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Signature registry

The signature matrix is a matrix that contains the expression of genes for each cell type. It is used to predict the cell type composition of a sample. PyDeconv provides a registry of signature matrices that can be used to predict the cell type composition of a sample.

The signature matrices are stored in CSV files and can be loaded using the pydeconv.signature_matrix.registry module.

Commercialy available signature matrices

The following signature matrices are commercially available. You can use them without any restrictions.

Laugney Lung Cancer

  • indication: lung
  • dataset used:
  • n patients:
  • n cells:
  • extraction comments:
from pydeconv.signature_matrix.registry import sig_matrix_laughney_lung_cancer
Output Celltypes

TNK, B, MonoMacro, Mast, Endothelial, Malignant, Stroma, DC, Epithelial

Cross tissue immune main CP

  • indication:
  • dataset used:
  • n patients:
  • n cells:
  • extraction comments:
from pydeconv.signature_matrix.registry import sig_matrix_cti_granularity_1
Output Celltypes

TNK, B, MonoMacro, DC, Mast

Cross tissue immune main 2nd granularity

  • indication:
  • dataset used:
  • n patients:
  • n cells:
  • extraction comments:
from pydeconv.signature_matrix.registry import sig_matrix_cti_granularity_2
Output Celltypes

CD4T, CD8T, B, Plasma, DC, NK, Mono, Mast, Tregs

Cross tissue immune main 3rd granularity

  • indication:
  • dataset used:
  • n patients:
  • n cells:
  • extraction comments:

Research only signature matrices

The following signature matrices are for research purposes only.

Private only signature matrices

The following signature matrices are private and can only be used by