Package: Statial 1.7.0

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]

Statial_1.7.0.tar.gz
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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

Datasets:

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

On BioConductor:Statial-1.7.0(bioc 3.20)Statial-1.6.0(bioc 3.19)

bioconductor-package

15 exports 2.14 score 134 dependencies

Last updated 2 months agofrom:a8188d2614

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

Dependencies:abind askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocParallel bit bit64 blob bslib cachem class classInt cli codetools colorspace concaveman cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir digest dplyr e1071 evaluate fansi farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue goftest gtable highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plotly polyclip promises proxy purrr R6 ranger rappdirs RColorBrewer Rcpp RcppEigen rjson rlang rmarkdown RSQLite s2 S4Arrays S4Vectors sass scales sf SingleCellExperiment snow SparseArray SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.utils statmod stringi stringr SummarizedExperiment sys tensor tibble tidyr tidyselect tinytex UCSC.utils units utf8 V8 vctrs viridisLite withr wk xfun XVector yaml zlibbioc

Statial

Farhan Ameen, Sourish Iyengar, Alex Qin, Ellis Patrick

Rendered fromStatial.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-11-15
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
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