CMSE Bioinformatics Workshops

CMSE Bioinformatics Workshops

July 31st, 8:30AM to August 18th, 12:30PM

The Department of Computational Mathematics, Science & Engineering will host three week-long workshops that provide training in Linux/R programming, statistics/visualization, and RNA-Seq.

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Event Categories:  Trainings Workshops

Workshop must be paid via an MSU grant account. A limited number of fee waivers are available. 

Lunch and snacks will be provided.

Cost: $50 per person per workshop
  • Week 1 (July 31 - Aug 4): Programming : intro & best practices
  • Week 2 (Aug 7 - Aug 11): Data analysis: handy concepts & skills
  • Week 3 (Aug 14 - Aug 18): Analysis of large-scale gene-expression data

Week 1 - Programming: Introduction & Best Practices

In Week 1, we will introduce you to UNIX commands and R programming, and show how to integrate them to create automated, reproducible workflows.


● Download, organize, modify data files using Linux utilities

● Use RStudio and R Notebooks to write & execute R programs

● Implement file input/output, loops, control statement, and functions in R

● Import and use external R packages

● Manipulate data and make multiple types of plots


Week 2 - Data Analysis: Handy Concepts & Skills

In Week 2, we will introduce you to a range of fundamental concepts in statistics and demonstrate how to apply them for routine data analyses.


● Summarize data using descriptive statistics and plots

● Learn common continuous & discrete distributions and use them in R

● Perform parametric and nonparametric hypothesis testing

● Learn and perform multivariable data analysis (regression, clustering, & PCA)


Week 3 - Analysis of Gene Expression Data

In Week 3, we demonstrate all the steps involved in turning RNA-Seq raw reads into gene-expression levels, differentially-expressed genes, enriched pathways, and gene/sample clusters.


● Execute quality control and mapping of RNA-seq reads

● Quantify gene, transcript, and exon expression levels

● Perform differential expression and pathway enrichment analyses

● Perform advanced analyses including clustering, PCA, and network analysis


The full syllabus here:

Questions? Contact Alexis Black (, Arjun Krishnan (, and Jianrong Wang (

1502/1503 Engineering Building East Lansing, MI
United States
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