diff --git a/api/python/notebooks/api_demo/census_gget_demo.ipynb b/api/python/notebooks/api_demo/census_gget_demo.ipynb index 33fb1f388..77150a2e1 100644 --- a/api/python/notebooks/api_demo/census_gget_demo.ipynb +++ b/api/python/notebooks/api_demo/census_gget_demo.ipynb @@ -9,13 +9,13 @@ "source": [ "# Querying data using the gget cellxgene module\n", "\n", - "*By Laura Luebbert, lauraluebbert@caltech.edu.*\n", + "*By Laura Luebbert, lauralubbert@gmail.com.*\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", @@ -25,7 +25,7 @@ "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." ] }, { @@ -905,7 +905,7 @@ "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:" ] },