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change loading in differential expression chapter
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AnnaChristina committed Oct 6, 2023
1 parent aefddec commit d5e31b2
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Showing 2 changed files with 19 additions and 14 deletions.
32 changes: 18 additions & 14 deletions jupyter-book/conditions/differential_gene_expression.ipynb
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Expand Up @@ -107,12 +107,17 @@
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"During startup - Warning message:\n",
"Setting LC_CTYPE failed, using \"C\" \n"
]
"data": {
"text/html": [
"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"><span style=\"color: #808000; text-decoration-color: #808000; font-weight: bold\">To use sccoda or tasccoda please install ete3 with </span><span style=\"color: #008000; text-decoration-color: #008000; font-weight: bold\">pip install ete3</span>\n",
"</pre>\n"
],
"text/plain": [
"\u001b[1;33mTo use sccoda or tasccoda please install ete3 with \u001b[0m\u001b[1;32mpip install ete3\u001b[0m\n"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
Expand All @@ -127,6 +132,7 @@
"import numpy as np\n",
"import random\n",
"import sc_toolbox\n",
"import pertpy \n",
"\n",
"import rpy2.rinterface_lib.callbacks\n",
"import anndata2ri\n",
Expand Down Expand Up @@ -212,7 +218,7 @@
}
],
"source": [
"adata = sc.read(\"kang.h5ad\")\n",
"adata = pertpy.data.kang_2018()\n",
"adata"
]
},
Expand All @@ -227,7 +233,7 @@
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Expand Down Expand Up @@ -1397,8 +1403,7 @@
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Expand Down Expand Up @@ -2386,8 +2391,7 @@
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Expand Down Expand Up @@ -2502,7 +2506,7 @@
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"kernelspec": {
"display_name": "Python 3",
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"language": "python",
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},
Expand All @@ -2516,7 +2520,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.16 (main, Dec 7 2022, 01:11:51) \n[GCC 9.4.0]"
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1 change: 1 addition & 0 deletions jupyter-book/conditions/differential_gene_expression.yml
Original file line number Diff line number Diff line change
Expand Up @@ -17,3 +17,4 @@ dependencies:
- conda-forge::pip
- pip:
- sc-toolbox
- pertpy==0.5.0

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