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Update AuxiliaryFunctions.ipynb
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michaelgmz authored Sep 1, 2022
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"cell_type": "markdown",
"metadata": {},
"source": [
"This notebook will you through a few auxiliary functions provided by UniTVelo. They are used to facilitate the RNA velocity research and relevant analysis when hardware is a bottleneck, especially GPU resources. The script of choosing the suitable modes is also provided.\n",
"This notebook will walk you through a few auxiliary functions provided by UniTVelo. They are used to facilitate the RNA velocity research and relevant analysis when hardware is a bottleneck, especially GPU resources. The script of choosing the suitable modes is also provided.\n",
"\n",
"We will use human erythroid development dataset in this tutorial (4 clusters & 37k cells in total)."
]
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"\n",
"We define two special scenarios when independent time should be used (see Methods section of manuscript), and we provide a reference script `utv.utils.choose_mode(adata, label)` for choosing modes,\n",
"- Datasets with cell cycle phase included.\n",
"- Datasets with very sparse cell types visualized in low dimentional embeddings.\n",
"- Datasets with very sparse cell types visualized in low dimensional embeddings.\n",
"\n",
"This script should work as a reference only. Sometimes both modes should be tried."
]
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