CCBR Bioinformatics Workflows and Training Courses on NIDAP

NIH Integrated Data Analysis Platform (NIDAP)

NIDAP, the NIH Integrated Data Analysis Platform, is an innovative, cloud-based, and collaborative data aggregation and analysis platform. The platform hosts user-friendly bioinformatics workflows and other component analysis and visualization tools that have been created and maintained by the NCI developer community based on open source tools. These workflows and other tools can be made immediately available to biologist end-users across the Institute. Robust controls allow users to work individually or collaboratively with PII/PHI while also maintaining proper security and ownership over their datasets. New users can access NIDAP by registering at http://nidap.nih.gov.

CCBR Bioinformatics Workflows on NIDAP

CCBR has built a number of workflows and tools on NIDAP in collaboration with NCI biologists that have requested our help. This is a service CCBR makes available to NCI Investigators at no cost to them. Please reach out to us if you have specific needs to discuss. For some of the most frequently requested analyses, we have created and maintain public workflows and self-guided training tutorials that we hope can both educate and empower NCI scientists to understand and execute on these bioinformatics analyses themselves.

It is always recommended to seek a consultation from CCBR before you carry your results forward towards publication. We can review your analysis to provide a second opinion on some of the analytical choices that are made during an analysis or to discuss any questions you may have. Additionally, when you are ready to publish, CCBR can assist you in making the code and data required to reproduce your results publicly available. Like all of CCBR’s services, these are available to NCI Investigators at no cost.

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Training for CCBR Workflows on NIDAP

Bulk RNA-Seq Analysis Workflow:

Our Bulk RNA-seq workflow is appropriate for analyzing RNA-seq data given expression in raw counts like those provided by the Sequencing Facility in Frederick. We have developed a Bulk RNA-seq Analysis on NIDAP training course consisting of a series of training videos that will provide you with the background to understand the analysis, takes you through an analysis using a training dataset, and then show you how to apply the same workflow to your own data.

We have recently added the ability to process TCGA and other publicly available datasets and Proteomics datasets using this workflow. We plan to create tutorials for these options in the near future, but in the meantime, please reach out to CCBR if you would like to access these features.

Training Resources for the CCBR Bulk RNA-seq Analysis Workflow on NIDAP:

Single-cell RNA-Seq (scRNA-seq) Analysis Workflow:

Our Single-cell RNA-seq (scRNA-seq) Analysis workflow on NIDAP is appropriate for analyzing Illumina 10x single-cell RNA-seq data. The standard analysis expects input provided by the user in the form of H5 or MEX files like those produced by the upstream Cell Ranger pipeline. To empower NCI researchers in learning to analyze their own data, CCBR has also developed a series of training videos that provide a brief overview of the scRNA-seq analysis, a step-by-step tutorial where you will analyze a training dataset, and a guide to how to import your own scRNA-seq data into NIDAP for analysis. Additional videos will highlight certain parts of the analysis or introduce additional functionalities as they are developed by CCBR and the NIDAP Developer Community.

Training Resources for the CCBR scRNA-seq Analysis Workflow on NIDAP:

Digital Spatial Profiling Analysis Workflow:

Our Digital Spatial Profiling (DSP) analysis workflow is appropriate for analyzing probe count data exported from Nanostring’s GeoMx Digital Spatial Profiler. We have developed a DSP analysis workflow training course that consists of several videos and documents which will introduce users to DSP analysis on NIDAP, demonstrate how to perform a typical DSP analysis on NIDAP with all example data available for users to follow along, and demonstrates how to upload and import DSP data into NIDAP for users to begin with their own DSP analysis.

Training Resources for the CCBR DSP Analysis Workflow on NIDAP:

For more information on the DSP Workflow on NIDAP, the following videos are available (to access the video, copy and paste the link in a new tab):

  • Duplicate this example code workbook to begin a DSP analysis on NIDAP:
  • Training Videos (you must be on VPN or on NIH campus networks to view videos):
  • Feedback:
    • Please give us feedback on this course by filling out This Form.
  • Troubleshooting Tips:
    • Use only the Chrome web browser to access NIDAP; other browsers (e.g. Safari, Edge, Firefox, etc.) are not supported at this time.
    • To watch videos you must be on VPN or an NIH internal network.
      • You may access NIDAP regardless of VPN status, but the videos linked here are hosted on NIH’s internal video streaming site.

Additional Types of Analyses Supported on NIDAP

Please contact us to discuss projects involving these datatypes:

  • Proteomics
  • nCounter Gene Expression (Nanostring)
  • mirSeq
  • Transcript-Level Bulk RNA-seq (Analysis of Isoforms)
  • Visium

Additional Tools

Additional interactive tools, including the 3D-TSNE plot viewer and cell selector (SC3D) tools, are also available. Please reach out to CCBR if you are interested in learning how to use them.

Collaboration with CCBR in NIDAP & Reproducible Workflows

Collaborating in NIDAP allows CCBR analysts to share public and custom workflows with users. On the platform, we can more easily assist users in the completion or review of their analyses. We can also help in the creation and retention of a permanent record (R3: Reproducible Research Repository) within NIDAP for future reference and for deposition of the code necessary for reproduction into a public code repository. Several publications have been completed to date fully utilizing the tools within NIDAP, driven mostly by the biologist end-users in collaboration with CCBR.

The following graphic shows the preferred series of steps that leverages the existing bioinformatics tools within NIDAP (colored in yellow).  Other workflows are under construction and coming soon.

Please reach out to CCBR if it sounds like a collaboration may help your research.

DUET

DUET, the Developer User Exchange for Research Tools, provides an easy to navigate the NIDAP tool catalog that hosts a wide variety of bioinformatics tools that can be utilized in an analysis.

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