Package: smoppix 0.99.41

Stijn Hawinkel

smoppix: Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index

Test for univariate and bivariate spatial patterns in spatial omics data with single-molecule resolution. The tests implemented allow for analysis of nested designs and are automatically calibrated to different biological specimens. Tests for aggregation, colocalization, gradients and vicinity to cell edge or centroid are provided.

Authors:Stijn Hawinkel [cre, aut]

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smoppix.pdf |smoppix.html✨
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NEWS

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

Peer review:

Bug tracker:https://github.com/sthawinke/smoppix/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • Eng - Spatial transcriptomics data of mouse fibroblast cells
  • EngRois - Spatial transcriptomics data of mouse fibroblast cells
  • Yang - Spatial transcriptomics data of Selaginella moellendorffii roots

On BioConductor:smoppix-0.99.37(bioc 3.21)

transcriptomicsspatialsinglecellcpp

5.18 score 1 stars 4 scripts 51 downloads 21 exports 112 dependencies

Last updated 2 days agofrom:3e84ca86fd. Checks:1 OK, 3 NOTE, 2 WARNING, 2 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 31 2025
R-4.5-win-x86_64ERRORJan 31 2025
R-4.5-mac-x86_64WARNINGJan 31 2025
R-4.5-mac-aarch64WARNINGJan 31 2025
R-4.5-linux-x86_64NOTEJan 31 2025
R-4.4-win-x86_64ERRORJan 31 2025
R-4.4-mac-x86_64NOTEJan 31 2025
R-4.4-mac-aarch64NOTEJan 31 2025

Exports:addCelladdNucleiaddWeightFunctionbuildDataFramebuildHyperFrameestGradientsestPisevalWeightFunctionfindOverlapfitLMMsgetFeaturesgetGpgetPvaluesGradientgetResultsmakePairsplotCellsplotExploreplotTopResultsplotWfsundwriteToXlsx

Dependencies:abindaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobbootcachemclicodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArraydeldirdplyrextraDistrfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegoftestgtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelme4lmerTestmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminqamunsellnlmenloptrnumDerivopensslopenxlsxpillarpkgconfigplogrpolyclippurrrR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrjsonrlangrpartRSQLiteS4ArraysS4VectorsscalesscamSingleCellExperimentsnowSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.modelspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsystensortibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzip

Vignette of the smoppix package

Stijn Hawinkel

Rendered fromsmoppixVignette.Rmdusingknitr::rmarkdownon Jan 31 2025.

Last update: 2025-01-28
Started: 2024-02-20

Readme and manuals

Help Manual

Help pageTopics
Add cell boundaries and event-wise cell identifiers to a hyperframe.addCell
Add design variables to hyperframeaddDesign
Add nuclei to a hyperframe already containing cells.addNuclei
Add tables with gene counts to the hyperframe, presort by gene and x-ccordinate and add design varibalesaddTabObs
Build a data frame for a certain gene and PI, in preparation for mixed model building.buildDataFrame
Build a formula from different componentsbuildFormula
Build a hyperframe containing all point patterns of an experiment.buildHyperFrame buildHyperFrame,data.frame-method buildHyperFrame,list-method buildHyperFrame,matrix-method buildHyperFrame,SpatialExperiment-method
Build a data frame with Moran's I as outcome variablebuildMoransIDataFrame
Build a weight matrix for Moran's I calculationsbuildMoransIWeightMat
Calculate individual PI entries of a single point patterncalcIndividualPIs
Estimate the PI for the nearest neighbour distances, given a set of ranks, using the negative hypergeometric distributioncalcNNPI
Estimate the PI for the distance to a fixed object of interest, such as a cell wall or centroidcalcWindowDistPI
Center numeric variablescenterNumeric
Check if features are present in hyperframecheckFeatures
Check if the required PI's are present in the objectcheckPi
Check for or construct design matrixconstructDesignVars
Convert windows to spatstat.geom owin formatconvertToOwins
A wrapper for C-functions calculating cross-distance matrix fastcrossdistWrapper
Spatial transcriptomics data of mouse fibroblast cellsEng EngRois
Estimate gradients over multiple point patterns, and extract the p-valuesestGradients estGradientsSingle getPvaluesGradient
Estimates probabilistic indices for single-molecule localization patterns, and add the variance weighting function.addWeightFunction estPis estPisSingle
Evaluate a variance weighting functionevalWeightFunction
Extract results from a list of fitted LMMs. For internal use mainly.extractResults
Construct empirical cumulative distribution functions (ecdfs) for distances within the cellfindEcdfsCell
Find overlap between list of windowsfindOverlap
Test for presence of gradient in a hyperframe of point patternsfitGradient
Fit linear (mixed) models for all probabilistic indices (PIs) and all genesfitLMMs fitLMMsSingle getResults
Fit a linear model for an individual gene and PI combinationfitPiModel
Extract coordinates from a point pattern or data framegetCoordsMat
Return all design variables, both at the level of the point pattern and the level of the eventgetDesignVars getEventVars getPPPvars
Extract en element from a matrix or vectorgetElement
Extract all unique features from an objectgetFeatures
Helper function to get gene pair from a vector or listgetGp
Extract the hyperframegetHypFrame
Parallel processing with BiocParallel with load balancingloadBalanceBplapply
Make design variable by combining different design variablesmakeDesignVar
An aux function to build gene pairsmakePairs
Calculate the Moran's I test statistic for spatial autocorrelationmoransI
A version of contr.sum that retains names, a bit controversial but also clearernamed.contr.sum
Nest random effects within fixed variables, in case the names are the samenestRandom
Plot the n cells with highest abundance of a featureplotCells
Plot the hyperframe with chosen features highlightedplotExplore
Plot the most significant findings for a certain PIplotTopResults
Plot the variance weighting functionplotWf
Split a number of plots into rows and columnssplitWindow
Subsample a point pattern when it is too largesubSampleP
Helper function to spit gene pairssund
Write effect sizes and p-values results to excel worksheetwriteToXlsx
Spatial transcriptomics data of Selaginella moellendorffii rootsYang