Audit notebook all notebooks (#377)

Co-authored-by: Emanuele Bezzi <[email protected]>
chanzuckerberg · Apr 18, 2023 · 0f49ea1 · 0f49ea1
1 parent 8f7af94
commit 0f49ea1
Show file tree

Hide file tree

Showing 10 changed files with 2,258 additions and 2,539 deletions.
diff --git a/api/python/notebooks/analysis_demo/comp_bio_explore_and_load_lung_data.ipynb b/api/python/notebooks/analysis_demo/comp_bio_explore_and_load_lung_data.ipynb
diff --git a/api/python/notebooks/analysis_demo/comp_bio_normalizing_full_gene_sequencing.ipynb b/api/python/notebooks/analysis_demo/comp_bio_normalizing_full_gene_sequencing.ipynb
@@ -1,27 +1,24 @@
 {
  "cells": [
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Normalizing full-length gene sequencing data from the Census\n",
+    "# Normalizing full-length gene sequencing data\n",
     "\n",
-    "The Census is a versioned container for the single-cell data hosted at [CELLxGENE Discover](https://cellxgene.cziscience.com/). The Census utilizes [SOMA](https://github.com/single-cell-data/SOMA/blob/main/abstract_specification.md) powered by [TileDB](https://tiledb.com/products/tiledb-embedded) for storing, accessing, and efficiently filtering data.\n",
+    "This tutorial shows you how to fetch full-length gene sequencing data from the Census and normalize it to account for gene length.\n",
     "\n",
-    "This notebook shows you how to fetch full-length gene sequencing data from the Census and normalize it to account for gene length.\n",
     "\n",
+    "**Contents**\n",
     "\n",
-    "## Contents\n",
-    "\n",
-    "- Opening the census\n",
-    "- Fetching example full-length sequencing data (Smart-Seq2)\n",
-    "- Normalizing expression to account for gene length\n",
-    "- Validation through clustering analysis\n",
+    "1. Opening the census\n",
+    "2. Fetching example full-length sequencing data (Smart-Seq2)\n",
+    "3. Normalizing expression to account for gene length\n",
+    "4. Validation through clustering exploration\n",
     "\n",
     "## Opening the census\n",
     "\n",
-    "First we open the Census, if you are not familiar with the basics of the Census API you should take a look at the notebook \"Learning about the CELLxGENE Census\" in `comp_bio_census_info.ipynb`."
+    "First we open the Census, if you are not familiar with the basics of the Census API you should take a look at notebook [Learning about the CZ CELLxGENE Census](https://cellxgene-census.readthedocs.io/en/latest/notebooks/analysis_demo/comp_bio_census_info.html)"
    ]
   },
   {
@@ -46,7 +43,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -66,7 +62,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -236,7 +231,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -260,7 +254,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -355,7 +348,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -455,7 +447,7 @@
    "source": [
     "All done! You can see that we now have real numbers instead of integers.\n",
     "\n",
-    "## Validation through clustering analysis\n",
+    "## Validation through clustering exploration\n",
     "\n",
     "Let's perform some basic clustering analysis to see if cell types cluster as expected using the normalized counts.\n",
     "\n",
@@ -621,7 +613,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.10.10"
   },
   "vscode": {
    "interpreter": {