Man pages for ImmuneDynamics/Spectre
High-dimensional cytometry and imaging analysis.

create.dtcreate.dt - convert a Seurat or SingleCellExperiment to a...
create.statscreate.stats - perform statistical analysis and generate an...
create.sumtablecreate.sumtables - create a data.table 'summarising' cellular...
demo.asinhdemo.asinh - Demo dataset with asinh transformed values
demo.batches.1demo.batches.1 - Samples from two batches with synthetically...
demo.clustereddemo.clustered - Demo data.table with cells (rows) x markers...
demo.expdemo.exp - Demo marker expression table with markers...
demo.startdemo.start - Starting demo dataset.
demo.sumdemo.sum - Demo summary dataset with features/measurments...
do.add.colsdo.add.cols
do.add.masksdo.add.masks
do.add.percelldo.add.percell
do.aggregateAggregate data using data.table functions - summarises the...
do.aligndo.align - Function to align multiple batches of a dataset.
do.asinhdo.asinh - Transform data in selected columns using ArcSinH
do.calculate.areado.calculate.area
do.clipdo.clip - Clips data using a specified lower and upper value
do.combine.colsdo.combine.cols - Combine the values of two columns into a...
do.create.outlinesdo.create.outlines
do.embed.columnsdo.embed.columns
do.extractdo.extract
do.extract.cell.datdo.extract.cell.dat
do.filterdo.filter - filtering data.table using multiple match values
do.filter.percelldo.filter.percell
do.label.from.polygondo.label.from.polygon
do.list.summarySummarise the column names and row numbers for elements of a...
do.list.switchList switch or inversion
do.logicleUsing logicle to transform data
do.merge.filesdo.merge.files - Function to merge a list of data.tables (one...
do.pull.datado.pull.data
do.reorderdo.reorder - custom row re-ordering of a data.table
do.rescaledo.rescale - Re-scale data in selected columns between two...
do.statsStatistical analysis
do.subsampleSubsample data
do.zscoredo.zscore - Calculate z.score for a dataset
fftRtsneFIt-SNE Based on Kluger Lab FIt-SNE
make.autographmake.autograph - Creates plots using ggplot2
make.colour.plotCreate a dot plot (X vs Y) coloured by a selected continuous...
make.multi.plotMake multiple plots for multiple columns and/or multiple...
make.network.plotDraw network diagram
make.pheatmapmake.pheatmap - Create a 'pretty' heatmap (pheatmap)
make.spatial.plotmake.spatial.plot
make.volcano.plotMake an enhanced volcano plot
package.checkpackage.check - a function to check the installation of all...
package.installpackage.install - a function to install packages required for...
package.loadpackage.load - a function to load (library) all required...
prep.cytonormprep.cytonorm - Prepare reference data into a FlowSOM object
read.filesread.files - Function to read data from CSV or FCS files into...
read.spatial.filesRead TIFF files into R and and create spatial data object
run.alignrun.align - Run the alignment model on a target data.table
run.chronoclustRun the ChronoClust algorithm
run.cytonormrun.cytonorm - Run the alignment model on a target data.table
run.fitsneRun FIt-SNE, Fourier Transform TSNE.
run.flowsomRun the FlowSOM algorithm
run.harmonyrun.harmony - dun Harmony alignment on a data.table
run.knn.classifierrun.knn.classifier - Run KNN classifier
run.pcaRun the PCA algorithm (using stats::prcomp)
run.phenographrun.phenograph - Run phenograph clustering
run.prepare.chronoclustrun.prepare.chronoclust
run.rpcarun rpca
run.ruvrun.ruv - Run the the CytofRUV alignment method.
run.spatial.analysisrun.spatial.analysis
run.tsneRun the tSNE algorithm (using Rtsne::Rtsne())
run.umapRun the UMAP algorithm (using umap::umap())
spatial-classspatial object
train.cytonormtrain.cytonorm - Prepare reference data into a FlowSOM object
train.knn.classifiertrain.knn.classifier - Train KNN classifier
write.fileswrite.files - Write .csv or .fcs files
write.hdf5write.hdf5
write.sumtableswrite.sumtables - Export generated data as a .csv file
ImmuneDynamics/Spectre documentation built on Nov. 12, 2023, 8:12 a.m.