diff --git a/docs/posts/prepare.md b/docs/posts/prepare.md index 46483904..c7f30d3d 100644 --- a/docs/posts/prepare.md +++ b/docs/posts/prepare.md @@ -10,7 +10,7 @@ If your data is in `h5ad` file (from the [`anndata`](https://anndata.readthedocs - Expression values (raw or normalized) in `anndata.X` - At least one embedding (e.g., tSNE, UMAP) in `anndata.obsm`, specified with the prefix `X_` (e.g., by default scanpy stores UMAP coordinates in `anndata.obsm['X_umap']`) - A unique identifier is required for each cell, which by default will be pulled from the `obs` DataFrame index. If the index is not unique or does not contain the cell ID, an alternative column can be specified with `--obs-names` -- A unique identifier is required for each gene, which by default will be pulled from the `var` DataFrame index. If the index is not unique or does not contain the cell ID, an alternative column can be specified with `--var-names` +- A unique identifier is required for each gene, which by default will be pulled from the `var` DataFrame index. If the index is not unique or does not contain the gene ID, an alternative column can be specified with `--var-names` #### What about R objects from seurat / bioconductor!? We hear you! We'd also love to be able to ingest these files directly. This isn't currently possible, but in the meantime, you can use [sceasy](https://bioconda.github.io/recipes/r-sceasy/README.html) ([docs](https://cellgeni.readthedocs.io/en/latest/visualisations.html)) to convert to `h5ad`. Seurat also has some [handy conversion tools](https://satijalab.org/seurat/v3.0/conversion_vignette.html) that you can try out.