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ekiernan committed Mar 25, 2020
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Each Release dataset has gene expression matrices containing cell clustering information and annotated cell types. This annotated expression matrix is provided in two file formats: a loom and a h5ad. Both file types are named with an `“_annotated_v1”` suffix and can be found under Release Files on the <link-to-browser relativelink="/releases/2020-mar">March 2020 Release</link-to-browser> page. The normalized matrices were generated using the Cumulus workflow and annotated using published cell types (see more details in the [Methods](methods.md)).

Use the suggested code below to view annotated loom and h5ad files in [Pegasus](https://pegasus.readthedocs.io/en/latest/), [Seurat](https://satijalab.org/seurat/), and [SCANPY](https://github.com/theislab/scanpy). You can view the [Cumulus documentation](https://cumulus.readthedocs.io/en/latest/cumulus.html#load-cumulus-results-into-pegasus) to learn more about importing the annotated expression matrices into these Python and R resources. For the examples below, we use files from the <link-to-browser relativelink="/explore/projects/4d6f6c96-2a83-43d8-8fe1-0f53bffd4674/m/releases/2020-mar/datasets/2020-Mar-Landscape-Adult-Liver-10x/release-files">2020-Mar-Landscape-Adult-Liver-10x</link-to-browser> dataset.
Use the suggested code below to view annotated loom and h5ad files in [Pegasus](https://pegasus.readthedocs.io/en/latest/), [Seurat](https://satijalab.org/seurat/), and [SCANPY](https://github.com/theislab/scanpy). You can view the [Cumulus documentation](https://cumulus.readthedocs.io/en/latest/cumulus.html#load-cumulus-results-into-pegasus) to learn more about importing the annotated expression matrices into these Python and R resources. For the examples below, we use files from the <link-to-browser relativelink="/projects/4d6f6c96-2a83-43d8-8fe1-0f53bffd4674/m/releases/2020-mar/datasets/2020-Mar-Landscape-Adult-Liver-10x/release-files">2020-Mar-Landscape-Adult-Liver-10x</link-to-browser> dataset.

### Pegasus
[Pegasus](https://pegasus.readthedocs.io/en/latest/) is a Python package used by Cumulus for analyzing very large single-cell transcriptomes. The following example files were tested using Python v3.7.5 and Pegasus v0.16.11.
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