How to import dataset from collection?

[YXC33]

Hi! I met a problem when I tried to import a dataset from a collection. Normally, when the dataset is not from a collection, I can get the dataset using these codes: curated_seurat_object <- metadata |> dplyr::filter( dataset_id == '37b21763-7f0f-41ae-9001-60bad6e2841d' ) |> get_seurat()

However, if I change the dataset_id to a dataset from collections, I can't get the dataset. For example: curated_seurat_object <- metadata |> dplyr::filter( dataset_id == '9fcb0b73-c734-40a5-be9c-ace7eea401c9' ) |> get_seurat()

And the web page of this dataset is: https://cellxgene.cziscience.com/e/9fcb0b73-c734-40a5-be9c-ace7eea401c9.cxg/

'9fcb0b73-c734-40a5-be9c-ace7eea401c9' %in% unique(dplyr::pull(metadata, "dataset_id")) [1] FALSE Since this code returned FALSE, I know it's not because of the size.

Could you please tell me how to get the dataset from collections?

[stemangiola]

have you tried the column collection_id?

[YXC33]

have you tried the column collection_id?

Thanks for the suggestion. However, I have tried the collection_id, and used this code: '71f4bccf-53d4-4c12-9e80-e73bfb89e398' %in% unique(dplyr::pull(metadata, "collection_id")) [1] FALSE This the collection page, https://cellxgene.cziscience.com/collections/71f4bccf-53d4-4c12-9e80-e73bfb89e398

And I checked there are only 76 collections in the collection_id column.

[stemangiola]

@myushen ?

[myushen]

Hi @YXC33, it seems that dataset_id 9fcb0b73-c734-40a5-be9c-ace7eea401c9 does not exist in our metadata, thus it won't be able to generate Seurat.

This could happen if the dataset was published recently and our API haven't incorporated it.

[stemangiola]

We will have the updated CELLxGENE in one week or so

[YXC33]

May I ask what's the frequency of updating? Also, for the datasets, we only have 329 unique datasets, but in Cellxgene, there are 1486 datasets.

[stemangiola]

Hello, we are completing the most recent update. Probably 2 weeks from publication.