Example Usage

Example usage of the Molecular Expression Assay Loader application.

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

Running the application (CLI or GUI)

CLI

1. If launching the app from outside the Platform, first download and set up dx-toolkit. 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:

# Whitespace between between "-i" and variable name is optional.
# Example: "-ivariable" and "-i variable" are equivalent.
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"

GUI

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

2. Navigate to the tool.
3. 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

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 Assay Dataset Merger 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.

Working with Molecular Expression Datasets

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 tutorial notebook in OpenBio.