Package: VoltRon 0.2.6

Artür Manukyan

VoltRon: VoltRon for Spatial Omics Data Integration and Analysis

VoltRon is a spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is capable of analyzing multiple types and modalities of spatially-aware datasets. VoltRon visualizes and analyzes regions of interests (ROIs), spots, cells, molecules and event tiles.

Authors:Artür Manukyan, Ella Bahry, Raj Prateek Rai, Wei-Che Ko, Markus Landthaler, Altuna Akalin

VoltRon_0.2.6.tar.gz
VoltRon_0.2.6.zip(r-4.7)VoltRon_0.2.6.zip(r-4.6)VoltRon_0.2.5.zip(r-4.5)
VoltRon_0.2.6.tgz(r-4.6-x86_64)VoltRon_0.2.6.tgz(r-4.6-arm64)VoltRon_0.2.5.tgz(r-4.5-x86_64)VoltRon_0.2.5.tgz(r-4.5-arm64)
VoltRon_0.2.6.tar.gz(r-4.7-arm64)VoltRon_0.2.6.tar.gz(r-4.7-x86_64)VoltRon_0.2.6.tar.gz(r-4.6-arm64)VoltRon_0.2.6.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
VoltRon/json (API)
NEWS

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

Bug tracker:https://github.com/bimsbbioinfo/voltron/issues

Uses libs:
  • opencv– Computer vision shape descriptors and matchers library
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

opencvcpp

6.31 score 121 stars 80 scripts 120 exports 168 dependencies

Last updated from:0d063637ce. Checks:8 ERROR, 1 OK, 4 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR1670
linux-devel-x86_64ERROR1494
source / vignettesOK838
linux-release-arm64ERROR1617
linux-release-x86_64ERROR1530
macos-release-arm64ERROR925
macos-release-x86_64ERROR2352
macos-oldrel-arm64FAIL79
macos-oldrel-x86_64FAIL187
windows-develERROR1144
windows-releaseERROR1136
windows-oldrelFAIL119
wasm-releaseFAIL261

Exports:addAssayaddBlockConnectivityaddFeatureaddMetadataaddSpatialLayerannotateSpatialDataas.AnnDataas.Giottoas.OmeTiffas.OmeZarras.Seuratas.SpatialExperimentas.VoltRonas.ZarrcombineChannelscombineGraphsconvertAnnDataToVoltRonfixVoltRonflipCoordinatesformAssayformImageformVoltRonFromSegmentToCropgenerateCosMxImagegenerateGeoJSONgenerateSegmentsgenerateTileDatagenerateXeniumImagegetBasiliskgetClustersgetDeconvolutiongetDiffExpgetFeaturesgetHotSpotAnalysisgetNicheAssaygetOmeTiffChannelsgetPCAgetProfileNeighborsgetRcppAutomatedRegistrationgetRcppManualRegistrationgetSpatialNeighborsgetUMAPgetVariableFeaturesimport10Xh5importCosMximportDBITSeqimportGenePSimportGeoMximportImageDataimportOpenSTimportPhenoCyclerimportQuPathIFimportSTOmicsimportVisiumimportVisiumHDimportXeniumloadVoltRonmergeMetadataMetadata<-modulateImagenormalizeDataopen_zarrregisterSpatialDataresizeImageSampleMetadatasaveVoltRonsubsettransferDataupdateAssayvrAssayNamesvrAssayParamsvrAssayTypesvrBarPlotvrCoordinatesvrCoordinates<-vrDatavrEmbeddingFeaturePlotvrEmbeddingNamesvrEmbeddingPlotvrEmbeddingsvrEmbeddings<-vrFeatureDatavrFeatureData<-vrFeaturesvrFeatureTypeNamesvrGraphvrGraph<-vrGraphNamesvrHeatmapPlotvrImageChannelNamesvrImageNamesvrImagesvrImages<-vrMainAssayvrMainAssay<-vrMainChannelvrMainChannel<-vrMainFeatureTypevrMainFeatureType<-vrMainImagevrMainImage<-vrMainSpatialvrMainSpatial<-vrNeighbourhoodEnrichmentvrNeighbourhoodEnrichmentPlotvrProportionPlotvrSampleNamesvrScatterPlotvrSegmentsvrSegments<-vrSpatialFeaturePlotvrSpatialNamesvrSpatialPlotvrSpatialPointsvrSpatialPoints<-vrViolinPlotwarpImagewarpSimpleITKImagezarrcreateGroup

Dependencies:abindaskpassassortheadbackportsbase64encbeachmatBHBiocGenericsBiocParallelBiocSingularbitopsbootbroombslibcachemcarcarDatacaToolsclicodetoolscolorsGencolorspacecommonmarkcorrplotcowplotcpp11curldata.tableDelayedArrayDerivdigestdoBydplyrdqrngEBImageevaluatefarverfastmapfftwtoolsFNNfontawesomeforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsggplot2ggpubrggrepelggsciggsignifgluegplotsgridExtragtablegtoolshighrhtmltoolshtmlwidgetshttpuvidsigraphIRangesirlbaisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelifecyclelme4lmtestlocfitmagickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrnlmenloptrnnetnumDerivopensslotelpbkrtestpillarpkgconfigpngPolychromepolynompromisespurrrquantregR6RANNrappdirsrbibutilsRCDTRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressRCurlRdpackreformulasrglrjsonrlangrmarkdownRSpectrarstatixrsvdRvcgS4ArraysS4VectorsS7sassScaledMatrixscalesscatterplot3dshinyshinyjssitmosnowsourcetoolsspSparseArraySparseMstringistringrsurvivalsystibbletidyrtidyselecttifftimeDatetinytexurcautf8uuiduwotvctrsviridisLitewithrxfunxtableXVectoryamlzoo

Readme and manuals

Help Manual

Help pageTopics
VoltRon: VoltRon for Spatial Omics Data Integration and AnalysisVoltRon-package
Add AssayaddAssay addAssay,VoltRon-method addAssay,vrMetadata-method
addBlockConnectivityaddBlockConnectivity
addFeatureaddFeature addFeature,VoltRon-method addFeature,vrAssayV2-method
addMetadataaddMetadata
addSpatialLayeraddSpatialLayer
annotateSpatialDataannotateSpatialData
as.AnnDataas.AnnData
as.Giottoas.Giotto
as.OmeTiffas.OmeTiff
as.OmeZarras.OmeZarr
as.Seuratas.Seurat
as.SpatialExperimentas.SpatialExperiment
as.VoltRonas.VoltRon as.VoltRon.Seurat as.VoltRon.SpatialExperiment
as.Zarras.Zarr as.Zarr.magick-image
combineChannelscombineChannels combineChannels,VoltRon-method combineChannels,vrAssay-method combineChannels,vrAssayV2-method combineChannels,vrImage-method combineChannels,vrSpatial-method
combineGraphscombineGraphs
convertAnnDataToVoltRonconvertAnnDataToVoltRon
demuxVoltRondemuxVoltRon
Fast creation of dummy variablesdummy_cols
fixVoltRonfixVoltRon
flipCoordinatesflipCoordinates flipCoordinates,VoltRon-method flipCoordinates,vrAssay-method flipCoordinates,vrAssayV2-method
formAssayformAssay
formImageformImage
formVoltRonformVoltRon
FromSegmentToCropFromSegmentToCrop
generateCosMxImagegenerateCosMxImage
generateGeoJSONgenerateGeoJSON
generateSegmentsgenerateSegments
generateTileDatagenerateTileData generateTileData,VoltRon-method generateTileData,vrAssay-method generateTileData,vrAssayV2-method
generateXeniumImagegenerateXeniumImage
get the Python Basilisk environmentgetBasilisk
getClustersgetClusters
getDeconvolutiongetDeconvolution
getDiffExpgetDiffExp
getFeaturesgetFeatures getFeatures,VoltRon-method getFeatures,vrAssay-method getFeatures,vrAssayV2-method
getHotSpotAnalysisgetHotSpotAnalysis
getNicheAssaygetNicheAssay
getOmeTiffChannelsgetOmeTiffChannels
getPCAgetPCA
Get profile specific neighborsgetProfileNeighbors
getRcppAutomatedRegistrationgetRcppAutomatedRegistration
getRcppManualRegistrationgetRcppManualRegistration
Get spatial neighborsgetSpatialNeighbors
getUMAPgetUMAP
getVariableFeaturesgetVariableFeatures
import10Xh5import10Xh5
importCosMximportCosMx
importDBITSeqimportDBITSeq
importGenePSimportGenePS
importGeoMximportGeoMx
importImageDataimportImageData
importOpenSTimportOpenST
importPhenoCyclerimportPhenoCycler
importImageDataimportQuPathIF
importSTOmicsimportSTOmics
importVisiumimportVisium
importVisiumHDimportVisiumHD
importXeniumimportXenium
knn_annoyknn_annoy
loadVoltRonloadVoltRon
Example MELC Datamelc_data
Merging VoltRon objectsmerge merge,VoltRon,ANY-method
Merging vrBlock objectsmerge,vrBlock,ANY-method
Merging vrMetadata objectsmerge,vrMetadata,ANY-method
Merging vrSample objectsmerge,vrSample,ANY-method
Example Transfer Datamerged_object
MetadataMetadata Metadata,VoltRon-method Metadata<- Metadata<-,VoltRon-method
modulateImagemodulateImage modulateImage,VoltRon-method modulateImage,vrAssay-method modulateImage,vrAssayV2-method modulateImage,vrImage-method modulateImage,vrSpatial-method
Normalize DatanormalizeData normalizeData,VoltRon-method normalizeData,vrAssay-method normalizeData,vrAssayV2-method
open_zarropen_zarr
registerSpatialDataregisterSpatialData
resizeImageresizeImage resizeImage,VoltRon-method resizeImage,vrAssay-method resizeImage,vrAssayV2-method resizeImage,vrImage-method resizeImage,vrSpatial-method
SampleMetadataSampleMetadata
saveVoltRonsaveVoltRon
slotApplyslotApply
slotToListslotToList
Subsetting VoltRon objectssubset subset,VoltRon-method
Subsetting vrAssay objectssubset,vrAssay-method
Subsetting vrAssayV2 objectssubset,vrAssayV2-method
Subsetting vrBlock objectssubset,vrBlock-method
Subsetting vrImage objectssubset,vrImage-method
Subsetting vrLayer objectssubset,vrLayer-method
Subsetting vrMetadata objectssubset,vrMetadata-method
Subsetting vrSample objectssubset,vrSample-method
Subsetting vrSpatial objectssubset,vrSpatial-method
subsetCoordinatessubsetCoordinates
subsetSegmentssubsetSegments
transferDatatransferData
Update AssayupdateAssay updateAssay,VoltRon-method updateAssay,vrAssay-method updateAssay,vrAssayV2-method
Example Visium Datavisium_data
The VoltRon ClassVoltRon VoltRon-class
Methods for VoltRon$.VoltRon $<-.VoltRon .DollarNames.VoltRon VoltRon-methods [[,VoltRon,character,character-method [[,VoltRon,character,missing-method [[,VoltRon-methods [[<-,VoltRon,character,character-method [[<-,VoltRon,character,missing-method [[<-,VoltRon-methods
The vrAssay (VoltRon Assay) ClassvrAssay vrAssay-class
Get Assay namesvrAssayNames vrAssayNames,VoltRon-method vrAssayNames,vrAssay-method vrAssayNames,vrAssayV2-method vrAssayNames,vrMetadata-method vrAssayNames<-,vrAssay-method vrAssayNames<-,vrAssayV2-method
Get assay parametersvrAssayParams
Get assay typesvrAssayTypes vrAssayTypes,VoltRon-method vrAssayTypes,vrAssay-method vrAssayTypes,vrAssayV2-method
The vrAssayV2 (VoltRon Assay) ClassvrAssayV2 vrAssayV2-class
vrBarPlotvrBarPlot
The vrBlock (VoltRon Block) ClassvrBlock vrBlock-class
vrCoordinatesvrCoordinates vrCoordinates,VoltRon-method vrCoordinates,vrAssay-method vrCoordinates,vrAssayV2-method vrCoordinates,vrImage-method vrCoordinates,vrSpatial-method vrCoordinates<- vrCoordinates<-,VoltRon-method vrCoordinates<-,vrAssay-method vrCoordinates<-,vrAssayV2-method vrCoordinates<-,vrImage-method vrCoordinates<-,vrSpatial-method
vrDatavrData vrData,VoltRon-method vrData,vrAssay-method vrData,vrAssayV2-method
vrEmbeddingFeaturePlotvrEmbeddingFeaturePlot
Get Embedding namesvrEmbeddingNames vrEmbeddingNames,VoltRon-method vrEmbeddingNames,vrAssay-method vrEmbeddingNames,vrAssayV2-method
vrEmbeddingPlotvrEmbeddingPlot
vrEmbeddingsvrEmbeddings vrEmbeddings,VoltRon-method vrEmbeddings,vrAssay-method vrEmbeddings,vrAssayV2-method vrEmbeddings<- vrEmbeddings<-,VoltRon-method vrEmbeddings<-,vrAssay-method vrEmbeddings<-,vrAssayV2-method
Feature DatavrFeatureData vrFeatureData,VoltRon-method vrFeatureData,vrAssay-method vrFeatureData,vrAssayV2-method vrFeatureData<- vrFeatureData<-,VoltRon-method vrFeatureData<-,vrAssay-method vrFeatureData<-,vrAssayV2-method
vrFeaturesvrFeatures vrFeatures,VoltRon-method vrFeatures,vrAssay-method vrFeatures,vrAssayV2-method
vrFeatureTypeNamesvrFeatureTypeNames vrFeatureTypeNames,VoltRon-method vrFeatureTypeNames,vrAssay-method vrFeatureTypeNames,vrAssayV2-method
vrGraphvrGraph vrGraph<-
vrGraphNamesvrGraphNames
HeatmapPlotvrHeatmapPlot
The vrImage (VoltRon Image) ClassvrImage vrImage-class
vrImageChannelNamesvrImageChannelNames vrImageChannelNames,VoltRon-method vrImageChannelNames,vrAssay-method vrImageChannelNames,vrAssayV2-method vrImageChannelNames,vrImage-method vrImageChannelNames,vrSpatial-method
vrImageNamesvrImageNames vrImageNames,VoltRon-method vrImageNames,vrAssay-method vrImageNames,vrAssayV2-method
vrImagesvrImages vrImages,VoltRon-method vrImages,vrAssay-method vrImages,vrAssayV2-method vrImages,vrImage-method vrImages,vrSpatial-method vrImages<- vrImages<-,vrAssay-method vrImages<-,vrAssayV2-method vrImages<-,vrImage-method vrImages<-,vrSpatial-method
The vrLayer (VoltRon Layer) ClassvrLayer vrLayer-class
Methods for vrLayer objectsvrLayer-methods [[,vrLayer,character,ANY-method [[<-,vrLayer,character,ANY-method
Main AssayvrMainAssay vrMainAssay,VoltRon-method vrMainAssay<- vrMainAssay<-,VoltRon-method
vrMainChannelvrMainChannel vrMainChannel,vrAssay-method vrMainChannel,vrAssayV2-method vrMainChannel,vrImage-method vrMainChannel,vrSpatial-method vrMainChannel<- vrMainChannel<-,vrAssay-method vrMainChannel<-,vrAssayV2-method vrMainChannel<-,vrImage-method vrMainChannel<-,vrSpatial-method
vrMainFeatureTypevrMainFeatureType vrMainFeatureType,VoltRon-method vrMainFeatureType,vrAssay-method vrMainFeatureType,vrAssayV2-method vrMainFeatureType<- vrMainFeatureType<-,VoltRon-method vrMainFeatureType<-,vrAssay-method vrMainFeatureType<-,vrAssayV2-method
vrMainImagevrMainImage vrMainImage,VoltRon-method vrMainImage,vrAssay-method vrMainImage,vrAssayV2-method vrMainImage<- vrMainImage<-,VoltRon-method vrMainImage<-,vrAssay-method vrMainImage<-,vrAssayV2-method
vrMainSpatialvrMainSpatial vrMainSpatial,VoltRon-method vrMainSpatial,vrAssay-method vrMainSpatial,vrAssayV2-method vrMainSpatial<- vrMainSpatial<-,VoltRon-method vrMainSpatial<-,vrAssay-method vrMainSpatial<-,vrAssayV2-method
The vrMetadata (VoltRon Metadata) ClassvrMetadata vrMetadata-class
vrNeighbourhoodEnrichmentvrNeighbourhoodEnrichment
vrNeighbourhoodEnrichmentPlotvrNeighbourhoodEnrichmentPlot
vrPercentagePlotvrProportionPlot
The vrSample (VoltRon Sample) ClassvrSample vrSample-class
Methods for vrSample objectsvrSample-methods [[,vrBlock,character,ANY-method [[,vrSample,character,ANY-method [[<-,vrBlock,character,ANY-method [[<-,vrSample,character,ANY-method
Get Sample namesvrSampleNames vrSampleNames,vrMetadata-method
vrScatterPlotvrScatterPlot
vrSegmentsvrSegments vrSegments,VoltRon-method vrSegments,vrAssay-method vrSegments,vrAssayV2-method vrSegments,vrImage-method vrSegments,vrSpatial-method vrSegments<- vrSegments<-,VoltRon-method vrSegments<-,vrAssay-method vrSegments<-,vrAssayV2-method vrSegments<-,vrImage-method vrSegments<-,vrSpatial-method
The vrSpatial (VoltRon Spatial) ClassvrSpatial vrSpatial-class
vrSpatialFeaturePlotvrSpatialFeaturePlot
vrSpatialNamesvrSpatialNames vrSpatialNames,VoltRon-method vrSpatialNames,vrAssay-method vrSpatialNames,vrAssayV2-method
vrSpatialPlotvrSpatialPlot
vrSpatialPointsvrSpatialPoints vrSpatialPoints,VoltRon-method vrSpatialPoints,vrAssay-method vrSpatialPoints,vrAssayV2-method vrSpatialPoints,vrBlock-method vrSpatialPoints,vrImage-method vrSpatialPoints,vrLayer-method vrSpatialPoints,vrMetadata-method vrSpatialPoints,vrSample-method vrSpatialPoints,vrSpatial-method vrSpatialPoints<- vrSpatialPoints<-,vrAssay-method vrSpatialPoints<-,vrAssayV2-method vrSpatialPoints<-,vrImage-method vrSpatialPoints<-,vrSpatial-method
vrViolinPlotvrViolinPlot
warpImagewarpImage
getRcppWarpImagewarpSimpleITKImage
Example Xenium Dataxenium_data
zarrcreateGroupzarrcreateGroup