Programming with Python and R: Reusing code you find online

Published: 26 September 2019
on channel: Programming and Linear Algebra for Biologists

This video covers several different scenarios showing how to reuse code you find online. How can you tell the difference between an installable package, a function definition, and a script? How can you use each of those things? How can you judge whether the code is trustworthy? We will work through some specific examples to answer these questions.

Special thanks to Massimiliano Loss, Vincenzo Bonnici, Monica Pendrazzini, Lilin Yin, Aaron Kusmec, and Joseph Gage for permission to use their code in this video, and to Yongli Zhao for pointing me to some code she had reused.

If pip doesn't work for you, see this video: • R and Python #0.1: What to install for Python
If Rscript doesn't work for you, see this video: • R and Python #0.2: What to install for R

Here are some links if you want to learn more about Git and GitHub:
https://happygitwithr.com/
https://swcarpentry.github.io/git-nov...
https://www.freecodecamp.org/news/git...

Table of Contents:

00:00 - Programming in Python and R: Using code you find online
00:26 - Objectives of this video
01:04 - General advice
04:24 - The Python Package Index
11:50 - R packages on CRAN
19:04 - Getting R functions with source
24:35 - Installing R packages from GitHub
27:48 - R packages on Bioconductor
33:24 - What is GitHub?
37:37 - Using Python scripts
50:14 - Using an R script
1:07:18 - NSF Acknowledgment

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