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On this page
  • Running the application (CLI or GUI)
  • CLI
  • GUI
  • Using the Dataset in the Cohort Browser
  • Integration with an Existing Dataset
  • Working with Molecular Expression Datasets

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  1. Developer
  2. Ingesting Data
  3. Molecular Expression Assay Loader

Example Usage

Example usage of the Molecular Expression Assay Loader application.

Last updated 1 year ago

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An Apollo license is required to use the Molecular Expression Assay Loader on the DNAnexus Platform. Org approval may also be required. for more information.

Running the application (CLI or GUI)

CLI

  1. If launching the app from outside the Platform, first download and set up . If running the app from the Platform (Cloud Workspace, JupyterLab, etc.) dx-toolkit is already installed and ready for use.

  2. From CLI, launch the app using dx run. For example:

dx run app-molecular-expression-assay-loader \
--name="My Molecular Expression Assay Loader Job" \
-i source_expression_data=example_matrix.csv \
-i assay_title="My Expression Project" \
-i database="my_expression_project" \
-i reference="GRCh38.p13" \
-i feature_type="mRNA" \
-i feature_id_type="transcript_ENST" \
-i feature_value_type="tpm" \
-i dataset_name="My Expression Project Dataset"

//Note that there does not need to be a space between -i and the variable name
// "-ivariable" and "-i variable" are both acceptable

GUI

  1. If launching the app from the GUI, log on to the DNAnexus Platform.

  2. Follow instructions provided on the Run App dialogue to get to the Inputs page.

Using the Dataset in the Cohort Browser

A Dataset created by the Molecular Expression Assay Loader App may be used in the Cohort Browser just like any other Dataset, however only the phenotypic data will be available for cohort browsing and cohort criteria selection. Either double click on the Dataset (a Record entity on the Platform) or right click on More Actions and select Explore Data.

Integration with an Existing Dataset

Working with Molecular Expression Datasets

Navigate to the .

The Dataset created by the Molecular Expression Assay Loader app can be linked to an existing Dataset that contains either phenotypic or phenotypic and assay data to create a combined new Dataset for use. This can be done by adding this Dataset as an input to the app. This allows for the creation of a rich clinico-omic Dataset where both the molecular information and clinical data related to your study are linked together to accelerate analysis.

A Spark-enabled JupyterLab instance may be used to parse assay metadata and access molecular expression data, as referenced in a Molecular Expression Assay Loader Dataset. See the in OpenBio.

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