What's New (March 2022)

CWL Support

We’ve released dxCompiler 2.10.0, which provides support for compiling CWL (Common Workflow Language) workflows and executing them on the platform. For setup instructions, including a getting-started example, see the dxCompiler documentation.

Improved Support for Secondary Analysis of Bulk RNA-Seq Data

We’ve added several apps to our Tool Library, and upgraded others, to improve support for secondary analysis of bulk RNA-Seq data. Users can now leverage popular tools like Kallisto, Salmon, a new version of STAR that includes a gene count feature, and a new version of RSEM for expression quantification. For more info, see the Tools Library for a full list of available RNA-Seq apps, and detail on each.

Add New Data Entities to Existing Datasets

The new Clinical Dataset Merger app allows you quickly and easily to update an existing Apollo Dataset with new data, whether it be new sample data, EHR extracts, or perhaps results from a clinical trial. See the Clinical Dataset Merger documentation for more information, including detail on inputs and outputs, and best practices for using the app.

Apollo Datasets Now Support Bulk RNA-Seq Data

Apollo users can now leverage the new Molecular Expression Assay Loader app, which supports the easy ingestion of bulk mRNA gene and transcript expression data into an Apollo Dataset. This data can then be analyzed as part of a broader Dataset in the Apollo Cohort Browser, a JupyterLab notebook, or any of a wide range of analysis applications. Learn more about the app, and how best to use it, from the Molecular Expression Assay Loader documentation; an example analysis is available in the OpenBio Github repository.

Easily Add Assay Data to Apollo Datasets

The new Assay Dataset Merger app makes it easier to integrate assay data into Apollo Datasets. The app allows Apollo users to link assays with any entity in an Apollo Dataset, in either a one-to-one or one-to-many relationship. Link bulk RNA-Seq data to clinical visit information to model a longitudinal study, or turn an existing Dataset into a multi-omic Dataset by adding molecular expression and pop gen data. See the Assay Dataset Merger documentation for more on how to set up and use the app.

Quickly Move Cohorts from One Dataset to Another

When you expand an existing Apollo Dataset to create a new Dataset, moving previously defined cohorts to the new Dataset used to be difficult. The Rebase Cohorts and Dashboards app makes this liftover easy. Select the cohorts you want to move, select the target Dataset, and run the app. See the Rebase Cohorts and Dashboards documentation for more on how to set up and use it.

Using the DNAnexus Platform

Get to know features you’ll use every day, in a series of short, task-oriented tutorials.
Learn to access and use the Platform via both its command-line interface and its user interface.
Learn to manage data, users, and work on the Platform, via its API. Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows.
This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.
Download, install, and get started using the DNAnexus Platform SDK, the DNAnexus upload and download agents, and dxCompiler.
Get details on new features, changes, and bug fixes for each Platform and toolkit release.
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