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Merged
merged 14 commits into from
Jan 30, 2023
Merged

Add scbasset batch, autotune tutorials #95

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c4cbae1
Add scbasset batch, autotune tutorials
Jan 17, 2023
31d8feb
Update note on api overview
Jan 17, 2023
87c6253
Merge main
Jan 17, 2023
c3476b7
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 17, 2023
d5189e8
Train and update scbasset batch
Jan 25, 2023
79bf699
Precommit changes
Jan 25, 2023
842cac3
Update scvi autotune
Jan 25, 2023
1ad918c
Precommit
Jan 25, 2023
c424a5e
Address comments
Jan 30, 2023
4b5a75e
Add analysis
Jan 30, 2023
c7fc8e5
Precommit
Jan 30, 2023
23e064d
Update isort
Jan 30, 2023
d4fdffa
Update scbasset, add new model autotune
Jan 30, 2023
b2c4638
Merge branch 'main' into scbasset
martinkim0 Jan 30, 2023
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30 changes: 12 additions & 18 deletions api_overview.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -13,18 +13,6 @@
"While we focus on scVI in this tutorial, the API is consistent across all models."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"\n",
"install()"
]
},
{
"cell_type": "code",
"execution_count": 1,
Expand All @@ -40,8 +28,10 @@
},
"outputs": [],
"source": [
"import scanpy as sc\n",
"import scvi"
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"\n",
"install()"
]
},
{
Expand All @@ -64,6 +54,9 @@
}
],
"source": [
"import scanpy as sc\n",
"import scvi\n",
"\n",
"sc.set_figure_params(figsize=(4, 4))\n",
"\n",
"# for white background of figures (only for docs rendering)\n",
Expand Down Expand Up @@ -151,6 +144,7 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {
"id": "hu4Dcg8QnNsz"
Expand All @@ -160,7 +154,7 @@
"\n",
"Important\n",
"\n",
"Unless otherwise specified, scvi-tools models require the raw counts (not log library size normalized).\n",
"Unless otherwise specified, scvi-tools models require the raw counts (not log library size normalized). scvi-tools models will run for non-negative real-valued data, but we strongly suggest checking that these possibly non-count values are intended to represent pseudocounts (e.g. SoupX-corrected counts), and not some other normalized data, in which the variance/covariance structure of the data has changed dramatically.\n",
"\n",
"</div>"
]
Expand Down Expand Up @@ -1686,7 +1680,7 @@
"provenance": []
},
"kernelspec": {
"display_name": "scvi-tools-dev",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -1700,7 +1694,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.6 | packaged by conda-forge | (main, Aug 22 2022, 20:36:39) [GCC 10.4.0]"
"version": "3.8.10 (default, Nov 14 2022, 12:59:47) \n[GCC 9.4.0]"
},
"pycharm": {
"stem_cell": {
Expand All @@ -1726,7 +1720,7 @@
},
"vscode": {
"interpreter": {
"hash": "b5142939ddaa1787bd1bfcf4c0ad4d35be0fa2237c553f986d37efcb39f03f79"
"hash": "e7370f93d1d0cde622a1f8e1c04877d8463912d04d973331ad4851f04de6915a"
}
}
},
Expand Down
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