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wee-snufkin authored Dec 17, 2023
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Expand Up @@ -68,7 +68,7 @@ In this tutorial we will perform trajectory analysis using [monocle3](https://co
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{: .agenda}

## Get data
# Get data
We will continue to work on the case study data from a mouse model of fetal growth restriction {% cite Bacon2018 %} (see [the study in Single Cell Expression Atlas](https://www.ebi.ac.uk/gxa/sc/experiments/E-MTAB-6945/results/tsne) and [the project submission](https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6945/)).

In the previous tutorials, we first created an AnnData object and performed downstream analysis on that file. However, Monocle3 uses another datatype which is Cell Data Set (CDS). To be able to infer trajectories in Monocle, we need to transform our AnnData object into CDS file. And guess what - we already have a tutorial for that! We did it in [format conversion tutorial]({% link topics/single-cell/tutorials/scrna-data-ingest/tutorial.md %}), in the [Anndata -> Cell Data Set (CDS) subsection]{% topics/single-cell/tutorials/scrna-data-ingest/tutorial.md %}#cds-input-for-monocle3-tutorial-use-for-pre-processed-data .
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