Module : TPM CPM

Module : TPM/CPM

This module estimates size factors for all cells.

• Internal name : TPM

or

• Internal name : CPM

• Avalaible : local mode

• Input Ports :

  • matrix : filtered expression matrix (tsv)
  • cells : filtered cells metadata (tsv)
  • genes : features metadata (tsv)

• Output Ports :

  • cellsoutput : normalized cells metadata (tsv)

• Optional parameters :

Parameter	Type	Description	Default Value
mode	string	Use Endogenous or Nuclear genes	Endogenous
color_by	string	Name of the column to use for cell plotting	Condition
length_correction	boolean	Whether to correct for feature length or not before plotting (increases computation time)	False

• Configuration example

<step id="normalization" skip="false">
        <module>TPM</module>
        <parameters>
           <parameter>
              <name>mode</name>
              <value>Endogenous</value>
           </parameter>
        </parameters>
</step>