Package: Statial 1.15.1

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]

Statial_1.15.1.tar.gz
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Statial_1.15.1.tgz(r-4.6-emscripten)
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

Uses libs:

c++– GNU Standard C++ Library v3

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 cpp

5.67 score 6 stars 31 scripts 448 downloads 17 exports 225 dependencies

Last updated from:8913bb81aa. Checks:1 WARNING, 14 ERROR, 1 OK. Indexed: yes.
A new build is currently in progress.

Target	Result	Time
bioc-checks	WARNING	193
linux-devel-arm64	ERROR	188
linux-devel-x86_64	ERROR	268
source / vignettes	ERROR	528
linux-release-arm64	ERROR	180
linux-release-x86_64	ERROR	252
macos-release-arm64	ERROR	133
macos-release-x86_64	ERROR	295
macos-oldrel-arm64	ERROR	116
macos-oldrel-x86_64	ERROR	315
windows-devel-arm64	ERROR	257
windows-devel-x86_64	ERROR	183
windows-release-arm64	ERROR	225
windows-release-x86_64	ERROR	134
windows-oldrel-x86_64	ERROR	157
wasm-release	OK	220

Exports:calcContamination calcStateChanges getAbundances getDistances getMarkerMeans getParentPhylo isKontextual kontextCurve kontextPlot Kontextual kontextualTest 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 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 spicyR 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

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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
Test Kontextual relationships between conditions or with survival	kontextualTest
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 1.15.1

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

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