Recommended Resources
These are resources I frequently share.
I'll update this page as I discover new tools and tutorials.
Genomics - designing analysis workflows
Some guides for getting ideas of how to analyze your genomics data when you don't know where to start
Cornell EGC's analysis docs
Shameless plug: This is a collection of small vignettes for doing genomics analysis on data from services offered by the EGC (ChIP-exo, ATAC-seq, etc). There are also some disucssion topics on epigenomics analysis in general like selecting normalization or peak calling strategies.
Software best practices
Some guides for organizing your analysis or structuring your code. Think FAIR.
Noble. (2009) A quick guide to organizing computational biology projects
If nothing else from this section, read this paper. Even/especially wet-bench scientists doing their own analysis.
INTERSECT Bootcamp tutorials
The people who compiled this are committed to training research software developers in best practices so it's great for anyone doing tool development. Even if you are just making a repo for a publication, there are useful resources in here. This link is for the bootcamp year that I attended but check out the other years to see how they've expanded their topics.