update results

Author: rcannood

results/spatial_simulators/data/dataset_info.json

@@ -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",
-    "file_size": 20645737
+    "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",
@@ -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",
     "file_size": 23748327
   },
   {
-    "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",
-    "file_size": 28476822
+    "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",
@@ -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
   },
   {
-    "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",
-    "file_size": 2341323
+    "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",
@@ -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
   },
   {
@@ -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
   }
 ]

results/spatial_simulators/data/method_info.json

@@ -11,9 +11,9 @@
     "code_url": "https://github.com/JSB-UCLA/scDesign2",
     "documentation_url": "https://htmlpreview.github.io/?https://github.com/JSB-UCLA/scDesign2/blob/master/vignettes/scDesign2.html",
     "image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/scdesign2:build_main",
-    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/df6409b000a8951078f2d233bb961eb8a706315a/src/methods/scdesign2",
+    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/methods/scdesign2",
     "code_version": "build_main",
-    "commit_sha": "df6409b000a8951078f2d233bb961eb8a706315a"
+    "commit_sha": "bf1f6d13221baeab459bdadf6993650f03ddb1f2"
   },
   {
     "task_id": "methods",
@@ -27,9 +27,9 @@
     "code_url": "https://github.com/SONGDONGYUAN1994/scDesign3",
     "documentation_url": "https://www.bioconductor.org/packages/release/bioc/html/scDesign3.html",
     "image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/scdesign3:build_main",
-    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/df6409b000a8951078f2d233bb961eb8a706315a/src/methods/scdesign3",
+    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/methods/scdesign3",
     "code_version": "build_main",
-    "commit_sha": "df6409b000a8951078f2d233bb961eb8a706315a"
+    "commit_sha": "bf1f6d13221baeab459bdadf6993650f03ddb1f2"
   },
   {
     "task_id": "methods",
@@ -43,9 +43,9 @@
     "code_url": "https://gitlab.com/sysbiobig/sparsim",
     "documentation_url": "https://gitlab.com/sysbiobig/sparsim/-/blob/master/vignettes/sparsim.Rmd",
     "image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/sparsim:build_main",
-    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/df6409b000a8951078f2d233bb961eb8a706315a/src/methods/sparsim",
+    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/methods/sparsim",
     "code_version": "build_main",
-    "commit_sha": "df6409b000a8951078f2d233bb961eb8a706315a"
+    "commit_sha": "bf1f6d13221baeab459bdadf6993650f03ddb1f2"
   },
   {
     "task_id": "methods",
@@ -59,9 +59,9 @@
     "code_url": "https://github.com/Oshlack/splatter",
     "documentation_url": "https://bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatter.html",
     "image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/splatter:build_main",
-    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/df6409b000a8951078f2d233bb961eb8a706315a/src/methods/splatter",
+    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/methods/splatter",
     "code_version": "build_main",
-    "commit_sha": "df6409b000a8951078f2d233bb961eb8a706315a"
+    "commit_sha": "bf1f6d13221baeab459bdadf6993650f03ddb1f2"
   },
   {
     "task_id": "methods",
@@ -75,9 +75,9 @@
     "code_url": "https://github.com/xzhoulab/srtsim",
     "documentation_url": "https://xzhoulab.github.io/SRTsim",
     "image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/srtsim:build_main",
-    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/df6409b000a8951078f2d233bb961eb8a706315a/src/methods/srtsim",
+    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/methods/srtsim",
     "code_version": "build_main",
-    "commit_sha": "df6409b000a8951078f2d233bb961eb8a706315a"
+    "commit_sha": "bf1f6d13221baeab459bdadf6993650f03ddb1f2"
   },
   {
     "task_id": "methods",
@@ -91,9 +91,9 @@
     "code_url": "https://github.com/YosefLab/SymSim",
     "documentation_url": "https://github.com/YosefLab/SymSim/blob/master/vignettes/SymSimTutorial.Rmd",
     "image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/symsim:build_main",
-    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/df6409b000a8951078f2d233bb961eb8a706315a/src/methods/symsim",
+    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/methods/symsim",
     "code_version": "build_main",
-    "commit_sha": "df6409b000a8951078f2d233bb961eb8a706315a"
+    "commit_sha": "bf1f6d13221baeab459bdadf6993650f03ddb1f2"
   },
   {
     "task_id": "methods",
@@ -107,9 +107,9 @@
     "code_url": "https://github.com/drisso/zinbwave",
     "documentation_url": "https://bioconductor.org/packages/release/bioc/html/zinbwave.html",
     "image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/methods/zinbwave:build_main",
-    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/df6409b000a8951078f2d233bb961eb8a706315a/src/methods/zinbwave",
+    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/methods/zinbwave",
     "code_version": "build_main",
-    "commit_sha": "df6409b000a8951078f2d233bb961eb8a706315a"
+    "commit_sha": "bf1f6d13221baeab459bdadf6993650f03ddb1f2"
   },
   {
     "task_id": "control_methods",
@@ -123,9 +123,9 @@
     "code_url": "https://github.com/openproblems-bio/task_spatial_simulators",
     "documentation_url": null,
     "image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/control_methods/positive:build_main",
-    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/df6409b000a8951078f2d233bb961eb8a706315a/src/control_methods/positive",
+    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/control_methods/positive",
     "code_version": "build_main",
-    "commit_sha": "df6409b000a8951078f2d233bb961eb8a706315a"
+    "commit_sha": "bf1f6d13221baeab459bdadf6993650f03ddb1f2"
   },
   {
     "task_id": "control_methods",
@@ -139,8 +139,8 @@
     "code_url": "https://github.com/openproblems-bio/task_spatial_simulators",
     "documentation_url": null,
     "image": "https://ghcr.io/openproblems-bio/task_spatial_simulators/control_methods/negative:build_main",
-    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/df6409b000a8951078f2d233bb961eb8a706315a/src/control_methods/negative",
+    "implementation_url": "https://github.com/openproblems-bio/task_spatial_simulators/blob/bf1f6d13221baeab459bdadf6993650f03ddb1f2/src/control_methods/negative",
     "code_version": "build_main",
-    "commit_sha": "df6409b000a8951078f2d233bb961eb8a706315a"
+    "commit_sha": "bf1f6d13221baeab459bdadf6993650f03ddb1f2"
   }
 ]