Module : Lineage with Monocle

Lineage with Monocle

This module infers lineage using Monocle 2.

• Internal name : lineage-monocle

• Avalaible : local mode

• Input Ports :

  • matrix : filtered expression matrix (tsv)
  • cells : normalized cells metadata (tsv)

• Output Ports :

  • none

• Optional parameters :

Parameter	Type	Description	Default Value
exp_family	text	Expression model family, should be one of : negbinomial, negbinomial_size	negbinomial
detection_threshold	float	Gene detection parameter	0.1
bypass	text	Use monocle native (native) normalization or bypass (bypass) using eoulsan normalization	bypass
select_genes	boolean	Weither to reduce gene set or not for dimensionnality reduction	False
mean_threshold	float	Minimum mean expression value to keep a gene	0.5
dispersion_fold_threshold	float	Minimum fold of dispersion to keep a gene	1
max_dim	int	Maximum number of dimensions to keep after dimensionnality reduction	2
reduction_method	int	Dimensionnality reduction method to use, should be one of : DDRTree or ICA	DDRTree
norm_method	string	Variance stabilizing method to use, should be one of : vstExprs, log, or none	vstExprs
reverse	boolean	Weither to represent cells in inverted order or not	False
color_by	string	Column to use to color cells on plot	State

• Configuration example

<step id="QC" skip="false">
	<module>lineage-monocle</module>
	<parameters>
		<parameter>
			<name>bypass</name>
			<value>bypass</value>	
		</parameter>
		<parameter>
			<name>select_genes</name>
			<value>False</value>	
		</parameter>
		<parameter>
			<name>color_by</name>
			<value>fluorescence</value>	
		</parameter>
	  </parameters>
</step>

Interpreting output files

Coming soon