Package: smoppix 1.5.3

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]

smoppix_1.5.3.tar.gz
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smoppix_1.5.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
smoppix/json (API)

# Install 'smoppix' in R:

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

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-1.5.2(bioc 3.24)smoppix-1.4.0(bioc 3.23)

transcriptomics spatial singlecell cpp

5.52 score 1 stars 1 packages 6 scripts 27 exports 107 dependencies

Last updated from:7ece295dd4. Checks:12 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	236
linux-devel-arm64	NOTE	408
linux-devel-x86_64	NOTE	676
source / vignettes	OK	498
linux-release-arm64	NOTE	412
linux-release-x86_64	NOTE	649
macos-release-arm64	NOTE	247
macos-release-x86_64	NOTE	616
macos-oldrel-arm64	NOTE	389
macos-oldrel-x86_64	NOTE	567
windows-devel	NOTE	1691
windows-release	NOTE	1678
windows-oldrel	NOTE	1754
wasm-release	OK	221

Exports:addCell addNuclei addWeightFunction buildDataFrame buildHyperFrame centerNumeric estGradients estPis evalWeightFunction findOverlap fitLMMs getFeatures getGp getPvaluesGradient getResults lm_from_wfit loadBalanceBplapply makePairs named.contr.sum plotCells plotExplore plotTopResults plotWf pnhyper selfName sund writeToXlsx

Dependencies:abind askpass BH Biobase BiocFileCache BiocGenerics BiocParallel bit bit64 blob boot cachem cli codetools cpp11 curl DBI dbplyr DelayedArray deldir dplyr farver fastmap filelock formatR futile.logger futile.options generics GenomicRanges ggplot2 glue goftest gtable httr2 IRanges isoband labeling lambda.r lattice lifecycle lme4 lmerTest magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv minqa nlme nloptr numDeriv openssl openxlsx pillar pkgconfig polyclip purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel Rdpack reformulas Rfast rjson rlang rpart RSQLite S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment snow SparseArray SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.model spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment sys tensor tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector zigg zip

Vignette of the smoppix package

Rendered fromsmoppixVignette.Rmdusingknitr::rmarkdown

Last update: 2026-06-25
Started: 2024-02-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add cell boundaries and event-wise cell identifiers to a hyperframe.	addCell
Add design variables to hyperframe	addDesign
Add nuclei to a hyperframe	addNuclei
Add tables with gene counts to the hyperframe, presort by gene and x-ccordinate and add design varibales	addTabObs
Extract a data frame for a certain gene and PI from a fitted object	buildDataFrame
Build a formula from different components	buildFormula
Build a hyperframe containing all point patterns of an experiment.	buildHyperFrame buildHyperFrame,data.frame-method buildHyperFrame,list-method buildHyperFrame,matrix-method buildHyperFrame,SpatialExperiment-method
Calculate individual PI entries of a single point pattern	calcIndividualPIs
Estimate the PI for nearest neighbour distances with the negative hypergeometric distribution	calcNNPI
Estimate the PI for the distance to a fixed object of interest, such as a cell wall or centroid	calcWindowDistPI
Center numeric variables	centerNumeric
Check if features are present in hyperframe	checkFeatures
Check if the required PI's are present in the object	checkPi
Check for or construct design matrix	constructDesignVars
Convert windows to spatstat.geom owin format	convertToOwins
A wrapper for C-functions calculating cross-distance matrix fast	crossdistWrapper
Spatial transcriptomics data of mouse fibroblast cells	Eng EngRois
Estimate gradients over multiple point patterns, and test for significance	estGradients estGradientsSingle getPvaluesGradient
Estimate probabilistic indices and add a variance weighting function.	addWeightFunction estPis estPisSingle
Evaluate a variance weighting function	evalWeightFunction
Extract results from a list of fitted LMMs. For internal use mainly.	extractResults
Construct empirical cumulative distribution functions (ecdfs) for within-cell distances	findEcdfsCell
Find overlap between list of windows	findOverlap
Test for presence of gradient in a hyperframe of point patterns	fitGradient
Fit linear (mixed) models for all probabilistic indices (PIs) and all genes	fitLMMs fitLMMsSingle getResults
Fit a linear model for an individual gene and PI combination	fitPiModel
Take an existing frame, add outcome and weight and fit lmer model	fitSingleLmmModel
Extract coordinates from a point pattern or data frame	getCoordsMat
Extract design variables from a hyperframe	getDesignVars getEventVars getPPPvars
Extract en element from a matrix or vector	getElement
Extract all unique and estimated features from an object	getFeatures
Get a gene pair from a vector or list	getGp
Extract the hyperframe	getHypFrame
Build a matrix with pi and weights	getPiAndWeights
Add compoments to a result from lm.wfit to make it a minimally valid lm object	lm_from_wfit
Parallel processing with BiocParallel with load balancing	loadBalanceBplapply
Make design variable by combining different design variables	makeDesignVar
An aux function to build gene pairs	makePairs
A version of contr.sum that retains names, a bit controversial but also clearer	named.contr.sum
Negative hypergeometric distribution (taken from orphaned extraDistr package)	NegHyper pnhyper
Nest random effects within fixed variables, in case the names are the same	nestRandom
Plot the n cells with highest abundance of a feature	plotCells
Plot a hyperframe with chosen features highlighted	plotExplore
Plot the most significant findings for a certain PI	plotTopResults
Plot the variance weighting function	plotWf
Name a character vector after itself	selfName
Sort feature pairs alphabetically	sortGp
Split a number of plots into rows and columns	splitWindow
Subsample a point pattern when it is too large	subSampleP
Helper function to spit gene pairs	sund
Write effect sizes and p-values results to an excel worksheet	writeToXlsx
Spatial transcriptomics data of Selaginella moellendorffii roots	Yang