Package index • AutoSpectral

All functions

AutoSpectral-package AutoSpectral: AutoSpectral: Tools for Unmixing Spectral Flow Cytometry Data
af.qc.plot(): Autofluorescence QC Plot
apply.gate(): Apply Gate
assess.mismatch(): Assess Spectral Mismatch Between Reference and Test Spectra
assess.mismatch.angle(): Assess Spectral Angle Between Reference and Test Spectra
assess.mismatch.clusters(): Cluster-Based Permutation Test for Spectral Mismatch Regions
assess.variability(): Assess Within-Fluorophore Spectral Variability
assess.variability.alignment(): Spectral-Location Alignment Between Variability and Mismatch
assess.variability.mad(): Denoised Per-Detector Variability (MAD)
assign.af.fluorophores(): Assign AF Spectrum By Fluorophore Projection
assign.af.joint.cov(): Assign AF Spectrum By Joint Covariance-Weighted Error
assign.af.joint.cov.l2(): Assign AF Spectrum By Joint Covariance-Weighted Squared 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
bead.cell.dist(): Per-Detector Spectral Distance Between Particle Types
benchmark.af.scatter.match(): Benchmark Scatter-Match Against Existing AF Assignment Methods
benchmark.af.spectra(): Benchmark AF Assignment Accuracy Against Spectral Panel Size
biexp.transform(): Fast, uncapped biexponential (logicle) transform
build.variant.basis(): Build Variant Covariance Basis
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
check.spectra.duplicates(): Check Spectra for Duplicate Fluorophores
clean.controls(): Clean Controls
compare.af(): Compare Autofluorescence Spectra Sets
compare.unmix(): Compare Unmixing Quality Across Two Spectral References
compare.unmixed.data(): Compare Two or More Sets of Already-Unmixed Data
concatenateFCS(): Concatenate Multiple FCS Files
correct.spectra.glasso(): Correct Spectra by Graphical Lasso
correct.spectra.mean.delta(): Correct Reference Spectra for Systematic Variant Offset
correct.unmixing.signatures(): Correct Unmixing Signatures
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
deconvolve.af.background(): Deconvolve Autofluorescence Background
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
.AS.check.github.update(): Check GitHub for a newer tagged release of a package
.build.control.sample.names(): Build Unique Control Sample Names
.contour.polygons.from.grid(): Contour Polygons From a Density Grid
.cosine.sim.rows(): dot Cosine Similarity Rows
.new_issue(): New Issue
.save.ggplot.fast(): Save a ggplot Directly to a Raster Device
downsample.control(): Downsample Control Data
estimate.noise.model(): Estimate Detector Noise Model
estimate.residual.spillover(): Estimate Residual Spillover From a Known-Negative Mask
estimate.unmix.time(): Estimate Unmixing Time
extract.raw.signature(): Extract Raw Signature
fit.af.spline(): Fit Spline to Autofluorescence Data
fit.robust.linear.model(): Fit Robust Linear Model
fix.my.unmix(): Fix My Unmix
fix.my.unmix.test(): Fix My Unmix (Test Version)
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.basis(): Get Autofluorescence Basis
get.af.basis.empirical(): Build A Continuous Autofluorescence Basis From Raw Events
get.af.basis.library(): Build A Continuous Autofluorescence Basis From The Discrete Library
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.aurora(): Get Autospectral Parameters for Aurora Cytometer
get.autospectral.param.auroraNL(): Get Autospectral Parameters for the Aurora Northern Lights Cytometer
get.autospectral.param.cytostellar(): Get Autospectral Parameters for CytoStellar Cytometer
get.autospectral.param.discover(): Get Autospectral Parameters for BD FACSDiscover Cytometers
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.xenith(): Get Autospectral Parameters for Xenith Cytometer
get.brightness.automated(): Get Brightness (Automated)
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.scatter.occupancy(): Get Scatter Occupancy
get.spectra.automated(): Get Fluorophore Spectra - Automated Workflow
get.spectral.variants(): Get Spectral Variations for Fluorophores
get.spread.thresholds(): Spread-Scaled Positivity Thresholds
get.top.events(): Get Top (Brightest) Events
get.universal.negative(): Get Universal Negative Control
get.variant.leakage.prior(): Variant Leakage Prior
handle.gating.error(): Handle and Plot Gating Failures
l2.normalize.spectra(): Renormalize Spectra to Unit L2 (Euclidean) Norm
match.fluorophores(): Match Fluorophores
match.markers(): Match Markers
mismatch.plot(): Plot Spectral Mismatch, Angle, Variability, Alignment, and Brightness by Dye Class
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
refine.fluorophore.spectra(): Refine Fluorophore Spectra
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
spectra.automated.steps.plot(): Plot Automated Spectra Extraction Pipeline Steps
spectra.legacy.steps.plot(): Plot Legacy Spectra Extraction Pipeline Steps
spectra.standard.workflow.plot(): Plot Standard (Manual-Gating) Spectra Extraction Workflow
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(): Tune Landmark Gate
unmix.af.basis(): Unmix With A Continuous Autofluorescence Basis
unmix.af.fwl(): Unmix With Per-Cell Autofluorescence By Frisch-Waugh
unmix.af.gls(): Unmix Autofluorescence by GLS with Per-Node Covariance
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.gls(): Unmix by Generalised Least Squares
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