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[docs] Update links to gget website and author email #1171

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Jun 4, 2024
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[docs] Update links to gget website and author email #1171

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10 changes: 5 additions & 5 deletions api/python/notebooks/api_demo/census_gget_demo.ipynb
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"source": [
"# Querying data using the gget cellxgene module\n",
"\n",
"*By Laura Luebbert, [email protected].*\n",
"*By Laura Luebbert, [email protected].*\n",
"\n",
"[gget](https://github.com/pachterlab/gget) is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.\n",
"\n",
"The [gget cellxgene](https://pachterlab.github.io/gget/cellxgene.html) module builds on the [CZ CELLxGENE Discover Census](https://chanzuckerberg.github.io/cellxgene-census/) to query data from [CZ CELLxGENE Discover](https://cellxgene.cziscience.com/). This notebook briefly introduces the [gget cellxgene](https://pachterlab.github.io/gget/cellxgene.html) module by providing one simple example for each supported query type.\n",
"The [gget cellxgene](https://pachterlab.github.io/gget/en/cellxgene.html) module builds on the [CZ CELLxGENE Discover Census](https://chanzuckerberg.github.io/cellxgene-census/) to query data from [CZ CELLxGENE Discover](https://cellxgene.cziscience.com/). This notebook briefly introduces the [gget cellxgene](https://pachterlab.github.io/gget/en/cellxgene.html) module by providing one simple example for each supported query type.\n",
"\n",
"If you use gget cellxgene in a publication, please [cite gget](https://pachterlab.github.io/gget/cite.html) in addition to [citing CZ CELLxGENE](https://cellxgene.cziscience.com/docs/08__Cite%20cellxgene%20in%20your%20publications).\n",
"If you use gget cellxgene in a publication, please [cite gget](https://pachterlab.github.io/gget/en/cite.html) in addition to [citing CZ CELLxGENE](https://cellxgene.cziscience.com/docs/08__Cite%20cellxgene%20in%20your%20publications).\n",
"\n",
"You can also [open this notebook in Google Colab](https://colab.research.google.com/github/chanzuckerberg/cellxgene-census/blob/main/api/python/notebooks/api_demo/census_gget_demo.ipynb).\n",
"\n",
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"2. Fetch an [AnnData](https://anndata.readthedocs.io/en/latest/) object by selecting gene(s), tissue(s) and cell type(s).\n",
"3. Plot a dot plot similar to those shown on the CZ CELLxGENE Discover [Gene Expression](https://cellxgene.cziscience.com/gene-expression).\n",
"4. Fetch only cell metadata (corresponds to AnnData.obs).\n",
"5. Use [gget cellxgene](https://pachterlab.github.io/gget/cellxgene.html) from the command line."
"5. Use [gget cellxgene](https://pachterlab.github.io/gget/en/cellxgene.html) from the command line."
]
},
{
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"id": "2QjJEJdS-He7"
},
"source": [
"## Use [gget cellxgene](https://pachterlab.github.io/gget/cellxgene.html) from the command line\n",
"## Use [gget cellxgene](https://pachterlab.github.io/gget/en/cellxgene.html) from the command line\n",
"All gget modules support use from the command line. Note that the command line interface requires the `-o/--out` argument to specify a path to save the fetched data. Here are the command line versions of the queries demonstrated above:"
]
},
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