Single-Cell RNA-sequencing (scRNA-seq) on the NIH Integrated Data Analysis Portal (NIDAP)

This page contains links to recorded video lectures and tutorials that will require approximately 3.5 hours in total to complete.  It is your responsibility to complete all parts of this training prior to attending the Discussion course that you registered for. During the live Discussion seminar, you can ask any questions about scRNA-seq or the NIDAP workflow. You can also reach out to us at with any questions.  We look forward to seeing you in class and hope you find these materials helpful in better understanding single-cell RNA-sequencing and the downstream analysis of scRNA-seq workflows on NIDAP.

Please begin with the recorded lecture on the background and methodology of scRNA-seq.  Then, follow instructions on how to log-into NIDAP and use Parts 1-3 of the tutorial to guide your own downstream analysis of an scRNA-seq training dataset.  At the end of this course, please consider responding to the survey link at the bottom of this page to provide us with feedback and suggestions for improving this course in the future.

Troubleshooting Tips:

    • For security purposes, you must be on the secure NIH network to access NIDAP.  This means that you must either be:
      • On-campus and able to connect to the NIH secure network there
      • Off-campus while using a VPN to gain access to the NIH secure network
    • Use only the Chrome web browser to access NIDAP; other browsers (e.g. Safari, Edge, Firefox, etc.) are not supported at this time


Lecture: Single-Cell RNA-seq Analysis – Background & Methodology (Lecture Video, PowerPoint Slides)

    • Introduction to course
    • scRNA-seq: Background and Theory
    • scRNA-seq: How does it work?
    • scRNA-seq: Receiving and processing data
    • scRNA-seq: Batch Correction


Guided Tutorial:  Next, you will need to follow along with a guided video tutorial that will walk you through each step of the downstream analysis of scRNA-seq datasets on NIDAP.  The videos for each part of this tutorial and a list of the topics discussed in each section are below.  To follow-along with these videos, open another tab in your Chrome web browser and log-in to NIDAP using your NIH credentials here:

Remember that you will either need to be either on an NIH campus and connected to the secure network there or connected to the NIH network from off-campus using a VPN in order to access NIDAP.  This is necessary to ensure the privacy of the data hosted on NIDAP.


Tutorial Part 1:  Single-Cell RNA-seq Analysis on NIDAP – Accessing NIDAP, Filtering, & Quality Control (Tutorial Part 1 Video)

    • How to access NIDAP
    • Orientation to the NIDAP home page
    • Accessing the scRNA-seq training dataset
    • Launching your first code workbook with the training dataset
    • Orientation to the code workbook
    • Filtering and QC of your sample datasets
    • Normalization of sample datasets and PCAs
    • Renormalization of your combined dataset


Tutorial Part 2: Single-Cell RNA-seq Analysis on NIDAP – Batch Correction (Tutorial Part 2 Video)

    • Renormalization of your combined dataset (continued)
    • Batch Correction


Tutorial Part 3: Single-Cell RNA-seq Analysis on NIDAP – Annotation, Visualization, and DEG (Tutorial Part 3 Video)

    • Differential Expression of Genes (DEG) analysis
    • Making and understanding your first Volcano plot
    • Making a Venn diagram of your DE genes across multiple contrasts


Advanced Tutorials: Coming Soon!

    • How to import your own datasets into NIDAP and begin analysis.
    • Advanced visualization and analysis of single-cell RNA-seq datasets.

Course Survey:  Single-Cell RNA-seq Analysis on NIDAP (Course Survey)

    • Please consider taking this short survey to provide us with feedback and suggestions on how to improve this course in the future (will take less than 3 minutes to complete).


Thank you for your time and attention!  We hope to see you in this or another class soon!