Update Spatially Variable Genes results (#359)

* update results * update dataset metadata * fix path * fix path
openproblems-bio · Oct 18, 2024 · d9adbb5 · d9adbb5
1 parent 49a20b6
commit d9adbb5
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Showing 158 changed files with 11,315 additions and 11,309 deletions.
diff --git a/datasets/10x_datasets/human_colorectal_cancer_visium/index.qmd b/datasets/10x_datasets/human_colorectal_cancer_visium/index.qmd
diff --git a/..._cancer_xenium/data/dataset_metadata.json → ...n_colon_cancer/data/dataset_metadata.json b/..._cancer_xenium/data/dataset_metadata.json → ...n_colon_cancer/data/dataset_metadata.json
@@ -8,17 +8,17 @@
         "name": "counts",
         "schema_type": "integer",
         "shape": [
-          5514,
-          14015
+          5561,
+          14016
         ],
         "type": "sparsematrix"
       },
       {
         "dtype": "float32",
         "name": "normalized",
         "shape": [
-          5514,
-          14015
+          5561,
+          14016
         ],
         "type": "sparsematrix"
       }
@@ -28,103 +28,103 @@
         "dtype": "int64",
         "name": "in_tissue",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "int64",
         "name": "array_row",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "int64",
         "name": "array_col",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "int32",
         "name": "n_genes_by_counts",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float64",
         "name": "log1p_n_genes_by_counts",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "total_counts",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "log1p_total_counts",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float64",
         "name": "pct_counts_in_top_50_genes",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float64",
         "name": "pct_counts_in_top_100_genes",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float64",
         "name": "pct_counts_in_top_200_genes",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float64",
         "name": "pct_counts_in_top_500_genes",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "int64",
         "name": "n_genes",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "size_factors",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       }
@@ -134,7 +134,7 @@
         "dtype": "int64",
         "name": "spatial",
         "shape": [
-          5514,
+          5561,
           2
         ],
         "type": "densematrix"
@@ -236,79 +236,79 @@
         "name": "feature_id",
         "schema_type": "string",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "category",
         "name": "feature_types",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "category",
         "name": "genome",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "int64",
         "name": "n_cells_by_counts",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "mean_counts",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "log1p_mean_counts",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "float64",
         "name": "pct_dropout_by_counts",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "total_counts",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "log1p_total_counts",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "int64",
         "name": "n_cells",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
@@ -318,7 +318,7 @@
         "name": "feature_name",
         "schema_type": "string",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       }
@@ -328,14 +328,14 @@
   },
   "uns": {
     "dataset_description": "This dataset is provided as part of the Technical Note: Post-Xenium In Situ Applications: Immunofluorescence, H&E, and Visium CytAssist Spatial Gene Expression (CG000709). Post-Xenium samples were compared to controls (samples not processed through the Xenium workflow) using 5 \u00b5m (FFPE) serial sections.",
-    "dataset_id": "10x_datasets/human_colon_cancer_xenium",
-    "dataset_name": "10X Xenium - Human Colon",
+    "dataset_id": "tenx_visium/post_xenium/human_colon_cancer",
+    "dataset_name": "10X Post Xenium - Human Colon",
     "dataset_organism": "Homo sapiens",
     "dataset_reference": "10x2023colon",
     "dataset_summary": "Gene expression library of Post Xenium Human Colon Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set - Replicate 1",
     "dataset_url": "https://www.10xgenomics.com/datasets/visium-cytassist-gene-expression-libraries-of-post-xenium-human-colon-cancer-ffpe-using-the-human-whole-transcriptome-probe-set-2-standard",
-    "date_created": "20-08-2024",
-    "file_size": 86811935,
+    "date_created": "23-09-2024",
+    "file_size": 86834646,
     "normalization_id": "log_cp10k"
   }
 }
diff --git a/...human_brain_cancer_visium/data/state.yaml → ...xenium/human_colon_cancer/data/state.yaml b/...human_brain_cancer_visium/data/state.yaml → ...xenium/human_colon_cancer/data/state.yaml
diff --git a/...asets/human_colon_cancer_xenium/index.qmd → .../post_xenium/human_colon_cancer/index.qmd b/...asets/human_colon_cancer_xenium/index.qmd → .../post_xenium/human_colon_cancer/index.qmd
@@ -1,8 +1,8 @@
 ---
-dataset-id: "10x_datasets/human_colon_cancer_xenium"
-title: "10X Xenium - Human Colon"
+dataset-id: "tenx_visium/post_xenium/human_colon_cancer"
+title: "10X Post Xenium - Human Colon"
 subtitle: "Gene expression library of Post Xenium Human Colon Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set - Replicate 1"
-categories: ["10x_datasets"]
+categories: ["tenx_visium"]
 css: [/datasets/datasets.css]
 title-block-banner: transparent
 toc: false
@@ -12,8 +12,8 @@ citation-location: document
 
 ```{r}
 #| include: false
-params <- list(data_dir = "datasets/10x_datasets/human_colon_cancer_xenium/data", results_dir = "results")
-params <- list(data_dir = "./data", results_dir = "../../../results")
+params <- list(data_dir = "datasets/tenx_visium/post_xenium/human_colon_cancer/data", results_dir = "results")
+params <- list(data_dir = "./data", results_dir = "../../../../results")
 ```
 
 {{< include /datasets/_include/_index_template.qmd >}}
diff --git a/...e_brain_xenium/data/dataset_metadata.json → ...um/mouse_brain/data/dataset_metadata.json b/...e_brain_xenium/data/dataset_metadata.json → ...um/mouse_brain/data/dataset_metadata.json
@@ -328,13 +328,13 @@
   },
   "uns": {
     "dataset_description": "This dataset is provided as part of the Technical Note: Post-Xenium In Situ Applications: Immunofluorescence, H&E, and Visium CytAssist Spatial Gene Expression (CG000709). Post-Xenium samples were compared to controls (samples not processed through the Xenium workflow) using 10 \u00b5m fresh-frozen (FF) serial sections.",
-    "dataset_id": "10x_datasets/mouse_brain_xenium",
-    "dataset_name": "10X Xenium - Mouse Brain",
+    "dataset_id": "tenx_visium/post_xenium/mouse_brain",
+    "dataset_name": "10X Post Xenium - Mouse Brain",
     "dataset_organism": "Mus musculus",
     "dataset_reference": "10x2023mousebrain",
     "dataset_summary": "Gene expression library of Post Xenium Mouse Brain (CytAssist Fresh Frozen) using the Mouse Whole Transcriptome Probe Set - Replicate 1",
     "dataset_url": "https://www.10xgenomics.com/datasets/visium-cytassist-gene-expression-libraries-of-post-xenium-mouse-brain-ff-using-the-mouse-whole-transcriptome-probe-set-2-standard",
-    "date_created": "20-08-2024",
+    "date_created": "23-09-2024",
     "file_size": 132646296,
     "normalization_id": "log_cp10k"
   }

diff --git a/...an_breast_cancer_1_visium/data/state.yaml → ...m/post_xenium/mouse_brain/data/state.yaml b/...an_breast_cancer_1_visium/data/state.yaml → ...m/post_xenium/mouse_brain/data/state.yaml
diff --git a/...10x_datasets/mouse_brain_xenium/index.qmd → ..._visium/post_xenium/mouse_brain/index.qmd b/...10x_datasets/mouse_brain_xenium/index.qmd → ..._visium/post_xenium/mouse_brain/index.qmd
@@ -1,8 +1,8 @@
 ---
-dataset-id: "10x_datasets/mouse_brain_xenium"
-title: "10X Xenium - Mouse Brain"
+dataset-id: "tenx_visium/post_xenium/mouse_brain"
+title: "10X Post Xenium - Mouse Brain"
 subtitle: "Gene expression library of Post Xenium Mouse Brain (CytAssist Fresh Frozen) using the Mouse Whole Transcriptome Probe Set - Replicate 1"
-categories: ["10x_datasets"]
+categories: ["tenx_visium"]
 css: [/datasets/datasets.css]
 title-block-banner: transparent
 toc: false
@@ -12,8 +12,8 @@ citation-location: document
 
 ```{r}
 #| include: false
-params <- list(data_dir = "datasets/10x_datasets/mouse_brain_xenium/data", results_dir = "results")
-params <- list(data_dir = "./data", results_dir = "../../../results")
+params <- list(data_dir = "datasets/tenx_visium/post_xenium/mouse_brain/data", results_dir = "results")
+params <- list(data_dir = "./data", results_dir = "../../../../results")
 ```
 
 {{< include /datasets/_include/_index_template.qmd >}}
diff --git a/..._cancer_visium/data/dataset_metadata.json → ...n_brain_cancer/data/dataset_metadata.json b/..._cancer_visium/data/dataset_metadata.json → ...n_brain_cancer/data/dataset_metadata.json
@@ -328,14 +328,14 @@
   },
   "uns": {
     "dataset_description": "10x Genomics obtained FFPE human brain cancer tissue from Avaden Biosciences. The tissue was sectioned as described in the Visium CytAssist Spatial Gene Expression for FFPE - Tissue Preparation Guide (CG000518). Tissue section of 5 \u00b5m was placed on a standard glass slide, then stained following the Deparaffinization, H&E Staining, Imaging & Decrosslinking Demonstrated Protocol (CG000520). The glass slide with tissue section was processed via Visium CytAssist instrument to transfer analytes to a Visium CytAssist Spatial Gene Expression Slide v2, with 11 mm capture areas following the Visium CytAssist Spatial Gene Expression Reagent Kits User Guide (CG000495).",
-    "dataset_id": "10x_datasets/human_brain_cancer_visium",
+    "dataset_id": "tenx_visium/visium/human_brain_cancer",
     "dataset_name": "10X Visium - Human Brain Cancer",
     "dataset_organism": "Homo sapiens",
     "dataset_reference": "10x2023brain",
     "dataset_summary": "Gene expression library of Human Glioblastoma (CytAssist FFPE) using the Human Whole Transcriptome Probe Set",
     "dataset_url": "https://www.10xgenomics.com/datasets/human-brain-cancer-11-mm-capture-area-ffpe-2-standard",
-    "date_created": "20-08-2024",
-    "file_size": 230684111,
+    "date_created": "23-09-2024",
+    "file_size": 230684127,
     "normalization_id": "log_cp10k"
   }
 }
diff --git a/...an_breast_cancer_2_visium/data/state.yaml → ...visium/human_brain_cancer/data/state.yaml b/...an_breast_cancer_2_visium/data/state.yaml → ...visium/human_brain_cancer/data/state.yaml
diff --git a/...asets/human_brain_cancer_visium/index.qmd → ...isium/visium/human_brain_cancer/index.qmd b/...asets/human_brain_cancer_visium/index.qmd → ...isium/visium/human_brain_cancer/index.qmd
@@ -1,8 +1,8 @@
 ---
-dataset-id: "10x_datasets/human_brain_cancer_visium"
+dataset-id: "tenx_visium/visium/human_brain_cancer"
 title: "10X Visium - Human Brain Cancer"
 subtitle: "Gene expression library of Human Glioblastoma (CytAssist FFPE) using the Human Whole Transcriptome Probe Set"
-categories: ["10x_datasets"]
+categories: ["tenx_visium"]
 css: [/datasets/datasets.css]
 title-block-banner: transparent
 toc: false
@@ -12,8 +12,8 @@ citation-location: document
 
 ```{r}
 #| include: false
-params <- list(data_dir = "datasets/10x_datasets/human_brain_cancer_visium/data", results_dir = "results")
-params <- list(data_dir = "./data", results_dir = "../../../results")
+params <- list(data_dir = "datasets/tenx_visium/visium/human_brain_cancer/data", results_dir = "results")
+params <- list(data_dir = "./data", results_dir = "../../../../results")
 ```
 
 {{< include /datasets/_include/_index_template.qmd >}}