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Update tutorial
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grst committed Oct 11, 2024
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"### Clonotype Diversity\n",
":::{note}\n",
"Clonotype diversity is a rather complicated subject and different approaches work with different assumptions. Noteable is that in sc-AIRR analysis the term population can be defined in different ways depending on the scientific question (i.e. individuals, patient groups, clonotype cluster). Further, many different alpha diversity indices for many different applications have been developed and each might introduce bias if used unwarily {cite}`Finotello.2016`. Either way it is recommended to use a combination of many different indices as each index provides different information {cite}`Pelissier.2023`\n",
"Clonotype diversity is a rather complicated subject and different approaches work with different assumptions. In sc-AIRR analysis the term \"population\" can be defined in different ways depending on the scientific question (i.e. individuals, patient groups, clonotype cluster). Further, many different alpha diversity indices for many different applications have been developed and may come with different pitfalls {cite}`Finotello.2016`. We recommend to consult a combination of different indices as each index provides different information {cite}`Pelissier.2023`\n",
":::\n",
"\n",
"Scirpy comes with an innate alpha diversity calculation tool ({func}`scirpy.tl.alpha_diversity`) and a corresponding visualization tool ({func}`scirpy.pl.alpha_diversity`), which can utilize any diversity index implemented into the python package [`scikit-bio`](https://scikit.bio/docs/latest/generated/skbio.diversity.alpha.html#module-skbio.diversity.alpha) However, `scikit-bio` is not an initial requirement for `Scirpy` and needs to be installed and imported separately."
"Scirpy provides ({func}`scirpy.tl.alpha_diversity`) to calculate alpha diversity and a corresponding visualization function ({func}`scirpy.pl.alpha_diversity`), which can utilize any diversity index implemented into the python package [`scikit-bio`](https://scikit.bio/docs/latest/generated/skbio.diversity.alpha.html#module-skbio.diversity.alpha) However, `scikit-bio` is not an initial requirement for `Scirpy` and needs to be installed and imported separately."
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