MAterials

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SFSU Affliations

Here are some different resources such as websites and podcasts for students who are interested in learning more about the programming languages (Python and R) used in Biology and Chemistry. 

• College of Science and Engineering (COSE)
• SFSU Department of Biology
• ​SFSU Department of Chemistry and Biochemistry

General Info for Python ​

Introduction and documentation​​​

• Learn Python 3 by CodeAcademy
• Python 3.8.3 Documentation & Tutorial
• When to Use “While” or “For” Loops in Python
• Python 3 Module of the Week
• Python Basics and other tutorials for data analysis and more
• Built-In Exceptions
• Improve Your Python: “Yield” and Generators Explained
• Python Cheat Sheets
• Python explanations and examples with W3Schools 

Python Enhancement Proposal (PEP) describing new features

• PEP 257 - Docstring Conventions
• PEP 8 - Style for Python Code

Biology Related

• Biopython Tutorial and Cookbook - Python Tools for Computational Molecular Biology
• Tutorial on how to manipulate, visualize and make sense of data by a Biologist

Data Science

• Introduction to Python for Data Science by DataCamp
• Earth Data Science Tutorials and other hands-on guides in Python

Coding Exercises

• Solve Python by HackerRank

Data Visualization

• Data Viz with Python and R

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General Info for R ​

Introduction and documentation

• Introduction to R by DataCamp
• R Programming by Johns Hopkins University via CourseEra
• List of Functions You Should Be Familiar With
• ggplot2 Cheat Sheet
• All Available and Published Cheat Sheets
• Named Colors for R Plots
• Books, Tutorials and Packages from Gaston Sanchez

Data Science

• R for Data Science
• Data Science: R Basics by HarvardX via edX
• Earth Analytics Course: Learn Data Science and other hands-on guides

Biology Related​

• Ecology-Related Resources R Labs for Community Ecologists
• enaR: An r package for Ecosystem Network Analysis
• A Checklist for Choosing Between R Packages in Ecology and Evolution by Christopher J. Lortie, Jenna Braun, Alessandro Filazzola, & Florencia Miguel
• CRAN Task View: Analysis of Ecological and Environmental Data​

Statistics

• Introduction to Bivariate Analysis
• An R Companion for the Handbook of Biological Statistics by Salvatore S. Mangiafico
• Hands-On Programming with R
• Handbook of Biological Statistics by John H. McDonald
• Applied Statistics with R

Coding Exercises

• Exercises that Practice and Extend Skills in R by John Maindonald

Online tools

• Online tools for analysisBioconductor provides tools/packages for bioinformatics analysis​

Miscellaneous and other media

• Daily coding challenges from easy to hard on Reddit
• freeCodeCamp - a nonprofit community that helps you learn to code by building projects
• The bioinformatics chat - computational biology, bioinformatics, and next generation sequencing podcast
• TidyTuesday Podcast to help R learners learn in real-world contexts
• Data-to-Viz - program that helps you determine the most appropriate graph for your data