Editorial changes to notebook comp_bio_data_integration_scvi.ipynb (#…

…370)
chanzuckerberg · Apr 11, 2023 · 093e181 · 093e181
1 parent a494ae3
commit 093e181
Showing 1 changed file with 8 additions and 18 deletions.
diff --git a/api/python/notebooks/analysis_demo/comp_bio_data_integration_scvi.ipynb b/api/python/notebooks/analysis_demo/comp_bio_data_integration_scvi.ipynb
@@ -1,20 +1,17 @@
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-    "# Integration of data from the Census\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",
+    "# Integrating multi-dataset slices of data\n",
     "\n",
     "The Census contains data from multiple studies providing an opportunity to perform inter-dataset analysis. To this end integration of data has to be performed first to account for batch effects.\n",
     "\n",
-    "This notebook provides a demonstration for integrating two Census datasets using [`scvi-tools`](https://docs.scvi-tools.org/en/stable/index.html). The goal is not to provide an exhaustive guide on proper integration, but to showcase what information in the Census can inform data integration.\n",
+    "This notebook provides a demonstration for integrating two Census datasets using [`scvi-tools`](https://docs.scvi-tools.org/en/stable/index.html). **The goal is not to provide an exhaustive guide on proper integration, but to showcase what information in the Census can inform data integration.**\n",
     "\n",
-    "We will go over the following:\n",
+    "**Contents**\n",
     "\n",
     "1. Finding and fetching data from mouse liver (10X Genomics and Smart-Seq2).\n",
     "1. Gene-length normalization of Smart-Seq2 data.\n",
@@ -24,7 +21,7 @@
     "   1. Integration with batch defined as `dataset_id` + `donor_id`.\n",
     "   1. Integration with batch defined as `dataset_id` + `donor_id` + `assay_ontology_term_id` + `suspension_type`.\n",
     "\n",
-    "## Finding and fetching data from mouse liver\n",
+    "## Finding and fetching data from mouse liver (10X Genomics and Smart-Seq2)\n",
     "\n",
     "Let's load all modules needed for this notebook."
    ]
@@ -61,12 +58,11 @@
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-    "Now we can 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\" at `comp_bio_census_info.ipynb`."
+    "Now we can 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](https://cellxgene-census.readthedocs.io/en/latest/notebooks/analysis_demo/comp_bio_census_info.html)."
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@@ -87,7 +83,6 @@
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@@ -229,7 +224,6 @@
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     "##  Gene-length normalization of Smart-Seq2 data.\n",
     "\n",
-    "Smart-seq2 read counts have to be normalized by gene length. For full details on gene-length normalization take a look at the notebook \"Normalizing full-length gene sequencing data from the Census\" at `comp_bio_normalizing_full_gene_sequencing.ipynb`.\n",
+    "Smart-seq2 read counts have to be normalized by gene length. For full details on gene-length normalization take a look at the notebook [Normalizing full-length gene sequencing data from the Census](https://cellxgene-census.readthedocs.io/en/latest/notebooks/analysis_demo/comp_bio_normalizing_full_gene_sequencing.html).\n",
     "\n",
     "Let's first get the gene lengths from `var.feature_length`."
    ]
@@ -413,7 +406,7 @@
     "\n",
     "Here we will use the \"single-cell Variational Inference\" model or scVI which uses a deep generative model for the integration of spatial transcriptomic data and scRNA-seq data.\n",
     "\n",
-    "For comprehensive usage and best practices of scVI please refer to the [doc site](https://docs.scvi-tools.org/en/stable/index.html) of `scvi-tools`.\n",
+    "**For comprehensive usage and best practices of scVI please refer to the [doc site](https://docs.scvi-tools.org/en/stable/index.html) of `scvi-tools`.**\n",
     "\n",
     "### Inspecting data prior to integration\n",
     "\n",
@@ -601,7 +594,6 @@
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@@ -1046,7 +1036,7 @@
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