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@rcannood
rcannood committed Dec 13, 2024
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98 changes: 49 additions & 49 deletions results/spatial_simulators/data/dataset_info.json
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@@ -1,43 +1,23 @@
[
{
"dataset_id": "hindlimbmuscle",
"dataset_name": "Hindlimbmuscle",
"dataset_summary": "Spatial RNA sequencing of regenerating mouse hindlimb muscle",
"dataset_description": "The spatial transcriptomics datasets regenerates mouse muscle tissue generated with the 10x Genomics Visium platform.",
"data_reference": "10.1101/2020.12.01.407460",
"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE161318",
"date_created": "25-11-2024",
"file_size": 20088216
},
{
"dataset_id": "cortex",
"dataset_name": "Cortex",
"dataset_summary": "Scripts and source data for image processing, barcode calling, and cell type annotations in a seqFISH+ experiment.",
"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.",
"data_reference": "10.1038/s41586-019-1049-y",
"data_url": "https://zenodo.org/records/2669683",
"date_created": "25-11-2024",
"file_size": 20271969
},
{
"dataset_id": "brain",
"dataset_name": "Brain",
"dataset_summary": "10X Visium spatial RNA-seq from adult mouse brain sections paired to single-nucleus RNA-seq",
"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.",
"data_reference": "10.1038/s41587-021-01139-4",
"data_url": "https://github.com/BayraktarLab/cell2location",
"date_created": "25-11-2024",
"date_created": "11-12-2024",
"file_size": 44683309
},
{
"dataset_id": "prostate",
"dataset_name": "Prostate",
"dataset_summary": "Spatially resolved gene expression of human protate tissue slices treated with steroid hormones for 8 hours",
"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.",
"data_reference": "10.1016/j.isci.2021.102640",
"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159697",
"date_created": "25-11-2024",
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"dataset_id": "cortex",
"dataset_name": "Cortex",
"dataset_summary": "Scripts and source data for image processing, barcode calling, and cell type annotations in a seqFISH+ experiment.",
"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.",
"data_reference": "10.1038/s41586-019-1049-y",
"data_url": "https://zenodo.org/records/2669683",
"date_created": "11-12-2024",
"file_size": 20271969
},
{
"dataset_id": "breast",
Expand All @@ -46,18 +26,18 @@
"dataset_description": "This study presents a spatially resolved transcriptomics analysis of human breast cancers.",
"data_reference": "10.1038/s41588-021-00911-1",
"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176078",
"date_created": "25-11-2024",
"date_created": "11-12-2024",
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},
{
"dataset_id": "fibrosarcoma",
"dataset_name": "Fibrosarcoma",
"dataset_summary": "Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of Tumor A1 of Tissue 1",
"dataset_description": "Spatial transcriptomics of Tumor A1 of Tissue 1.",
"data_reference": "10.1038/s41587-022-01272-8",
"data_url": "https://github.com/romain-lopez/DestVI-reproducibility",
"date_created": "25-11-2024",
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"dataset_id": "prostate",
"dataset_name": "Prostate",
"dataset_summary": "Spatially resolved gene expression of human protate tissue slices treated with steroid hormones for 8 hours",
"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.",
"data_reference": "10.1016/j.isci.2021.102640",
"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159697",
"date_created": "11-12-2024",
"file_size": 20645737
},
{
"dataset_id": "pdac",
Expand All @@ -66,18 +46,18 @@
"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..",
"data_reference": "10.1101/2020.12.01.407460",
"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111672",
"date_created": "25-11-2024",
"date_created": "11-12-2024",
"file_size": 18406025
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{
"dataset_id": "olfactorybulb",
"dataset_name": "Olfactorybulb",
"dataset_summary": "Single-cell and spatial transcriptomic of mouse olfactory bulb",
"dataset_description": "Single-cell and spatial transcriptomic of mouse olfactory bulb",
"data_reference": "10.1126/science.aaf2403",
"data_url": "http://ww1.spatialtranscriptomicsresearch.org/?usid=24&utid=8672855942",
"date_created": "25-11-2024",
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"dataset_id": "fibrosarcoma",
"dataset_name": "Fibrosarcoma",
"dataset_summary": "Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of Tumor A1 of Tissue 1",
"dataset_description": "Spatial transcriptomics of Tumor A1 of Tissue 1.",
"data_reference": "10.1038/s41587-022-01272-8",
"data_url": "https://github.com/romain-lopez/DestVI-reproducibility",
"date_created": "11-12-2024",
"file_size": 28476822
},
{
"dataset_id": "osteosarcoma",
Expand All @@ -86,7 +66,7 @@
"dataset_description": "Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression.",
"data_reference": "10.1073/pnas.1912459116",
"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176078",
"date_created": "25-11-2024",
"date_created": "11-12-2024",
"file_size": 21082263
},
{
Expand All @@ -96,7 +76,27 @@
"dataset_description": "Single-Cell omics Data across Mouse Gastrulation and Highly multiplexed spatially resolved gene expression profiling of Early Organogenesis.",
"data_reference": "10.1038/s41587-021-01006-2",
"data_url": "https://content.cruk.cam.ac.uk/jmlab/SpatialMouseAtlas2020/",
"date_created": "25-11-2024",
"date_created": "11-12-2024",
"file_size": 15690550
},
{
"dataset_id": "olfactorybulb",
"dataset_name": "Olfactorybulb",
"dataset_summary": "Single-cell and spatial transcriptomic of mouse olfactory bulb",
"dataset_description": "Single-cell and spatial transcriptomic of mouse olfactory bulb",
"data_reference": "10.1126/science.aaf2403",
"data_url": "http://ww1.spatialtranscriptomicsresearch.org/?usid=24&utid=8672855942",
"date_created": "11-12-2024",
"file_size": 2341323
},
{
"dataset_id": "hindlimbmuscle",
"dataset_name": "Hindlimbmuscle",
"dataset_summary": "Spatial RNA sequencing of regenerating mouse hindlimb muscle",
"dataset_description": "The spatial transcriptomics datasets regenerates mouse muscle tissue generated with the 10x Genomics Visium platform.",
"data_reference": "10.1101/2020.12.01.407460",
"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE161318",
"date_created": "11-12-2024",
"file_size": 20088216
}
]
36 changes: 18 additions & 18 deletions results/spatial_simulators/data/method_info.json
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Expand Up @@ -11,9 +11,9 @@
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Expand All @@ -27,9 +27,9 @@
"code_url": "https://github.com/SONGDONGYUAN1994/scDesign3",
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Expand All @@ -43,9 +43,9 @@
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Expand All @@ -59,9 +59,9 @@
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Expand All @@ -75,9 +75,9 @@
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Expand All @@ -91,9 +91,9 @@
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Expand All @@ -107,9 +107,9 @@
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Expand All @@ -123,9 +123,9 @@
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Expand All @@ -139,8 +139,8 @@
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]
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