hubmapconsortium/hubmap-api-py-client

client.select_genes(where='cluster', has='...?')

Opened this issue · 2 comments

mccalluc commented

I'd like to select genes from clusters, but I'm not sure what kind of query criteria to provide.

SFD5311 commented

These data are available in with genomic_modality='atac' for now. Working on reprocessing RNA data to follow the same format.

I believe the syntax using this client would be something like:
cluster_genes = client.select_genes(where='cluster', has=['d4493657cde29702c5ed73932da5317c-19'], genomic_modality='atac', p_value=0.05)

Cluster grouping_names are of the format dataset_uuid-original_cluster_number

SFD5311 commented

These data are available in with genomic_modality='atac' for now. Working on reprocessing RNA data to follow the same format.

I believe the syntax using this client would be something like:
cluster_genes = client.select_genes(where='cluster', has=['d4493657cde29702c5ed73932da5317c-19'], genomic_modality='atac', p_value=0.05)

Cluster grouping_names are of the format dataset_uuid-original_cluster_number