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‎results/spatial_simulators/data/dataset_info.json‎

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[
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{
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"dataset_id": "hindlimbmuscle",
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"dataset_name": "Hindlimbmuscle",
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"dataset_summary": "Spatial RNA sequencing of regenerating mouse hindlimb muscle",
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"dataset_description": "The spatial transcriptomics datasets regenerates mouse muscle tissue generated with the 10x Genomics Visium platform.",
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"data_reference": "10.1101/2020.12.01.407460",
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"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE161318",
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"date_created": "14-03-2025",
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},
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{
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"dataset_id": "brain",
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"dataset_name": "Brain",
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"dataset_summary": "10X Visium spatial RNA-seq from adult mouse brain sections paired to single-nucleus RNA-seq",
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"dataset_description": "This datasets were generated matched single nucleus (sn, this submission) and Visium spatial RNA-seq (10X Genomics) profiles of adjacent mouse brain sections that contain multiple regions from the telencephalon and diencephalon.",
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"data_reference": "10.1038/s41587-021-01139-4",
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"data_url": "https://github.com/BayraktarLab/cell2location",
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"date_created": "11-12-2024",
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"date_created": "14-03-2025",
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"file_size": 44683309
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},
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{
@@ -16,87 +26,77 @@
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"dataset_description": "The dataset includes processed image data, cell type annotations with Louvain clusters, gene IDs for transcript locations, and mRNA point locations, with additional data available on Zenodo.",
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"data_reference": "10.1038/s41586-019-1049-y",
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"data_url": "https://zenodo.org/records/2669683",
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"date_created": "11-12-2024",
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"file_size": 20271969
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{
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"dataset_id": "breast",
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"dataset_name": "Breast",
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"dataset_summary": "A spatially resolved atlas of human breast cancers",
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"dataset_description": "This study presents a spatially resolved transcriptomics analysis of human breast cancers.",
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"data_reference": "10.1038/s41588-021-00911-1",
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"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176078",
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"date_created": "11-12-2024",
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"file_size": 23748327
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},
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{
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"dataset_id": "prostate",
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"dataset_name": "Prostate",
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"dataset_summary": "Spatially resolved gene expression of human protate tissue slices treated with steroid hormones for 8 hours",
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"dataset_description": "Spatially resolved gene expression was prepard by dissociated hman prostate tissue to single cells, and collected & prepped for RNA-seq using the Visium Spatial Gene Expression kit.",
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"data_reference": "10.1016/j.isci.2021.102640",
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"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159697",
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"date_created": "11-12-2024",
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"date_created": "14-03-2025",
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{
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"dataset_id": "breast",
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"dataset_name": "Breast",
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"dataset_summary": "A spatially resolved atlas of human breast cancers",
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"dataset_description": "This study presents a spatially resolved transcriptomics analysis of human breast cancers.",
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"data_reference": "10.1038/s41588-021-00911-1",
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"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176078",
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"date_created": "14-03-2025",
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},
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{
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"dataset_id": "pdac",
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"dataset_name": "pancreatic ductal adenocarcinomas",
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"dataset_summary": "Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas",
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"dataset_description": "We developed a multimodal intersection analysis method combining scRNA-seq with spatial transcriptomics to map and characterize the spatial organization and interactions of distinct cell subpopulations in complex tissues, such as primary pancreatic tumors..",
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"data_reference": "10.1101/2020.12.01.407460",
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"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111672",
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"date_created": "11-12-2024",
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"date_created": "14-03-2025",
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},
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{
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"dataset_id": "olfactorybulb",
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"dataset_name": "Olfactorybulb",
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"dataset_summary": "Single-cell and spatial transcriptomic of mouse olfactory bulb",
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"dataset_description": "Single-cell and spatial transcriptomic of mouse olfactory bulb",
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"data_reference": "10.1126/science.aaf2403",
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"data_url": "http://ww1.spatialtranscriptomicsresearch.org/?usid=24&utid=8672855942",
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"date_created": "14-03-2025",
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},
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{
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"dataset_id": "fibrosarcoma",
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"dataset_name": "Fibrosarcoma",
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"dataset_summary": "Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of Tumor A1 of Tissue 1",
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"dataset_description": "Spatial transcriptomics of Tumor A1 of Tissue 1.",
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"data_reference": "10.1038/s41587-022-01272-8",
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"data_url": "https://github.com/romain-lopez/DestVI-reproducibility",
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"dataset_id": "osteosarcoma",
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"dataset_name": "Osteosarcoma",
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"dataset_summary": "Spatial profiling of human osteosarcoma cells.",
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"dataset_description": "Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression.",
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"data_reference": "10.1073/pnas.1912459116",
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},
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{
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"dataset_id": "gastrulation",
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"dataset_name": "Gastrulation",
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"dataset_summary": "single-cell and spatial transcriptomic molecular map of mouse gastrulation",
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"dataset_description": "Single-Cell omics Data across Mouse Gastrulation and Highly multiplexed spatially resolved gene expression profiling of Early Organogenesis.",
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"data_reference": "10.1038/s41587-021-01006-2",
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"data_url": "https://content.cruk.cam.ac.uk/jmlab/SpatialMouseAtlas2020/",
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"date_created": "11-12-2024",
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"date_created": "14-03-2025",
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{
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"dataset_id": "olfactorybulb",
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"dataset_name": "Olfactorybulb",
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"dataset_summary": "Single-cell and spatial transcriptomic of mouse olfactory bulb",
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"dataset_description": "Single-cell and spatial transcriptomic of mouse olfactory bulb",
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"data_reference": "10.1126/science.aaf2403",
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"data_url": "http://ww1.spatialtranscriptomicsresearch.org/?usid=24&utid=8672855942",
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"date_created": "11-12-2024",
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"file_size": 2341323
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},
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{
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"dataset_id": "hindlimbmuscle",
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"dataset_name": "Hindlimbmuscle",
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"dataset_summary": "Spatial RNA sequencing of regenerating mouse hindlimb muscle",
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"dataset_description": "The spatial transcriptomics datasets regenerates mouse muscle tissue generated with the 10x Genomics Visium platform.",
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"data_reference": "10.1101/2020.12.01.407460",
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"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE161318",
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"date_created": "11-12-2024",
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"file_size": 20088216
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"dataset_id": "osteosarcoma",
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"dataset_name": "Osteosarcoma",
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"dataset_summary": "Spatial profiling of human osteosarcoma cells.",
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"dataset_description": "Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression.",
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}
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]

‎results/spatial_simulators/data/method_info.json‎

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"code_url": "https://github.com/JSB-UCLA/scDesign2",
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{
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"method_name": "scDesign3",
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"method_id": "scdesign3_nb",
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"method_description": "scDesign3 offers a probabilistic model that unifies the generation and inference\nfor single-cell and spatial omics data. The model's interpretable parameters and\nlikelihood enable scDesign3 to generate customized in silico data and unsupervisedly\nassess the goodness-of-fit of inferred cell latent structures (for example, clusters,\ntrajectories and spatial locations).\n",
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"code_url": "https://github.com/SONGDONGYUAN1994/scDesign3",
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"image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/scdesign3_nb:build_main",
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"implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/0ac6b16e5e1ca015caff41382afd57f8292192ab/src/methods/scdesign3_nb",
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{
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"task_id": "methods",
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"method_id": "scdesign3_poisson",
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"method_name": "scDesign3 (Poisson)",
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"method_summary": "A probabilistic model that unifies the generation and inference for single-cell and spatial omics data",
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"method_description": "scDesign3 offers a probabilistic model that unifies the generation and inference\nfor single-cell and spatial omics data. The model's interpretable parameters and\nlikelihood enable scDesign3 to generate customized in silico data and unsupervisedly\nassess the goodness-of-fit of inferred cell latent structures (for example, clusters,\ntrajectories and spatial locations).\n",
40+
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41+
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"image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/scdesign3_poisson:build_main",
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"implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/0ac6b16e5e1ca015caff41382afd57f8292192ab/src/methods/scdesign3_poisson",
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{
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"task_id": "methods",
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"code_url": "https://gitlab.com/sysbiobig/sparsim",
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"documentation_url": "https://gitlab.com/sysbiobig/sparsim/-/blob/master/vignettes/sparsim.Rmd",
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"image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/sparsim:build_main",
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"implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/methods/sparsim",
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"implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/0ac6b16e5e1ca015caff41382afd57f8292192ab/src/methods/sparsim",
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{
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"task_id": "methods",
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"code_url": "https://github.com/Oshlack/splatter",
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"documentation_url": "https://bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatter.html",
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"image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/splatter:build_main",
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"implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/methods/splatter",
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{
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"task_id": "methods",
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"code_url": "https://github.com/xzhoulab/srtsim",
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"documentation_url": "https://xzhoulab.github.io/SRTsim",
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"image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/srtsim:build_main",
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"implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/methods/srtsim",
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"implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/0ac6b16e5e1ca015caff41382afd57f8292192ab/src/methods/srtsim",
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"commit_sha": "0ac6b16e5e1ca015caff41382afd57f8292192ab"
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{
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"task_id": "methods",
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"code_url": "https://github.com/YosefLab/SymSim",
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"documentation_url": "https://github.com/YosefLab/SymSim/blob/master/vignettes/SymSimTutorial.Rmd",
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"image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/symsim:build_main",
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"implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/methods/symsim",
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"implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/0ac6b16e5e1ca015caff41382afd57f8292192ab/src/methods/symsim",
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"commit_sha": "0ac6b16e5e1ca015caff41382afd57f8292192ab"
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{
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"task_id": "methods",
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"code_url": "https://github.com/drisso/zinbwave",
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"documentation_url": "https://bioconductor.org/packages/release/bioc/html/zinbwave.html",
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"image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/zinbwave:build_main",
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"implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/methods/zinbwave",
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"implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/0ac6b16e5e1ca015caff41382afd57f8292192ab/src/methods/zinbwave",
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"commit_sha": "0ac6b16e5e1ca015caff41382afd57f8292192ab"
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},
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{
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"task_id": "control_methods",
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"code_url": "https://github.com/openproblems-bio/task_spatial_simulators",
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"method_name": "negative_shuffle",
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"method_description": "This control method shuffles the input data as a negative control.\n",
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{
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"method_id": "negative",
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"method_name": "negative",
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"method_summary": "A negative control method.",
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"method_description": "A negative control method.\n",
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"method_id": "negative_normal",
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"method_name": "negative_normal",
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"method_summary": "A negative control which generates normal distributed data.",
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"method_description": "This control method generates normal distributed data as a negative control.\nThe mean and the sd are defined by the mean and sd of the input data.\n",
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]

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