls(): Unmix Using Weighted Least Squares
unmix.wls.fast(): Unmix WLS Fast
unmix.wls.per.cell(): Unmix WLS Per Cell
unmixed.mxn.plot(): m \(\times\) n Unmixed Biplot Grid
unmixed.nxn.plot(): n \(\times\) n Unmixed Biplot Triangle
validate.control.file(): Validate Control File
writeFCS(): Write FCS File