{ "_id": "6a12ac38acfb0bcc41d17fbf", "Package": "STRIDER", "Type": "Package", "Title": "Spatial Transcriptomics Deconvolution and Integration in R", "Version": "1.0.0", "Date": "2026-01-25", "Authors@R": "person(\"Zaoqu\", \"Liu\",\nemail = \"liuzaoqu@163.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4386-2787\"))", "Author": "Zaoqu Liu [aut, cre] ()", "Maintainer": "Zaoqu Liu ", "Description": "STRIDER (Spatial Transcriptomics deconvolutIon and\nintegration in R) provides comprehensive tools for analyzing\nspatial transcriptomics data. The package implements topic\nmodeling based deconvolution using Latent Dirichlet Allocation\n(LDA) to decompose spatial spots into cell type proportions. 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Tests updated for population SD\n\nAll 687 tests pass\nR CMD check: 0 errors, 4 warnings (RcppArmadillo related), 4 notes\n", "time": 1769282048 }, "_maintainer": { "name": "Zaoqu Liu", "email": "liuzaoqu@163.com", "login": "zaoqu-liu", "orcid": "0000-0002-4386-2787", "description": "AI4S", "uuid": 68080738 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "rlang", "version": ">= 1.0.0", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.4.0", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.0", "role": "Imports" }, { "package": "text2vec", "version": ">= 0.6.0", "role": 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}, { "page": "compute_rotation_svd_cpp", "title": "Compute Optimal Rotation via SVD", "topics": [ "compute_rotation_svd_cpp" ] }, { "page": "create_mapping_graph", "title": "Create Spot-Cell Neighborhood Graph", "topics": [ "create_mapping_graph" ] }, { "page": "create_strider_object", "title": "Create STRIDER Object", "topics": [ "create_strider_object" ] }, { "page": "data_io", "title": "Data Input/Output Functions for STRIDER", "topics": [ "data_io" ] }, { "page": "deconvolve", "title": "Cell Type Deconvolution Functions for STRIDER", "topics": [ "deconvolve" ] }, { "page": "euclidean_distance_cpp", "title": "Compute Euclidean Distance Matrix", "topics": [ "euclidean_distance_cpp" ] }, { "page": "evaluate_model_prediction", "title": "Evaluate Model Using Cell Type Prediction", "topics": [ "evaluate_model_prediction" ] }, { "page": "evaluate_topic_range", "title": "Evaluate Multiple Topic Numbers", "topics": [ "evaluate_topic_range" ] }, { "page": "filter_cells", "title": "Filter 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"topics": [ "get_default_colors" ] }, { "page": "get_extended_colors", "title": "Generate Color Palette", "topics": [ "get_extended_colors" ] }, { "page": "get_mapped_celltypes", "title": "Get Mapped Cell Information", "topics": [ "get_mapped_celltypes" ] }, { "page": "get_shared_genes", "title": "Get Shared Genes Between Datasets", "topics": [ "get_shared_genes" ] }, { "page": "integrate_samples", "title": "Integrate Multiple Spatial Transcriptomics Samples", "topics": [ "integrate_samples" ] }, { "page": "integration", "title": "Multi-Sample Integration Functions for STRIDER", "topics": [ "integration" ] }, { "page": "integration_quality", "title": "Calculate Integration Quality Metrics", "topics": [ "integration_quality" ] }, { "page": "kl_divergence_matrix_cpp", "title": "Compute KL Divergence Matrix", "topics": [ "kl_divergence_matrix_cpp" ] }, { "page": "lda_model", "title": "LDA Topic Model for STRIDER", "topics": [ "lda_model" ] }, { "page": "map_spots_to_cells", "title": "Map Spatial Spots to Similar Single Cells", "topics": [ "map_spots_to_cells" ] }, { "page": "mapping", "title": "Spot-to-Cell Mapping Functions for STRIDER", "topics": [ "mapping" ] }, { "page": "marker_find", "title": "Marker Gene Identification for STRIDER", "topics": [ "marker_find" ] }, { "page": "model_evaluate", "title": "Model Evaluation Functions for STRIDER", "topics": [ "model_evaluate" ] }, { "page": "normalize_counts", "title": "Normalize Counts", "topics": [ "normalize_counts" ] }, { "page": "plot", "title": "Visualization Functions for STRIDER", "topics": [ "plot" ] }, { "page": "plot_celltype_heatmap", "title": "Plot Cell Type Composition Heatmap", "topics": [ "plot_celltype_heatmap" ] }, { "page": "plot_cluster", "title": "Plot Cluster Results", "topics": [ "plot_cluster" ] }, { "page": "plot_deconv", "title": "Plot Deconvolution Results", "topics": [ "plot_deconv" ] }, { "page": "plot_deconv_pie", "title": "Scatter Pie Plot for Deconvolution", "topics": [ "plot_deconv_pie" 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