rm_old_tutorial

sergiomarco25 · sergiomarco25 · commit 4a0bc59c7129 · 2025-09-26T09:32:54.000+02:00
diff --git a/docs/.ipynb_checkpoints/index-checkpoint.md b/docs/.ipynb_checkpoints/index-checkpoint.md
@@ -12,7 +12,7 @@ Plotting  <api/plotting.md>
 
 ```
 ```{toctree}
-:maxdepth: 2
+:maxdepth: 3
 :caption: Tutorials
 notebooks/Basic_tutorial
 
diff --git a/docs/index.md b/docs/index.md
@@ -12,7 +12,7 @@ Plotting  <api/plotting.md>
 
 ```
 ```{toctree}
-:maxdepth: 2
+:maxdepth: 3
 :caption: Tutorials
 notebooks/Basic_tutorial
 
diff --git a/docs/notebooks/.ipynb_checkpoints/Basic_tutorial-checkpoint.ipynb b/docs/notebooks/.ipynb_checkpoints/Basic_tutorial-checkpoint.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Aim of the tutorial"
+    "# Basic tutorial"
    ]
   },
   {
@@ -18,7 +18,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 0. Dataset for the tutorial"
+    "## 0. Dataset for the tutorial"
    ]
   },
   {
@@ -32,7 +32,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 1. Import packages"
+    "## 1. Import packages"
    ]
   },
   {
@@ -53,7 +53,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 2. Load SpatialData object"
+    "## 2. Load SpatialData object"
    ]
   },
   {
@@ -104,7 +104,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 2. Processing cellular information & cell type definition"
+    "## 3. Processing cellular information & cell type definition"
    ]
   },
   {
@@ -245,7 +245,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 3. Segmentation-free analysis"
+    "## 4. Segmentation-free analysis"
    ]
   },
   {
@@ -367,14 +367,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 4. Gene-centric exploration of uRNA compopsition "
+    "## 5. Gene-centric exploration of uRNA compopsition "
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 4.1 Exploring uRNA abundance and proportion"
+    "### 5.1 Exploring uRNA abundance and proportion"
    ]
   },
   {
@@ -518,7 +518,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 4.2 Exploring spatial variability and uRNA patterning"
+    "### 5.2 Exploring spatial variability and uRNA patterning"
    ]
   },
   {
@@ -848,7 +848,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 4.3 Filtering uRNA genes"
+    "### 5.3 Filtering uRNA genes"
    ]
   },
   {
@@ -892,7 +892,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 5. Identifying uRNAs source"
+    "## 6. Identifying uRNAs source"
    ]
   },
   {
@@ -945,7 +945,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 5.1 Assesing diffusion"
+    "### 6.1 Assesing diffusion"
    ]
   },
   {
@@ -1051,7 +1051,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 5.2. Cell-specific uRNAs source score"
+    "### 6.2. Cell-specific uRNAs source score"
    ]
   },
   {
diff --git a/docs/notebooks/Basic_tutorial.ipynb b/docs/notebooks/Basic_tutorial.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Aim of the tutorial"
+    "# Basic tutorial"
    ]
   },
   {
@@ -18,7 +18,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 0. Dataset for the tutorial"
+    "## 0. Dataset for the tutorial"
    ]
   },
   {
@@ -32,7 +32,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 1. Import packages"
+    "## 1. Import packages"
    ]
   },
   {
@@ -53,7 +53,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 2. Load SpatialData object"
+    "## 2. Load SpatialData object"
    ]
   },
   {
@@ -104,7 +104,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 2. Processing cellular information & cell type definition"
+    "## 3. Processing cellular information & cell type definition"
    ]
   },
   {
@@ -245,7 +245,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 3. Segmentation-free analysis"
+    "## 4. Segmentation-free analysis"
    ]
   },
   {
@@ -367,14 +367,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 4. Gene-centric exploration of uRNA compopsition "
+    "## 5. Gene-centric exploration of uRNA compopsition "
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 4.1 Exploring uRNA abundance and proportion"
+    "### 5.1 Exploring uRNA abundance and proportion"
    ]
   },
   {
@@ -518,7 +518,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 4.2 Exploring spatial variability and uRNA patterning"
+    "### 5.2 Exploring spatial variability and uRNA patterning"
    ]
   },
   {
@@ -848,7 +848,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 4.3 Filtering uRNA genes"
+    "### 5.3 Filtering uRNA genes"
    ]
   },
   {
@@ -892,7 +892,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 5. Identifying uRNAs source"
+    "## 6. Identifying uRNAs source"
    ]
   },
   {
@@ -945,7 +945,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 5.1 Assesing diffusion"
+    "### 6.1 Assesing diffusion"
    ]
   },
   {
@@ -1051,7 +1051,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 5.2. Cell-specific uRNAs source score"
+    "### 6.2. Cell-specific uRNAs source score"
    ]
   },
   {

Original file line number	Diff line number	Diff line change
`@@ -4,7 +4,7 @@`
`4`	`4`	`"cell_type": "markdown",`
`5`	`5`	`"metadata": {},`
`6`	`6`	`"source": [`
`7`		`- "# Aim of the tutorial"`
	`7`	`+ "# Basic tutorial"`
`8`	`8`	`]`
`9`	`9`	`},`
`10`	`10`	`{`
`@@ -18,7 +18,7 @@`
`18`	`18`	`"cell_type": "markdown",`
`19`	`19`	`"metadata": {},`
`20`	`20`	`"source": [`
`21`		`- "# 0. Dataset for the tutorial"`
	`21`	`+ "## 0. Dataset for the tutorial"`
`22`	`22`	`]`
`23`	`23`	`},`
`24`	`24`	`{`
`@@ -32,7 +32,7 @@`
`32`	`32`	`"cell_type": "markdown",`
`33`	`33`	`"metadata": {},`
`34`	`34`	`"source": [`
`35`		`- "# 1. Import packages"`
	`35`	`+ "## 1. Import packages"`
`36`	`36`	`]`
`37`	`37`	`},`
`38`	`38`	`{`
`@@ -53,7 +53,7 @@`
`53`	`53`	`"cell_type": "markdown",`
`54`	`54`	`"metadata": {},`
`55`	`55`	`"source": [`
`56`		`- "# 2. Load SpatialData object"`
	`56`	`+ "## 2. Load SpatialData object"`
`57`	`57`	`]`
`58`	`58`	`},`
`59`	`59`	`{`
`@@ -104,7 +104,7 @@`
`104`	`104`	`"cell_type": "markdown",`
`105`	`105`	`"metadata": {},`
`106`	`106`	`"source": [`
`107`		`- "# 2. Processing cellular information & cell type definition"`
	`107`	`+ "## 3. Processing cellular information & cell type definition"`
`108`	`108`	`]`
`109`	`109`	`},`
`110`	`110`	`{`
`@@ -245,7 +245,7 @@`
`245`	`245`	`"cell_type": "markdown",`
`246`	`246`	`"metadata": {},`
`247`	`247`	`"source": [`
`248`		`- "# 3. Segmentation-free analysis"`
	`248`	`+ "## 4. Segmentation-free analysis"`
`249`	`249`	`]`
`250`	`250`	`},`
`251`	`251`	`{`
`@@ -367,14 +367,14 @@`
`367`	`367`	`"cell_type": "markdown",`
`368`	`368`	`"metadata": {},`
`369`	`369`	`"source": [`
`370`		`- "# 4. Gene-centric exploration of uRNA compopsition "`
	`370`	`+ "## 5. Gene-centric exploration of uRNA compopsition "`
`371`	`371`	`]`
`372`	`372`	`},`
`373`	`373`	`{`
`374`	`374`	`"cell_type": "markdown",`
`375`	`375`	`"metadata": {},`
`376`	`376`	`"source": [`
`377`		`- "## 4.1 Exploring uRNA abundance and proportion"`
	`377`	`+ "### 5.1 Exploring uRNA abundance and proportion"`
`378`	`378`	`]`
`379`	`379`	`},`
`380`	`380`	`{`
`@@ -518,7 +518,7 @@`
`518`	`518`	`"cell_type": "markdown",`
`519`	`519`	`"metadata": {},`
`520`	`520`	`"source": [`
`521`		`- "## 4.2 Exploring spatial variability and uRNA patterning"`
	`521`	`+ "### 5.2 Exploring spatial variability and uRNA patterning"`
`522`	`522`	`]`
`523`	`523`	`},`
`524`	`524`	`{`
`@@ -848,7 +848,7 @@`
`848`	`848`	`"cell_type": "markdown",`
`849`	`849`	`"metadata": {},`
`850`	`850`	`"source": [`
`851`		`- "# 4.3 Filtering uRNA genes"`
	`851`	`+ "### 5.3 Filtering uRNA genes"`
`852`	`852`	`]`
`853`	`853`	`},`
`854`	`854`	`{`
`@@ -892,7 +892,7 @@`
`892`	`892`	`"cell_type": "markdown",`
`893`	`893`	`"metadata": {},`
`894`	`894`	`"source": [`
`895`		`- "# 5. Identifying uRNAs source"`
	`895`	`+ "## 6. Identifying uRNAs source"`
`896`	`896`	`]`
`897`	`897`	`},`
`898`	`898`	`{`
`@@ -945,7 +945,7 @@`
`945`	`945`	`"cell_type": "markdown",`
`946`	`946`	`"metadata": {},`
`947`	`947`	`"source": [`
`948`		`- "## 5.1 Assesing diffusion"`
	`948`	`+ "### 6.1 Assesing diffusion"`
`949`	`949`	`]`
`950`	`950`	`},`
`951`	`951`	`{`
`@@ -1051,7 +1051,7 @@`
`1051`	`1051`	`"cell_type": "markdown",`
`1052`	`1052`	`"metadata": {},`
`1053`	`1053`	`"source": [`
`1054`		`- "## 5.2. Cell-specific uRNAs source score"`
	`1054`	`+ "### 6.2. Cell-specific uRNAs source score"`
`1055`	`1055`	`]`
`1056`	`1056`	`},`
`1057`	`1057`	`{`