Package: Spectre 1.3.0

Thomas Ashhurst

Spectre: High-dimensional cytometry and imaging analysis

A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.

Authors:Thomas Ashhurst [aut, cre], Felix Marsh-Wakefield [aut], Givanna Putri [aut]

Spectre_1.3.0.tar.gz
Spectre_1.3.0.zip(r-4.7-any)Spectre_1.3.0.zip(r-4.6-any)Spectre_1.3.0.zip(r-4.5-any)
Spectre_1.3.0.tgz(r-4.6-any)Spectre_1.3.0.tgz(r-4.5-any)
Spectre_1.3.0.tar.gz(r-4.7-any)Spectre_1.3.0.tar.gz(r-4.6-any)
Spectre_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Spectre/json (API)

# Install 'Spectre' in R:
install.packages('Spectre', repos = c('https://agshaas.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/immunedynamics/spectre/issues

Pkgdown/docs site:https://immunedynamics.io

Datasets:
  • demo.clustered - Demo.clustered - Demo data.table with cells (rows) x markers (columns), with clusters, populations, and UMAP values added

On CRAN:

Conda:

batch-alignmentclusteringcomputational-analysisdimensionality-reductionflow-cytometrymass-cytometry

5.13 score 71 stars 127 scripts 61 exports 171 dependencies

Last updated from:159dc9f6d7. Checks:7 ERROR, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develERROR435
source / vignettesOK490
linux-releaseERROR427
macos-releaseERROR378
macos-oldrelERROR422
windows-develERROR339
windows-releaseERROR305
windows-oldrelERROR326
wasm-releaseOK256

Exports:adjust.filescheck.filescreate.dtcreate.statscreate.sumtabledo.add.colsdo.add.masksdo.add.percelldo.aggregatedo.aligndo.asinhdo.calculate.areado.clipdo.combine.colsdo.create.outlinesdo.extractdo.extract.cell.datdo.filterdo.filter.percelldo.label.from.polygondo.list.summarydo.list.switchdo.logicledo.merge.filesdo.pull.datado.reorderdo.rescaledo.statsdo.subsampledo.zscorefast.colour.plotfast.multi.plotmake.autographmake.colour.plotmake.multi.plotmake.pheatmapmake.spatial.plotmake.volcano.plotpackage.checkpackage.installpackage.loadprep.cytonormread.filesread.spatial.filesrun.alignrun.cytonormrun.fitsnerun.flowsomrun.harmonyrun.knn.classifierrun.pcarun.phenographrun.rpcarun.spatial.analysisrun.tsnerun.umapspatialtrain.cytonormtrain.knn.classifierwrite.fileswrite.hdf5

Dependencies:abindALLaskpassbackportsbase64encBHBiobaseBiocGenericsbiocmakebootbroombslibcachemcarcarDatacliclustercolorRampscolorspaceConsensusClusterPluscorrplotcowplotcpp11crosstalkcytolibdata.tabledendextenddendsortDerivdigestdir.expirydoBydplyrdqrngDTellipseemmeansestimabilityevaluatefactoextraFactoMineRfarverfastmapfilelockflashClustflowCoreFlowSOMFNNfontawesomeforecastFormulafracdifffsgenericsggforceggnewscaleggplot2ggpointdensityggpubrggrepelggsciggsignifggthemesgluegridExtragtablegtoolsherehighrhtmltoolshtmlwidgetsigraphirlbaisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleapslifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmimeminqamodelrmultcompViewmvtnormnlmenloptrnnetnumDerivopensslotelpatchworkpbkrtestpheatmappillarpkgconfigpngpolyclippolynompromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressRcppTOMLRdpackreformulasreticulateRhdf5librlangrmarkdownrprojrootRProtoBufLibRSpectrarstatixrstudioapirsvdRtsneS4VectorsS7sassscalesscattermorescatterplot3dshowtextshowtextdbsitmoSparseMstringistringrsurvivalsyssysfontssystemfontstibbletidyrtidyselecttimeDatetinytextweenrumapurcautf8uwotvctrsviridisviridisLitewithrxfunXMLyamlzoo

Readme and manuals

Help Manual

Help pageTopics
adjust.filesadjust.files
check.filescheck.files
create.dt - convert a Seurat or SingleCellExperiment to a data.tablecreate.dt
create.stats - perform statistical analysis and generate an output data.tablecreate.stats
create.sumtable - create a data.table 'summarising' cellular data by sample and population/cluster.create.sumtable
demo.clustered - Demo data.table with cells (rows) x markers (columns), with clusters, populations, and UMAP values addeddemo.clustered
do.add.colsdo.add.cols
do.add.masksdo.add.masks
do.add.percelldo.add.percell
Aggregate data using data.table functions - summarises the mean, median, or sum expression of each marker on each cluster/populationdo.aggregate
do.align - Function to align multiple batches of a dataset.do.align
Transform data using ArcSinh transformationdo.asinh
do.calculate.areado.calculate.area
do.clip - Clips data using a specified lower and upper valuedo.clip
do.combine.cols - Combine the values of two columns into a single columndo.combine.cols
do.create.outlinesdo.create.outlines
do.extractdo.extract
do.extract.cell.datdo.extract.cell.dat
do.filter - filtering data.table using multiple match valuesdo.filter
do.filter.percelldo.filter.percell
do.label.from.polygondo.label.from.polygon
Summarise the column names and row numbers for elements of a listdo.list.summary
List switch or inversiondo.list.switch
Using logicle to transform datado.logicle
do.merge.files - Function to merge a list of data.tables (one data.table per 'sample') into a single large data.table.do.merge.files
do.pull.datado.pull.data
do.reorder - custom row re-ordering of a data.tabledo.reorder
do.rescale - Re-scale data in selected columns between two values, usually 0 and 1.do.rescale
Statistical analysisdo.stats
Subsample datado.subsample
do.zscore - Calculate z.score for a datasetdo.zscore
DEPRECATED fast colour plotfast.colour.plot
DEPRECATED fast multi plotfast.multi.plot
make.autograph - Creates plots using ggplot2make.autograph
Make colour plotmake.colour.plot
Make multiple plots for multiple columns and/or multiple sample/group/clustersmake.multi.plot
make.pheatmap - Create a 'pretty' heatmap (pheatmap)make.pheatmap
make.spatial.plotmake.spatial.plot
Make an enhanced volcano plotmake.volcano.plot
package.check - a function to check the installation of all required packages.package.check
package.install - a function to install packages required for Spectre.package.install
package.load - a function to load (library) all required packages.package.load
prep.cytonorm - Prepare reference data into a FlowSOM objectprep.cytonorm
Read CSV or FCS files into a list.read.files
Read TIFF files into R and and create spatial data objectread.spatial.files
run.align - Run the alignment model on a target data.tablerun.align
run.cytonorm - Run the alignment model on a target data.tablerun.cytonorm
Run FIt-SNE, Fourier Transform TSNE.run.fitsne
Run FlowSOMrun.flowsom
run.harmony - dun Harmony alignment on a data.tablerun.harmony
run.knn.classifier - Run KNN classifierrun.knn.classifier
Run the PCA algorithm (using stats::prcomp)run.pca
run.phenograph - Run phenograph clusteringrun.phenograph
Run rPCA for batch correctionrun.rpca
run.spatial.analysisrun.spatial.analysis
Run the tSNE algorithm (using Rtsne::Rtsne())run.tsne
Run UMAPrun.umap
spatial objectspatial spatial-class
train.cytonorm - Prepare reference data into a FlowSOM objecttrain.cytonorm
train.knn.classifier - Train KNN classifiertrain.knn.classifier
write.files - Write .csv or .fcs fileswrite.files
write.hdf5write.hdf5