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BIOF 048 | Single Cell RNA-seq Analysis

September 29, 2020 to October 2, 2020


Registration closed.

Registration occurs on a first-come, first-served basis. Programs are open to general public. The deadline for registration is one week before the first day of the course.  If you are unable to register before the deadline, please email: or call 301-496-7975 for space availability. 

NIH Fellows or NIH community members being sponsored by their lab and awaiting payment authorization can tentatively hold a seat using the “Reserve A Seat” option. Payments need to be received within 7 business days from date of reservation or before the start of a workshop, whichever comes first. Seat reservations will be cancelled if payment is not received prior to workshop.

Workshops generally run from 9:00am - 5:00pm.

Course Overview
Bulk transcriptomes have provided considerable insights and fostered the discovery and characterization of GRN (Gene Regulatory Network)s. However, bulk transcriptomes provide population-based averaged measurements which blur cell heterogeneity and developmental dynamics of asynchronous cell populations. Single-cell transcriptome technologies (scRNA-seq) capture cell heterogeneity and thus are useful for the discovery of cell populations, identification of cell mutants, and quantification of subpopulations. Leveraging on the ability of generating thousands of individual measurements from scRNA-seq, lots of methods have been developed to capture spatial or temporal information from cell populations. This course will introduce basic steps of the scRNA-seq processing, starting from fastq coming off 10x sequencer to spatial and temporal analysis using popular R packages. Then, we will discuss case studies that can be addressed using scRNA-seq.

Experience with R is required; experience with seq analysis in general is advantageous

Simultaneous access to two screens is highly recommended for adequate learning experience. Examples include two laptops, one computer with two screens, one laptop and one tablet, etc.

Course Schedule

Day 1 DAY 2 DAY  3 DAY 4

Lecture 1

  • ​Overview of course
  • Comparison of Bulk and single cell RNA-Seq
  • Overview of available scRNA-seq technologies (10x) and experimental protocols

Lecture 3

  • Processing Raw scRNA-seq Data

Lecture 5

  • Identifying cell populations

Lecture 6

  • Trajectory Analysis

Lab 1

  • Lab based around data wrangling from public data repositories: get data from 10x website and GEO
  • Shell and Unix commands to navigate directories, create folders, open files
  • Raw file formats


  • Introduction to R/Bioconductor

Lab 5

  • Introduction of Seurat

Lab 6

  • Introduction of Trajectory Analysis
  • Analysis of small dataset- min project

​Lecture 2

  • scRNA-Seq processing workflow starting with choice of sequencer
  • Overview of Popular tools and algorithms
  • Overview of Cell Ranger

Lecture 4

  • Construction of expression matrix

Lab 2

  • Data outputs from different scRNAseq technologies
  • Demultiplexing
  • FastQC


  • Data wrangling for scRNAseq data

Training Rate
Discounted Training Rates
$1,075.00 - NIH Community (Trainees, Employees, Contractors, Volunteers, etc.)
$1,195.00 - Academia, US Government, US Military

Technology Fee

Comprehensive File
A PDF file containing all notes, protocols, and reference material will be provided. No additional books are required. 

Although no grades are given for courses, each participant will receive Continuing Education Units (CEUs) based on the number of contact hours.   One CEU is equal to ten contact hours. Upon completion of the course each participant will receive a certificate, showing completion of the workshop and 2.8 CEUs.

Refund Policy
100% tuition refund for registrations cancelled 14 or more calendar days prior to the start of the workshop.
50% tuition refund for registrations cancelled between 4 to 13 calendar days prior to the start of the workshop.
No refund will be issued for registrations cancelled 3 calendar days or less prior to the start of the workshop.

All cancellations must be received in writing via email to Ms. Carline Coote at
Cancellations received after 4:00 pm (ET) on business days or received on non-business days are time marked for the following business day. 
All refund payments will be processed by the start of the initial workshop.


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