The cap-sc-client package provides a simple interface to interact with the Cell Annotation Platform (CAP) GraphQL API. The package allows to search for datasets, cell labels metadata and get molecular profiles of cell types published on CAP.
pip install -U cap-sc-clientThe main goal of this package is to provide an interace to access CAP datasets and cell annotation metadata (including marker genes, synonyms, rationales, etc.) via standard python tooling. The outputs are in the format pandas DataFrame, which could be converted to other formats (csv, JSON, etc.) if the user desires.
>>> from cap_sc_client import CapClient
>>> cp = CapClient()
>>> datasets = cp.search_datasets(limit=5, offset=0, organism=["Homo sapiens"])
>>> datasets.head()
id name cell_count project
0 1427 Skin fibroblasts - Pan-d... 337376.0 {'id': '613', 'name': 'Pan...
1 1426 Skin fibroblast scRNA-seq ... 153546.0 {'id': '613', 'name': 'Pan...
2 1157 Single cell atlas of the h... 72788.0 {'id': '544', 'name': 'Sin...
3 1156 snRNA-seq of human retina ... 3177310.0 {'id': '544', 'name': 'Sin...
4 1154 snRNA-seq of human retina ... 691008.0 {'id': '544', 'name': 'Sin...
>>> labels = cp.search_cell_labels(limit=10, offset=0)
>>> labels[["full_name", "ontology_term_exists", "marker_genes"]]
full_name ontology_term_exists marker_genes
0 cycling stromal ... True [MKI67, TOP2A, C...
1 alveolar type 1 ... True [PDPN, HOPX]
2 mesoderm 2 (ZEB2) False [ZEB2]
3 acinar cell True [PRSS1]
4 neuron True [STMN2]
5 smooth muscle cell True [DES, CNN1, ACTA...
6 ciliated cell True [FOXJ1]
7 Schwann cell True [MPZ]
8 pancreatic cells False [PDX1]
9 club cell True [SCGB1A1]
There is also an MDSession class that allows users to interact with the molecular profiles of cell types within a specific dataset. However, this class requires users to be familiar with the CAP MD page.
For more examples, please refer to "examples" and the GitHub wiki for detailed documentation.
Detailed documentation is available on GitHub Wiki.