Package: scSpatialSIM 0.1.3.4

Fridley Lab

scSpatialSIM: A Point Pattern Simulator for Spatial Cellular Data

Single cell resolution data has been valuable in learning about tissue microenvironments and interactions between cells or spots. This package allows for the simulation of this level of data, be it single cell or ‘spots’, in both a univariate (single metric or cell type) and bivariate (2 or more metrics or cell types) ways. As more technologies come to marker, more methods will be developed to derive spatial metrics from the data which will require a way to benchmark methods against each other. Additionally, as the field currently stands, there is not a gold standard method to be compared against. We set out to develop an R package that will allow users to simulate point patterns that can be biologically informed from different tissue domains, holes, and varying degrees of clustering/colocalization. The data can be exported as spatial files and a summary file (like 'HALO'). <https://github.com/FridleyLab/scSpatialSIM/>.

Authors:Alex Soupir [aut], Christopher Wilson [aut], Jordan Creed [aut], Julia Wrobel [aut], Oscar Ospina [aut], Brooke Fridley [aut, cph], Fridley Lab [cre]

scSpatialSIM_0.1.3.4.tar.gz
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scSpatialSIM.pdf |scSpatialSIM.html
scSpatialSIM/json (API)

# Install 'scSpatialSIM' in R:
install.packages('scSpatialSIM', repos = c('https://fridleylab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/fridleylab/scspatialsim/issues

Datasets:
  • wm - Round spatstat window

On CRAN:

5.08 score 4 stars 9 scripts 190 downloads 13 exports 78 dependencies

Last updated 2 months agofrom:2f236dfdea. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winOKNov 18 2024
R-4.5-linuxOKNov 18 2024
R-4.4-winOKNov 18 2024
R-4.4-macOKNov 18 2024
R-4.3-winOKNov 18 2024
R-4.3-macOKNov 18 2024

Exports:%>%CalculateDensityCreateSimulationObjectCreateSpatialListExtractParametersGenerateCellPositivityGenerateDistributionsGenerateHolesGenerateSpatialPatternGenerateTissuePlotSimulationSummariseSpatialUpdateSimulationWindow

Dependencies:abindbackportsbootbroomcarcarDataclicolorspacecorrplotcowplotcpp11crayondeldirDerivdoBydplyrfansifarverFormulagenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpbmcapplypillarpkgconfigpolyclippolynomproxypurrrquantregR6RColorBrewerRcppRcppEigenrlangrstatixscalesSparseMspatstat.dataspatstat.geomspatstat.randomspatstat.univarspatstat.utilsstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr

Introduction

Rendered froma01_Introduction.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-10-01
Started: 2023-07-04

Using with spatialTIME

Rendered froma02_Using_with_spatialTIME.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2023-08-31
Started: 2023-08-31