Practical Computing Skills for Omics Data
      Ohio State PLNTPTH 5006 - Autumn 2025

Week	Tue session	Thu session	Ex	GA/FP
01	08/26: Course intro & Omics data	08/28: The Ohio Supercomputer Center (OSC)
02	09/02: Project organization	09/04: VS Code + Markdown & Unix shell: Basics		GA 1
03	09/09: Sequence files & Unix shell: Working with files I	09/11: Unix shell: Working with files II	Ex 1
04	09/16: Version control: Git	09/18: Version control: GitHub		GA 2
05	09/23: A closer look at OSC	09/25: Using software with modules and containers	Ex 2
06	09/30: Shell scripting basics	10/02: Shell scripts to run CLI tools & Shell tips		GA 3
07	10/07: Slurm batch jobs I	10/09: Slurm Batch jobs II	Ex 3
08	10/14: Catch-up	Fall break		GA 4
09	10/21: Workflow management	10/23: Data management and transfer	Ex 4
10	10/28: Using generative AI	10/30: GenAI with GitHub Copilot		GA 5
11	11/04: Intro to R and RStudio & Data structures and types	11/06: Tabular data in R	Ex 5
12	Veteran’s day	11/13: R notebooks with Quarto	Ex 6	FP 1
13	11/18: Data visualization in R	11/20: Bioconductor: R for omics data		GA 6
14	11/25: RNA-Seq count data analysis in R	Thanksgiving	Ex 7	FP 2
15	12/02: Running nf-core pipelines I	12/04: Running nf-core pipelines II	Ex 8
16	12/09: Student presentations			FP 4

= Week overview page       Ex / = Exercises       GA/FP = Graded Assignment / Final Project