Merge branch 'master' into add-cell-level-to-differential-expression

.github/dependabot.yml

@@ -9,4 +9,5 @@ updates:
     directory: "/" # Location of package manifests
     schedule:
       interval: "weekly"
-
+    labels:
+      - "safe to run"

package.json

@@ -51,13 +51,13 @@
     "@babel/core": "^7.21.0",
     "@babel/plugin-transform-runtime": "^7.21.0",
     "@babel/polyfill": "^7.8.7",
-    "@next/bundle-analyzer": "^10.0.9",
+    "@next/bundle-analyzer": "^14.0.3",
     "@socialgouv/matomo-next": "^1.2.2",
     "@vitessce/heatmap": "^3.2.2",
     "@vitessce/scatterplot": "^3.2.2",
     "antd": "^4.24.8",
     "aws-amplify": "^5.3.11",
-    "axios": "^0.21.2",
+    "axios": "^1.6.2",
     "babel-plugin-add-module-exports": "^1.0.4",
     "babel-plugin-dynamic-import-node": "^2.3.3",
     "babel-plugin-import": "^1.13.6",
@@ -77,7 +77,7 @@
     "localforage": "^1.7.4",
     "lodash": "^4.17.13",
     "lru-memoize": "^1.1.0",
-    "mathjs": "^11.0.1",
+    "mathjs": "^12.1.0",
     "next": "^12.3.4",
     "next-images": "^1.4.0",
     "next-plugin-antd-less": "^1.8.0",

src/utils/upload/fileUploadSpecifications.js

@@ -55,7 +55,8 @@ const fileUploadSpecifications = {
     inputInfo: [
       ['<code>scdata$samples</code>: sample assignment. If absent, treated as unisample.'],
       ['<code>scdata[[\'RNA\']]@counts</code>: raw feature counts.'],
-      ['<code>scdata@reductions</code>: contains the embbedings for <code>pca</code> as well as either <code>umap</code> or <code>tsne</code>.'],
+      ['<code>scdata@reductions</code>: contains the embeddings for <code>pca</code>, as well as either <code>umap</code> or <code>tsne</code>.'],
+      ['<strong>Important notes on dimensionality reductions:</strong> ensure the default dimensionality reduction in your Seurat object is named exactly <code>umap</code> or <code>tsne</code>. If the default reduction name includes <code>umap</code> or <code>tsne</code> (e.g., <code>ref.umap</code>), it will be automatically renamed. If the default reduction is different and does not contain these names, the upload will not be successful.'],
       ['\uD83D\uDCA1cluster metadata in <code>[email protected]</code> is auto-detected.'],
       ['\uD83D\uDCA1sample level metadata in <code>[email protected]</code> that groups samples in <code>scdata$samples</code> is auto-detected for downstream analysis.'],
       ['\uD83D\uDCA1if file size is over 15GB, try removing any assays not indicated above.'],