Tools & Resources

The tools, packages, and guides we actually use for CRISPR, bioinformatics, and learning to code as a biologist.

Disclosure: Some links in this post are affiliate links. If you purchase through them, I may earn a commission at no extra cost to you. I only recommend tools I’ve actually used and believe deliver real value.

CRISPR guide design

Where we go to design and check guides before ordering oligos.

  • BenchlingFree

    All-in-one design, cloning, and lab notebook. Free academic tier.

  • CHOPCHOPFree

    Fast web tool for sgRNA design and off-target scoring.

  • CRISPORFree

    Guide scoring with well-documented, citable algorithms.

NGS & edit-analysis

For quantifying editing outcomes from Sanger and amplicon NGS.

  • CRISPResso2Free

    The standard for analyzing amplicon NGS from CRISPR experiments.

  • TIDE / ICEFree

    Estimate indel spectra straight from Sanger traces — no NGS needed.

Learn R & Python

How we recommend biologists get started with code.

  • swirlFree

    Learn R interactively, inside R itself. Best free starting point.

  • BioconductorFree

    The package ecosystem behind most bioinformatics in R.

  • Posit (RStudio)Free

    The IDE we use for every R tutorial on this site.

From BioTech Bench

Our own guides and the book.