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omnideconv / SimBu

Simulate pseudo-bulk RNAseq samples from scRNAseq expression data
http://omnideconv.org/SimBu/
GNU General Public License v3.0
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Creating a dataset with Seurat object asks for tpm_assay #29

Closed alex-d13 closed 2 years ago

alex-d13 commented 2 years ago

Creating a dataset from Seurat object does not work without a tpm assay:

> ds_seurat <- SimBu::dataset_seurat(seurat_obj = seurat_obj, 
+                                    count_assay = "counts", 
+                                    cell_id_col = 'ID', 
+                                    cell_type_col = 'cell_type',
+                                    name = "seurat_dataset")
Error in generate_summarized_experiment(annotation = annotation, count_matrix = count_matrix,  : 
  object 'tpm_matrix' not found

tpm matrix should be optional.