RSingleCellExperimentCreator module

This module allow to create a Bioconductor SingleCellExperiment from expression or matrix data.

  • Internal name: rsinglecellexperimentcreator
  • Available: Only in local mode

  • Input port:
    • additionalannotation: Additional annotation data (format: additional_annotation_tsv) from the design file. This data allow to describe the genes/features of the Bioconductor SingleCellExperiment object
    • matrix: Matrix data (format: expression_matrix_tsv) if matrix input is enabled
    • expression: Expression step output (format: expression_results_tsv) if matrix input is not enabled

  • Output port:
    • output: A Bioconductor SingleCellExperiment object in a RDS file (format: singlecellexperiment_rds)

  • Optional parameters:
    • Parameter Type Description Default value
    r.execution.mode string The R execution mode. The available mode values are: process, rserve and docker. process
    rserve.servername string The Rserve server name to use in rserve execution mode not set
    docker.image string The Docker image to use in Docker execution mode. genomicpariscentre/singlecellexperiment:3.7
    input.matrices boolean The input of the module is a matrix (e.g. 10X Genomics data). For SmartSeq2, this parameter is usually set to false true
    merge.matrices boolean When the input of the module is matrices, this option allow to merge all the input matrices in one output matrix true
    design.prefix string This parameter define the prefix of Eoulsan design columns that contains annotations about the cells. This cell annotations will be copied in the output Bioconductor object Not set
    use.additional.annotation boolean When this parameter is enabled, feature annotations will be copied in the output Bioconductor object to describe the genes/features of the Bioconductor SingleCellExperiment object true

  • Configuration example:
    • <!--  RSingleCellExperimentCreato step -->
<step id="myrsinglecellexperimentcreator" skip="false" discardoutput="false">
        <module>rsinglecellexperimentcreator</module>
        <parameters>
                <parameter>
                        <name>input.matrices</name>
                        <value>true</value>
                </parameter>
                <parameter>
                        <name>r.execution.mode</name>
                        <value>docker</value>
                </parameter>
        </parameters>
</step>