call_squidpy | R Documentation |
Call Squidpy Pipeline via reticulate with OmniPath and format results [[DEPRECATED]]
call_squidpy(
sce,
op_resource,
seed = 1004,
conda_env = NULL,
assay = "RNA",
assay.type = "logcounts",
...
)
sce |
SingleCellExperiment or Seurat Object as input |
op_resource |
Tibble or list of OmniPath resources, typically obtained via
|
seed |
seed passed to squidpy's ligrec function |
conda_env |
python conda environment to run Squidpy; set to liana_env by default |
assay |
assay name |
assay.type |
count slot (logcounts by default) |
... |
kwargs passed to Squidpy; For more information see: https://squidpy.readthedocs.io/en/latest/api/squidpy.gr.ligrec.html#squidpy.gr.ligrec |
CellPhoneDBv2 algorithm re-implementation in Python.
Note that 'cluster_key' is a parameter passed to the Squidpy function, by default this will be set to the default Ident of the Seurat object.
A list of Squidpy results for each resource
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