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docs(tutorial): update hyperlink
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CaibinSh committed Aug 14, 2024
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6 changes: 3 additions & 3 deletions docs/tutorials/scAR_tutorial_batch_denoising_scRNAseq.ipynb
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"\n",
"In this tutorial, we will guide you through the process of batch denoising scRNAseq datasets, which originate from different batches and laboratories.\n",
"\n",
"To demonstrate the process, we will use the [human breast cell atals](10.1038/s41588-024-01688-9), comprising over 800,000 human cells collected from 55 donors and sequenced across 45 batches. This dataset serves as a practical example for removing ambient noise during data integration. The original dataset can be accessed via [cellxgene](https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637).\n",
"To demonstrate the process, we will use the [human breast cell atals](https://www.nature.com/articles/s41588-024-01688-9), comprising over 800,000 human cells collected from 55 donors and sequenced across 45 batches. This dataset serves as a practical example for removing ambient noise during data integration. The original dataset can be accessed via [cellxgene](https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637).\n",
"\n",
"<div class=\"alert alert-info\">\n",
"\n",
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"The dataset can be downloaded from cellxgene by following command \n",
"`wget -O HBCA.h5ad https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad\n",
"` \n",
"The integrated dataset consists of 803,283 cells from 55 donors, sequenced across 45 batches. The batch information, labeled as 'processing_date' in Anndata.obs, is detailed in the Methods section of [Reed et al., Nature Genetics (2024)](10.1038/s41588-024-01688-9)"
"The integrated dataset consists of 803,283 cells from 55 donors, sequenced across 45 batches. The batch information, labeled as 'processing_date' in Anndata.obs, is detailed in the Methods section of [Reed et al., Nature Genetics (2024)](https://www.nature.com/articles/s41588-024-01688-9)"
]
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{
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"id": "cbf4a8b1",
"metadata": {},
"source": [
"scAR allows for denoising a specific subset of genes and samples, making pre-filtering advisable to save computational time. In this case, we have subsetted the data to include only marker genes and highly variable genes, as provided in Figure 2 of [Reed et al., Nature Genetics (2024)](10.1038/s41588-024-01688-9) and Anndata.var, respectively."
"scAR allows for denoising a specific subset of genes and samples, making pre-filtering advisable to save computational time. In this case, we have subsetted the data to include only marker genes and highly variable genes, as provided in Figure 2 of [Reed et al., Nature Genetics (2024)](https://www.nature.com/articles/s41588-024-01688-9) and Anndata.var, respectively."
]
},
{
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