1.2 Custom Pipeline Development in Python & R

Overview of Course

If you love automating data analysis, building reproducible workflows, and customizing scripts for biological data, this course is for you.

Custom Pipeline Development in Python & R teaches you how to design, code, and optimize bioinformatics pipelines tailored to specific research needs. You’ll learn to automate multi-step processes for tasks like sequence analysis, data cleaning, and reporting using powerful scripting and workflow management tools.

Skills you’ll need: Python, R Programming, Workflow Automation, Data Wrangling, Bioinformatics Tools, Shell Scripting, Reproducible Research, Snakemake, R Markdown, Pipeline Optimization

Completing this course will help you:

Who is the course for?

This course is perfect for bioinformatics students, researchers, and professionals who want to streamline data analysis with coding. It’s ideal for those with basic programming knowledge in Python or R, and who are ready to build reusable pipelines for genomic, transcriptomic, or other biological datasets.

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Course 1.1

Integrative Multi-Omics Analysis

How to analyze and integrate multiple omics datasets—such as genomics, transcriptomics, proteomics, and metabolomics, to uncover meaningful biological insights. You’ll learn how to preprocess and interpret complex biological data using computational tools, enabling a systems-level understanding of biological processes and disease mechanisms.

Integrative Multi-Omics Analysis

5 lessons - 4:11 hours

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Course 1.3

Reproducible Research with Workflow Managers

Reproducible Research with Workflow Managers teaches you how to structure and automate bioinformatics projects using tools like Snakemake, Nextflow, and CWL. You'll learn to organize code, manage dependencies, and build workflows that are sharable, scalable, and reproducible across systems.