Package: Statial 1.15.0

Farhan Ameen

Statial: A package to identify changes in cell state relative to spatial associations

Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.

Authors:Farhan Ameen [aut, cre], Sourish Iyengar [aut], Alex Qin [aut], Shila Ghazanfar [aut], Ellis Patrick [aut]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
Statial/json (API)

# Install 'Statial' in R:

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

Bug tracker:https://github.com/sydneybiox/statial/issues

Pkgdown/docs site:https://sydneybiox.github.io

Datasets:

kerenKontextual - Kontextual results from kerenSCE
kerenSCE - MIBI-TOF Breast cancer intensities

On BioConductor:Statial-1.15.0(bioc 3.24)Statial-1.14.0(bioc 3.23)

singlecell spatial classification single-cell

6.77 score 6 stars 31 scripts 402 downloads 16 exports 225 dependencies

Last updated from:97ee04a497. Checks:1 WARNING, 2 OK, 5 ERROR, 1 NOTE. Indexed: yes.
A new build is currently in progress.

Target	Result	Time
bioc-checks	WARNING	267
source / vignettes	OK	720
linux-release-x86_64	ERROR	437
macos-release-arm64	ERROR	275
macos-oldrel-arm64	NOTE	726
windows-devel	ERROR	1001
windows-release	ERROR	794
windows-oldrel	ERROR	856
wasm-release	OK	251

Exports:calcContamination calcStateChanges getAbundances getDistances getMarkerMeans getParentPhylo isKontextual kontextCurve kontextPlot Kontextual makeWindow parentCombinations plotStateChanges prepMatrix relabel relabelKontextual

Dependencies:abind ALL ape aplot askpass backports base64enc BH Biobase BiocFileCache BiocGenerics biocmake BiocParallel bit bit64 blob boot broom bslib cachem car carData circlize class classInt cli clue cluster codetools colorRamps colorspace ComplexHeatmap concaveman ConsensusClusterPlus corrplot cowplot cpp11 crayon crosstalk curl cytolib data.table DBI dbplyr DelayedArray deldir Deriv diffcyt digest dir.expiry doBy doParallel dplyr e1071 edgeR evaluate farver fastmap filelock flowCore FlowSOM fontawesome fontBitstreamVera fontLiberation fontquiver foreach forecast formatR Formula fracdiff fs futile.logger futile.options gdtools generics GenomicRanges GetoptLong ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggpubr ggrepel ggsci ggsignif ggtree GlobalOptions glue goftest gridExtra gridGraphics gtable highr hopach htmltools htmlwidgets httr httr2 igraph IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma lme4 lmtest locfit magick magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr multcomp mvtnorm nlme nloptr nnet numDeriv openssl otel patchwork pbkrtest pillar pkgconfig plotly plyr png polyclip polynom promises proxy purrr quantreg R6 ranger rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 Rhdf5lib rjson rlang rmarkdown RProtoBufLib RSQLite rstatix Rtsne s2 S4Arrays S4Vectors S7 sandwich sass scales Seqinfo sf shape SingleCellExperiment snow SparseArray SparseM SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils statmod stringi stringr SummarizedExperiment survival sys systemfonts tensor TH.data tibble tidyr tidyselect tidytree timeDate tinytex treeio treekoR tweenr units urca utf8 V8 vctrs viridisLite withr wk xfun XML XVector yaml yulab.utils zoo

Statial

Rendered fromStatial.Rmdusingknitr::rmarkdown

Last update: 2025-07-07
Started: 2022-09-18

Help page	Topics
Calculate the level of marker contamination of each cell	calcContamination
First layer wrapper function to build linear models measuring state changes	calcStateChanges
Calculate pairwise distance between cell types	distanceCalculator
Wrapper to calculate imhomogenous K function between a cell and surrounding types on each image	getAbundances
Wrapper to calculate pairwise distance between cell types by image	getDistances
Extract the average expression for all markers for each cell type in each region defined by lisaClust	getMarkerMeans
Extract parent and all children from a Phylo object	getParentPhylo
Test whether an object is a kontextualResult	isKontextual
Kontextual results from kerenSCE	kerenKontextual
MIBI-TOF Breast cancer intensities	kerenSCE
Evaluation of Kontextual over a range of radii.	kontextCurve
Plotting the original and kontextual L values over a range of radii.	kontextPlot
Evaluation of pairwise cell relationships, conditional on a 3rd population.	Kontextual
Creates a window for a PPP object	makeWindow
Create all combinations of cell type relationships from a list of parents	parentCombinations
Visualise Cell-Cell Marker Relationships	plotStateChanges
Convert Kontextual or state changes result to a matrix for classification	prepMatrix
Cell permutation for Kontextual	relabel relabelKontextual

Package: Statial 1.15.0

Statial: A package to identify changes in cell state relative to spatial associations

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