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
In addition, we also teach short courses for Harvard Catalyst.
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:
|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
August 23rd - 24th, 2017: Introduction to RNA-seq using high-performance computing [Registration is now closed]
September 13th - 14th, 2017: Introduction to R [Registration is now closed]
October 25th, 2017: Using DESeq2 for Differential Gene Expression (Prerequisite: Introduction to R)
Harvard Catalyst Workshops
Introduction to Omics Research : An online course about the scope, analytical methods, & challenges of omics research. [Registration is now closed]
September 25th - 27th, 2017: Introduction to UNIX and RNA-seq Analysis Workshop [Registration is now closed]
November 1st - 3rd, 2017: Introduction to R: Basics, Plots, and RNA-seq Differential Expression Analysis [Registration is now closed]
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.]
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.
- [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 email@example.com.