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Fix function reference
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grst committed Nov 1, 2024
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"Reannotation of BCR data is outside the scope of Scirpy. Instead we refer the reader to one of the following workflows which all rely on the [Immcantation suite](https://immcantation.readthedocs.io/en/stable/index.html). \n",
"\n",
" * [**Dandelion**](https://sc-dandelion.readthedocs.io/en/latest/) {cite}`Suo.2023` is a Python library for single-cell BCR analysis that also supports re-annotation as showcased in [their tutorial](https://sc-dandelion.readthedocs.io/en/latest/notebooks/1_dandelion_preprocessing-10x_data.html#). Dandelion has some overlap with Scirpy functionality and is interoperable with *Scirpy* by using the {func}`scirpy.io.from_dandelion`and {func}`scirpy.io.to_dandelion` functions that allow to easily switch to Scirpy after the reannotation step. \n",
" * [**nf-core/airrflow**](https://nf-co.re/airrflow/) {cite}`Gabernet2024` is a Nextflow pipeline that can process both bulk and single-cell TCR and BCR-seq data that generates a wide range of outputs, including QC metrics and analysis reports. It may be convenient to first check the outputs of *airrflow* to get an overview of the data, and then follow up with *Scirpy* for more custom analyses. The pipeline produces reannotated BCR data in {term}`AIRR` format that can be imported into *Scirpy* using {func}`ir.io.read_airr`. \n",
" * [**nf-core/airrflow**](https://nf-co.re/airrflow/) {cite}`Gabernet2024` is a Nextflow pipeline that can process both bulk and single-cell TCR and BCR-seq data that generates a wide range of outputs, including QC metrics and analysis reports. It may be convenient to first check the outputs of *airrflow* to get an overview of the data, and then follow up with *Scirpy* for more custom analyses. The pipeline produces reannotated BCR data in {term}`AIRR` format that can be imported into *Scirpy* using {func}`scirpy.io.read_airr`. \n",
" * Alternatively, the [**Immcantation suite**](https://immcantation.readthedocs.io/en/stable/index.html) can be used directly as showcased in [their tutorial](https://immcantation.readthedocs.io/en/stable/getting_started/10x_tutorial.html). Similar to *airrflow*, reannotation will result in an AIRR-compilant `.tsv` file, which can be loaded into Scirpy using {func}`scirpy.io.read_airr`."
]
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