These materials are for instruction in MDIBL's 2023 Reproducible and FAIR Bioinformatics Analysis of Omics Data course.
They are adapted from Alex's Lemonade Stand Foundation Childhood Cancer Data Lab training materials, Harvard Chan Bioinformatics Core lessons and Penn GCB 535 materials. (Sources used will be indicated in individual sections of instruction material.)
We manage environments with where participants will interact with materials in mind.
- For setting up the bulk RNA-seq materials, we use a conda environment that mirrors what is available on the FAIR Bioinformatics server (i.e., same R version, same versions of Salmon; see instructions). We assume that development is taking place on an Apple Silicon machine.
- For the machine learning materials, we assume that training participants will use their laptops with the most recent version of R and use
renvto manage packages.