Package: SpaceMarkers 1.3.1

Atul Deshpande

SpaceMarkers: Spatial Interaction Markers

Spatial transcriptomic technologies have helped to resolve the connection between gene expression and the 2D orientation of tissues relative to each other. However, the limited single-cell resolution makes it difficult to highlight the most important molecular interactions in these tissues. SpaceMarkers, R/Bioconductor software, can help to find molecular interactions, by identifying genes associated with latent space interactions in spatial transcriptomics.

Authors:Atul Deshpande [aut, cre], Ludmila Danilova [ctb], Dmitrijs Lvovs [ctb]

SpaceMarkers_1.3.1.tar.gz
SpaceMarkers_1.3.1.zip(r-4.5)SpaceMarkers_1.3.1.zip(r-4.4)
SpaceMarkers_1.3.1.tgz(r-4.5-any)SpaceMarkers_1.3.1.tgz(r-4.4-any)
SpaceMarkers_1.3.1.tar.gz(r-4.5-noble)SpaceMarkers_1.3.1.tar.gz(r-4.4-noble)
SpaceMarkers_1.3.1.tgz(r-4.4-emscripten)
SpaceMarkers.pdf |SpaceMarkers.html✨
SpaceMarkers/json (API)
NEWS

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

Bug tracker:https://github.com/deshpandelab/spacemarkers/issues

Datasets:

On BioConductor:SpaceMarkers-1.3.1(bioc 3.21)SpaceMarkers-1.2.1(bioc 3.20)

singlecellgeneexpressionsoftwarespatialtranscriptomics

6.32 score 5 stars 21 scripts 167 downloads 7 exports 88 dependencies

Last updated 4 months agofrom:5bd997fa9e. Checks:6 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 01 2025
R-4.5-winOKMar 01 2025
R-4.5-macOKMar 01 2025
R-4.5-linuxOKMar 01 2025
R-4.4-winOKMar 01 2025
R-4.4-macOKMar 01 2025

Exports:getInteractingGenesgetPairwiseInteractingGenesgetSpatialFeaturesgetSpatialParametersgetSpatialParametersExternalload10XCoordsload10XExpr

Dependencies:abindapebackportsbitbit64bootbroomcarcarDataclicolorspacecorrplotcowplotcpp11deldirDerivdigestdoBydplyrfansifarverFormulagenericsggplot2gluegoftestgtablehdf5risobandjsonlitelabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmatrixStatsmatrixTestsmgcvmicrobenchmarkminqamodelrmunsellnanoparquetnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplyrpolyclippurrrquantregqvalueR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasreshape2rlangrstatixscalesSparseMspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivaltensortibbletidyrtidyselectutf8vctrsviridisLitewithr

Inferring Immune Interactions in Breast Cancer

Orian Stapleton

Rendered fromSpaceMarkers_vignette.Rmdusingknitr::rmarkdownon Mar 01 2025.

Last update: 2024-07-16
Started: 2024-07-16