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Suggesting very minor edits to comp_bio_data_integration.Rmd #694

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Aug 6, 2023
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Suggesting very minor edits to comp_bio_data_integration.Rmd #694

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5 changes: 2 additions & 3 deletions api/r/cellxgene.census/vignettes_/comp_bio_data_integration.Rmd
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Expand Up @@ -40,12 +40,11 @@ This notebook provides a demonstration for integrating two Census datasets using

## Finding and fetching data from mouse liver (10X Genomics and Smart-Seq2)

Let's load all modules needed for this notebook.
Let's load all packages needed for this notebook.

```{r, warning=FALSE, message=FALSE}
library(cellxgene.census)
library(Seurat)
library(patchwork)
```

Now we can open the Census.
Expand All @@ -67,7 +66,7 @@ census_datasets <- as.data.frame(census_datasets$concat())
census_datasets[grep("Liver", census_datasets$dataset_title), ]
```

Now we can use the values from `dataset_id` to query and load an AnnData object with all the cells from those datasets.
Now we can use the values from `dataset_id` to query and load a Seurat object with all the cells from those datasets.

```{r, warning=FALSE, message=FALSE, message=FALSE, results='hide'}
tabula_muris_liver_ids <- c("4546e757-34d0-4d17-be06-538318925fcd", "6202a243-b713-4e12-9ced-c387f8483dea")
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