From f83ed20bd55e4637f5f030df77a2c5c2572d23e9 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 1 Nov 2024 22:00:41 +0100 Subject: [PATCH] Fix function reference --- docs/tutorials/tutorial_5k_bcr.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorials/tutorial_5k_bcr.ipynb b/docs/tutorials/tutorial_5k_bcr.ipynb index 3fab4e58e..dd4966584 100644 --- a/docs/tutorials/tutorial_5k_bcr.ipynb +++ b/docs/tutorials/tutorial_5k_bcr.ipynb @@ -88,7 +88,7 @@ "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`." ] },