Package: SpaceMarkers 2.3.1
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:
SpaceMarkers_2.3.1.tar.gz
SpaceMarkers_2.3.1.zip(r-4.7)SpaceMarkers_2.3.1.zip(r-4.6)SpaceMarkers_2.3.1.zip(r-4.5)
SpaceMarkers_2.3.1.tgz(r-4.6-any)SpaceMarkers_2.3.1.tgz(r-4.5-any)
SpaceMarkers_2.3.1.tar.gz(r-4.7-any)SpaceMarkers_2.3.1.tar.gz(r-4.6-any)
SpaceMarkers_2.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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
- curated_genes - Curated Genes for example purposes
- optParams - Optimal paramters of 5 patterns from CoGAPS.
On BioConductor:SpaceMarkers-2.3.1(bioc 3.24)SpaceMarkers-2.2.0(bioc 3.23)
singlecellgeneexpressionsoftwarespatialtranscriptomics
Last updated from:145f3da779. Checks:1 WARNING, 6 NOTE, 2 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 369 | ||
| linux-devel-x86_64 | NOTE | 570 | ||
| source / vignettes | OK | 918 | ||
| linux-release-x86_64 | NOTE | 531 | ||
| macos-release-arm64 | NOTE | 301 | ||
| macos-oldrel-arm64 | NOTE | 329 | ||
| windows-devel | NOTE | 543 | ||
| windows-release | NOTE | 410 | ||
| windows-oldrel | FAIL | 29 | ||
| wasm-release | OK | 277 |
Exports:add_featuresanalysis_typeanalysis_type<-assayassayscalculate_gene_scores_directedcalculate_gene_set_scorecalculate_gene_set_specificitycalculate_influencecalculate_lr_scorescalculate_overlap_directedcalculate_overlap_undirectedcalculate_thresholdscolDatacreate_lr_dataframedirected_scoresdirected_scores<-find_all_hotspotsfind_hotspots_gmmfind_pattern_hotspotsget_im_scoresget_interacting_genesget_pairwise_interacting_genesget_spatial_featuresget_spatial_parametersget_spatial_params_morans_ihotspotshotspots<-imgRasterinfluence_mapinfluence_map<-interactionsinteractions<-load_anndataload10Xload10XCoordsload10XExprlr_scoreslr_scores<-overlap_mapoverlap_scoresoverlap_scores<-paramsplot_cell_interaction_circosplot_im_scoresplot_overlap_scoresplot_source_to_target_circosplot_spatialplot_spatial_data_over_imageplot_target_from_sources_circosrowDatasave_anndataSpaceMarkersSpaceMarkersExperimentspatial_paramsspatial_params<-spatial_patternsspatial_patterns<-spatialCoordsundirected_scoresundirected_scores<-
Dependencies:abindapeaskpassbackportsbase64encBiobaseBiocFileCacheBiocGenericsbitbit64blobbmpbootbroombslibcachemcarcarDatacirclizeclicolorspacecorrplotcowplotcpp11crosstalkcurldata.tableDBIdbplyrDelayedArraydeldirDerivdigestdoBydplyreffsizeevaluatefarverfastmapfilelockfontawesomeforecastFormulafracdifffsgenericsGenomicRangesggplot2GlobalOptionsgluegoftestgridExtragtablehdf5rhighrhtmltoolshtmlwidgetshttrhttr2IRangesisobandjpegjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelme4lmtestmagickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmatrixTestsmemoisemgcvmicrobenchmarkmimeminqamixtoolsmodelrnanoparquetnlmenloptrnnetnumDerivopensslotelpbkrtestpillarpkgconfigplotlyplyrpngpolyclippromisespurrrquantregqvalueR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadbitmapreformulasreshape2rjsonrlangrmarkdownRSQLiterstatixS4ArraysS4VectorsS7sassscalessegmentedSeqinfoshapeSingleCellExperimentSparseArraySparseMSpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensortibbletidyrtidyselecttifftimeDatetinytexurcautf8vctrsviridisviridisLitewithrxfunXVectoryamlzoo
Inferring Immune Interactions in Breast Cancer
Rendered fromSpaceMarkers_vignette.Rmdusingknitr::rmarkdownon Jun 08 2026.Last update: 2026-04-28
Started: 2024-07-16
SpaceMarkers Functions Step-by-Step
Rendered fromSpaceMarkersStepByStep_vignette.Rmdusingknitr::rmarkdownon Jun 08 2026.Last update: 2026-04-29
Started: 2026-04-28
SpaceMarkers with SpatialExperiment Objects
Rendered fromSpaceMarkersExperiment_vignette.Rmdusingknitr::rmarkdownon Jun 08 2026.Last update: 2026-04-29
Started: 2026-04-28
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate interaction scores for a specific pattern pair | .calc_IM_scores |
| Compute the threshold for identifying outlier values or hotspots | .calc_threshold |
| Directed SpaceMarkers workflow | .directed_SpaceMarkers |
| .find_genes_of_interest Identify genes associated with pattern interaction. This function identifies genes exhibiting significantly higher values of testMat in the Interaction region of the two patterns compared to regions with exclusive influence from either pattern. It uses Kruskal-Wallis test followed by posthoc analysis using Dunn's Test to identify the genes. | .find_genes_of_interest |
| .pick_image | .pick_image |
| Perform row-wise t-tests from scratch | .row_t_test |
| Undirected SpaceMarkers workflow | .undirected_SpaceMarkers |
| Add spatial features to a SpaceMarkersExperiment | add_features |
| Access or set the analysis type on a SpaceMarkersExperiment | analysis_type analysis_type,SpaceMarkersExperiment-method analysis_type<- analysis_type<-,SpaceMarkersExperiment-method |
| Coercion from SingleCellExperiment to SpaceMarkersExperiment | as-SingleCellExperiment-SpaceMarkersExperiment |
| Coercion from SpatialExperiment to SpaceMarkersExperiment | as-SpatialExperiment-SpaceMarkersExperiment |
| Calculate interaction scores for all pattern pairs | calculate_gene_scores_directed calculate_gene_scores_directed,ANY-method calculate_gene_scores_directed,SpaceMarkersExperiment-method |
| calculate_gene_set_score | calculate_gene_set_score calculate_gene_set_score,ANY-method calculate_gene_set_score,SpaceMarkersExperiment-method |
| calculate_gene_set_specificity | calculate_gene_set_specificity calculate_gene_set_specificity,ANY-method calculate_gene_set_specificity,SpaceMarkersExperiment-method |
| Compute the spatial influence of a spatial feature | calculate_influence calculate_influence,data.frame-method calculate_influence,SpaceMarkersExperiment-method |
| calculate_lr_scores | calculate_lr_scores calculate_lr_scores,ANY-method calculate_lr_scores,SpaceMarkersExperiment-method |
| calculate_overlap_directed | calculate_overlap_directed calculate_overlap_directed,data.frame-method calculate_overlap_directed,SpaceMarkersExperiment-method |
| calculate_overlap_undirected | calculate_overlap_undirected calculate_overlap_undirected,data.frame-method calculate_overlap_undirected,SpaceMarkersExperiment-method |
| Compute the thresholds for all columns in a data frame | calculate_thresholds |
| Combine LR / ligand / receptor score matrices into a long table | create_lr_dataframe |
| Curated Genes for example purposes | curated_genes |
| Access directed interaction scores on a SpaceMarkersExperiment | directed_scores directed_scores,SpaceMarkersExperiment-method directed_scores<- directed_scores<-,SpaceMarkersExperiment-method |
| Find hotSpots for all spatial patterns | find_all_hotspots find_all_hotspots,data.frame-method find_all_hotspots,SpaceMarkersExperiment-method |
| Find hotspots for all patterns or influences based on values | find_hotspots_gmm find_hotspots_gmm,data.frame-method find_hotspots_gmm,SpaceMarkersExperiment-method |
| Identify hotspots of spatial pattern influence | find_pattern_hotspots |
| get_im_scores | get_im_scores get_im_scores,list-method get_im_scores,SpaceMarkersExperiment-method |
| Calculate Interaction Regions and Associated Genes | get_interacting_genes |
| get_pairwise_interacting_genes | get_pairwise_interacting_genes get_pairwise_interacting_genes,ANY-method get_pairwise_interacting_genes,SpaceMarkersExperiment-method |
| Load spatial features | get_spatial_features |
| Read optimal parameters for spatial kernel density from user input or .json file | get_spatial_parameters |
| Calculate the optimal parameters from spatial kernel density for cell-cell interactions | get_spatial_params_morans_i |
| Access hotspot assignments on a SpaceMarkersExperiment | hotspots hotspots,SpaceMarkersExperiment-method hotspots<- hotspots<-,SpaceMarkersExperiment-method |
| Access the per-spot influence map on a SpaceMarkersExperiment | influence_map influence_map,SpaceMarkersExperiment-method influence_map<- influence_map<-,SpaceMarkersExperiment-method |
| Access pairwise interaction results on a SpaceMarkersExperiment | interactions interactions,SpaceMarkersExperiment-method interactions<- interactions<-,SpaceMarkersExperiment-method |
| Load an AnnData file as a SpaceMarkersExperiment | load_anndata |
| Load 10X Visium data as a SpaceMarkersExperiment | load10X |
| Load 10x Visium Spatial Coordinates | load10XCoords |
| Load 10X Visium Expression Data | load10XExpr |
| Access ligand-receptor scores on a SpaceMarkersExperiment | lr_scores lr_scores,SpaceMarkersExperiment-method lr_scores<- lr_scores<-,SpaceMarkersExperiment-method |
| Curated Ligand-receptor interaction genes A list of vectors with genes associated with ligand-receptor interactions from CellChat database | lrdf |
| Optimal paramters of 5 patterns from CoGAPS. | optParams |
| Per-spot overlap classification map for a pattern pair | overlap_map |
| Access pattern overlap scores on a SpaceMarkersExperiment | overlap_scores overlap_scores,SpaceMarkersExperiment-method overlap_scores<- overlap_scores<-,SpaceMarkersExperiment-method |
| Access analysis hyperparameters on a SpaceMarkersExperiment | params params,SpaceMarkersExperiment-method |
| Plot Ligand-Receptor Interactions between Cell Types | plot_cell_interaction_circos |
| plot_im_scores | plot_im_scores |
| plot_overlap_scores | plot_overlap_scores |
| Plot Ligand-Receptor Interactions from a Single Source to Target Cell Types | plot_source_to_target_circos |
| plot_spatial | plot_spatial |
| plotSpatialDataOverImage | plot_spatial_data_over_image |
| Plot Ligand-Receptor Interactions from Multiple Source to a Single Target Cell Type | plot_target_from_sources_circos |
| Save a SpaceMarkersExperiment as an AnnData (.h5ad) file | save_anndata |
| Main dispatcher for SpaceMarkers | SpaceMarkers |
| Create a SpaceMarkersExperiment object | SpaceMarkersExperiment |
| Accessor generics for SpaceMarkersExperiment | SpaceMarkersExperiment-accessors spatial_patterns spatial_patterns,SpaceMarkersExperiment-method spatial_patterns<- spatial_patterns<-,SpaceMarkersExperiment-method |
| SpaceMarkersExperiment class | show,SpaceMarkersExperiment-method SpaceMarkersExperiment-class |
| Access or set the spatial-kernel parameters on a SpaceMarkersExperiment | spatial_params spatial_params,SpaceMarkersExperiment-method spatial_params<- spatial_params<-,SpaceMarkersExperiment-method |
| Access undirected interaction scores on a SpaceMarkersExperiment | undirected_scores undirected_scores,SpaceMarkersExperiment-method undirected_scores<- undirected_scores<-,SpaceMarkersExperiment-method |
