Package: Statial 1.9.0

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], Shila Ghazanfar [aut], Ellis Patrick [aut]

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Statial.pdf |Statial.html✨
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:https://sydneybiox.github.io

Datasets:

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

On BioConductor:Statial-1.9.0(bioc 3.21)Statial-1.8.0(bioc 3.20)

singlecell spatial classification single-cell

6.56 score 5 stars 20 scripts 180 downloads 16 exports 214 dependencies

Last updated 2 months agofrom:b4c031f4af. Checks:OK: 1 ERROR: 4 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 18 2024
R-4.5-win	ERROR	Dec 20 2024
R-4.5-linux	ERROR	Dec 20 2024
R-4.4-win	ERROR	Dec 20 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	ERROR	Dec 20 2024
R-4.3-mac	WARNING	Oct 31 2024

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 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 doBy doParallel dplyr e1071 edgeR evaluate fansi farver fastmap filelock flowCore FlowSOM fontawesome foreach formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggpubr ggrepel ggsci ggsignif ggtree GlobalOptions glue goftest gridExtra gridGraphics gtable highr hopach htmltools htmlwidgets httr igraph IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma lme4 locfit magick magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr multcomp munsell mvtnorm nlme nloptr nnet numDeriv openssl patchwork pbkrtest pillar pkgconfig plogr plotly plyr png polyclip polynom promises proxy purrr quantreg R6 ranger rappdirs RColorBrewer Rcpp RcppEigen reshape2 Rhdf5lib rjson rlang rmarkdown RProtoBufLib RSQLite rstatix Rtsne s2 S4Arrays S4Vectors sandwich sass scales 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 tinytex treeio treekoR tweenr UCSC.utils units utf8 uuid V8 vctrs viridisLite withr wk xfun XML XVector yaml yulab.utils zlibbioc zoo

Statial

Farhan Ameen, Sourish Iyengar, Alex Qin, Ellis Patrick

Rendered fromStatial.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-10-23
Started: 2022-09-18

Citation

Development and contributors

Readme and manuals

Help Manual

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