With funding from the HMS Tools and Technology Committee, the Harvard NeuroDiscovery Center (HNDC) and the Harvard Stem Cell Institute (HSCI) we have a dedicated bioinformatics training program for:

  • HMS researchers with a primary affiliation in one of the Basic and Social Science Departments on the Quad

  • researchers with an affiliation with the HNDC

  • HSCI researchers

In addition, we also teach short courses for Harvard Catalyst.

Upcoming workshops/courses:

For all researchers at Harvard University and affiliated institutions

We are excited to announce a new workshop series called “Current Topics in Bioinformatics”.

Each of these 2 to 3 hour, hands-on workshops are freestanding, but some of them will have prerequisites. They will be held monthly in the Longwood Medical Area at either HSPH or HMS. The workshops are first-come-first-served and there is no registration process, so we encourage you to be punctual!

Please find the list of upcoming workshops in this new series and their descriptions below:

Lessons Date Timing Location Prerequisites
Introduction to R & Visualizations with ggplot2 9/19/2017 2-4pm HSPH, Building FXB, Room G11 None
Advanced plotting (including volcano plots and heatmaps) 10/17/2017 1-4pm HSPH, Building FXB, Room G11 Beginner R or Intro R workshop
Functional analysis of gene lists 11/13/2017 1-4pm TMEC, Room 328 Beginner R or Intro R workshop
Reproducible research using R (Rmarkdown: report generation) 12/11/2017 1-4pm HSPH, Buliding FXB, Room G13 Beginner R or Intro R workshop

Introduction to R and visualizations with ggplot2 (September 19th, 2017):

In this brief introduction to the R programming environment, we will cover the basics of R and RStudio. R is a simple programming environment that enables the effective handling of data, while providing excellent graphical support. RStudio is a tool that provides a user-friendly environment for working with R. We will explore R syntax and data structures, functions and packages, and the basics of data wrangling. We will end with performing visualizations with the ggplot2 R package for the generation of publication-worthy figures.

Advanced plotting (October 17th, 2017):

For this workshop, we will be using R to perform a variety of advanced plotting methods. Using several R packages (ggplot2, ggrepel, pheatmap, etc.), we will learn how to change from a wide data format to a long data format for plotting purposes, how to label and/or repel individual data points on a scatter plot, and how to create heatmaps and volcano plots.

Functional analysis of gene lists (November 13th, 2017):

Functional analysis methods help us to gain insight about the biology underlying a list of genes. These genes could be output from a differential expression analysis, a GWAS analysis, proteomics analysis, etc. Regardless of the source of the gene list, functional analysis can explore whether particular pathways or processes are enriched among a list of genes. In this 3-hour workshop, we will use over-representation analysis (ORA) and functional class scoring methods to identify potential pathways that are associated with our list of genes. We will be using the clusterProfiler R package to determine whether there is enrichment of any gene ontology (GO) processes in a list of genes and generate plots from the results. We will also give a brief introduction to using clusterProfiler to perform functional class scoring with gene set enrichment analysis (GSEA) followed by the Pathview R package for visualization.

Reproducible research using R (December 11th, 2017):

Reproducible research is as important for computational analysis as it is at the bench. Integrating your R data analyses into a report format allows for easy retrieval of the packages/versions and code used to generate your results and figures. It allows for efficient communication of your results with your collaborators. The knitr R package allows for the easy generation of professional reports for any R analysis, while allowing for customization and easy revision. In this 3-hour workshop, we will cover the simple RMarkdown syntax and explore options for customizing your reports.

For HSCI, HNDC and on-quad HMS researchers

Harvard Catalyst Workshops

Training program description:

We provide bioinformatics training through both shorter workshops and in-depth courses. [Click here for a list of upcoming workshops/courses, or scroll down.]

1. Workshops

  • Next Generation Sequencing Introduction Series

    (Galaxy-based) workshops on RNA-Seq, ChIP-Seq to introduce basic concepts of Next-Generation Sequencing (NGS) analysis. The goal of these workshops are to enable researchers to design their studies appropriately and perform preliminary data analyses.

  • Basic Bioinformatics Skills Series

    Topics include R, data visualization using R, Python programming, Unix and high-performance computing (duration varies from half a day to three days).

2. In-Depth Next Generation Sequencing Analysis Courses

These intensive courses run for 10-12 days and are aimed at bench biologists interested in learning how to perform independent, best practice NGS-based analyses. Topics include:

  • Unix & High-Performance Computing (Orchestra)
  • NGS data analysis (RNA-Seq, ChIP-Seq, Variant calling)
  • Statistical analysis using R
  • Functional analysis

No prior NGS or command line expertise is required for our workshops or courses unless explicitly stated.

Past Workshops:


  • [HSCI/TnT/HNDC] May 31st - July 7th: In-depth NGS data analysis course
  • [HNDC] April 20th: Introduction to R
  • [TnT/HNDC/HSCI] April 3rd & 4th: Introduction to R
  • [HSCI] March 6th & 7th: Introduction to UNIX and Orchestra with HMS-RC
  • [HSCI/TnT/HNDC] February 15th: Introduction to Differential Gene Expression (DGE) analysis for RNA-Seq
  • [TnT/HNDC] February 10th & 13th: Introduction to R
  • [HSCI] January 24th & 25th: Introduction to R


  • [HSCI/TnT/HNDC] October 31st - December 2nd: In-depth NGS data analysis course (RNA-Seq)
  • [HSCI/TnT/HNDC] October 20th: Introduction to Differential Gene Expression (DGE) analysis for RNA-Seq
  • [TnT/HNDC] September 29th & 30th: Introduction to R
  • [HSCI] September 8th & 9th: Introduction to R
  • [HSCI] August 22nd & 23rd: Introduction to UNIX and Orchestra with HMS-RC
  • [HSCI/TnT/HNDC] June 22nd - August 12th: In-depth NGS data analysis course
  • [HSCI] May 23rd & 24th: Introduction to UNIX and Orchestra with HMS-RC
  • [TnT/HNDC] May 12th & 12th: Introduction to UNIX and Orchestra with HMS-RC
  • [HSCI/TnT/HNDC] February 8th - March 8th: In-depth NGS data analysis course


  • [HSCI] December 11th: Introduction to R
  • [HSCI] November 13th: *RNA-Seq with Galaxy**
  • [TnT/HNDC] November 23rd: RNA-Seq with Galaxy
  • [TnT/HNDC] October 8th & 9th: Introduction to UNIX and Orchestra with HMS-RC
  • [TnT/HNDC] October 2nd: RNA-Seq with Galaxy
  • [TnT/HNDC] September 21st: RNA-Seq with Galaxy
  • [TnT/HNDC] September 11th: ChIP-Seq with Galaxy
  • [TnT/HNDC] August 14th: RNA-Seq with Galaxy
  • [TnT/HNDC] July 22nd: A Hands-on Introduction to Python (in collaboration with IQSS)
  • [TnT/HNDC] July 17th: RNA-Seq with Galaxy
  • [TnT/HNDC] June 26th: Introduction to R and R graphics with ggplot2 (in collaboration with IQSS)


For any training-related questions, please email us at