Input Formats¶
As a marker-gene free method, cyclum only requires an expression matrix.
Expression matrix¶
- Cyclum accept expression matrix as input. Cyclum includes tools to
- covert count matrix to TPM/PKM value,
- log transform / Freeman-Tukey transform matrix,
- center and scale expression data .
For evaluation purpose, cyclum also accept cell labels.
Configuration file (to be supported)¶
The parameters for runing cyclum is specified in the configuration file. Fields are listed in the following table.
| Field | Type | Annotation |
|---|---|---|
| name | ||
| preproc | ||
| output |