About this website and course

Author

Affiliations

Jelmer Poelstra

CFAES Bioinformatics Core, Ohio State University

Dept. of Plant Pathology, Ohio State University

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Overview

This is the GitHub website for the course Practical Computing Skills for Omics Data (PLNTPTH 5006), a 3-credit course taught at Ohio State University during the Fall semester of 2026.

The course is taught by Jelmer Poelstra from the CFAES Bioinformatics Core and Department of Plant Pathology , with TA Kelsey Starr from the Department of Plant Pathology.

Course description

Omics data is everywhere, but can you actually analyze it? This course will teach you the skills to do so: using the Unix shell, writing shell and R scripts, and running jobs on the Ohio Supercomputer Center. You will also learn how to improve the reproducibility of your research using best-practice project organization, documentation, and version control. No prior coding experience required.

Main topics taught

• Reproducibility — project documentation with Markdown, file organization, data and management and sharing
• Unix shell — basics, scripting, running command-line programs
• HPC / Supercomputer usage — basics, software, and running Slurm batch jobs at OSC
• Version control — with Git and GitHub
• Running pipelines — using Nextflow/nf-core pipelines
• R — Basics, data wrangling & visualization, Quarto, and specifics to omics data
• Omics data and analysis basics — with a focus on high-throughput sequencing data
• AI — Using generative and agentic AI to help with coding

CarmenCanvas website

If you are a student in this course, you should also refer to its CarmenCanvas site .

Simple Syllabus

Simple Syllabus for this course .