Latest notebook update: Sun Jul 21 02:04:29 UTC 2024

pachterlab · Jul 21, 2024 · 2c66458 · 2c66458
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commit 2c66458
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Showing 32 changed files with 2,681 additions and 1,865 deletions.
diff --git a/vignettes/bivariate.ipynb b/vignettes/bivariate.ipynb
diff --git a/vignettes/create_sfe.ipynb b/vignettes/create_sfe.ipynb
diff --git a/vignettes/create_sfe_v2.ipynb b/vignettes/create_sfe_v2.ipynb
@@ -2,7 +2,7 @@
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     "---\n",
@@ -26,7 +26,7 @@
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+   "id": "b72fe2d3",
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      "remove_cell"
@@ -44,7 +44,7 @@
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+   "id": "280ab726",
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@@ -85,7 +85,7 @@
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     "name": "setup"
@@ -103,7 +103,7 @@
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    "source": [
     "## Downloading the data\n",
@@ -116,7 +116,7 @@
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@@ -128,7 +128,7 @@
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@@ -141,7 +141,7 @@
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@@ -156,7 +156,7 @@
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@@ -167,7 +167,7 @@
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@@ -180,7 +180,7 @@
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@@ -192,7 +192,7 @@
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@@ -210,7 +210,7 @@
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+   "id": "4111dd2e",
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    "source": [
     "Here, spot locations are provided as a CSV file. There are two columns of particular interest, namely `xcoord` and `ycoord`. The barcode column corresponds to the barcodes in the count matrix. Before calling the `SpatialFeatureExperiment` constructor, the spatial coordinates must be converted to a `sf` data frame using `df2sf()`. The coordinates are centroid positions, so we will indicate that `geometryType=\"POINT\"`.  "
@@ -219,7 +219,7 @@
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@@ -234,7 +234,7 @@
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@@ -245,7 +245,7 @@
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@@ -261,7 +261,7 @@
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@@ -272,7 +272,7 @@
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    "source": [