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CRISPR & Gene Editing

CRISPR & gene editing covers guide RNA design, delivery, validation, and off-target analysis for Cas9/Cas12/Cas13, base editors, prime editors and epigenome editors. It includes pooled CRISPR screens (MAGeCK), arrayed knockouts, and translational programs in cell & gene therapy and agriculture.

CRISPORMAGeCKCRISPResso2Benchling
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Default learning track

4 phases · ~16–22 weeks

A baseline path through this sector with milestones, prerequisites, and concrete projects. Click Personalize this roadmap above to have the AI tailor pace, depth, and resources to your background and goals.

1

Phase 1 — Foundations

3–4 weeks 30–40 hours

Build the conceptual and quantitative base needed to read papers and follow tutorials in the sector.

Prerequisites

  • Comfortable with basic biology / health-science vocabulary
  • Ability to install software and use a terminal

Skills you'll build

Python or R basicsLinux shellGit/GitHubReading scientific literature

Hands-on projects

Reproducible analysis notebook

Walk through a published tutorial in CRISPOR + MAGeCK + CRISPResso2 and reproduce its results on the provided sample data.

Deliverable: GitHub repo with a Jupyter/Quarto notebook, environment.yml, and README

Milestones

  • Set up reproducible Conda/Mamba environment and a public GitHub repo
  • Read and summarize 3 review papers covering the sector landscape
  • Complete an intro statistics or scripting course end-to-end
Citation · documentation
Addgene — CRISPR reagents & protocols
Addgene
Why: Exact sector match (CRISPR & Gene Editing)
Dataset · tool
CRISPOR — guide RNA design
Tefor / UCSC
Why: Exact sector match (CRISPR & Gene Editing)
2

Phase 2 — Core tools & datasets

4–6 weeks 60–80 hours

Learn the standard analytical stack of the sector and the canonical public datasets used by professionals.

Prerequisites

  • Completed Phase 1 reproducible notebook
  • Working Python/R environment

Skills you'll build

CRISPOR + MAGeCK + CRISPResso2Data wranglingQC & exploratory analysisVersion-controlled pipelines

Hands-on projects

Dataset deep-dive on DepMap CRISPR screens + ENCODE sgRNA libraries

Pick one study from DepMap CRISPR screens + ENCODE sgRNA libraries, reproduce the headline result, and write a short technical note on what you found.

Deliverable: GitHub repo + 3-page PDF write-up

Milestones

  • Run the official CRISPOR + MAGeCK + CRISPResso2 tutorial end-to-end on real data
  • Download and explore one full dataset from DepMap CRISPR screens + ENCODE sgRNA libraries
  • Document a clean QC + analysis pipeline that another person could rerun
Citation · training
Innovative Genomics Institute training
IGI · UC Berkeley
Why: Exact sector match (CRISPR & Gene Editing)
Dataset · tool
MAGeCK — CRISPR screen analysis
Liu Lab
Why: Exact sector match (CRISPR & Gene Editing)
3

Phase 3 — Applied projects

6–8 weeks 80–120 hours

Move from tutorials to original analyses on real questions. Start showing your work publicly.

Prerequisites

  • Phase 2 dataset deep-dive complete
  • Comfortable with the sector's primary tooling

Skills you'll build

End-to-end pipeline designStatistical interpretationScientific writingReproducible reports

Hands-on projects

CRISPR screen + edit-quant mini-pipeline

Re-analyze a public pooled CRISPR screen with MAGeCK, then quantify editing outcomes on a target with CRISPResso2 on public amplicon data.

Deliverable: Reproducible repo + hit table + edit-outcome figures + 3-page brief

Milestones

  • Ship one original mini-analysis on a public dataset with clearly stated hypothesis and limitations
  • Engage with the Innovative Genomics Institute and Addgene CRISPR community (post a question, answer one, or share a notebook)
  • Get peer feedback on at least one project and iterate
Citation · course
Coursera · Genome Editing (Hopkins / Harvard variants)
Coursera
Why: Exact sector match (CRISPR & Gene Editing)
Dataset · tool
CRISPResso2 — edit quantification
Pinello Lab
Why: Exact sector match (CRISPR & Gene Editing)
4

Phase 4 — Portfolio & career launch

3–5 weeks 30–50 hours

Package your work, target real roles, and prepare to interview in the sector.

Prerequisites

  • Phase 3 capstone project shipped
  • 2+ public repos under version control

Skills you'll build

Technical CVPortfolio siteInterview prep (case studies + technical questions)Networking

Hands-on projects

Job-ready portfolio package

Curate 2–3 of your strongest sector projects into a portfolio site with clear case-study writeups, plus a 1-page CV tailored to the target role.

Deliverable: Live portfolio URL + PDF CV + cover letter template

Milestones

  • Publish a portfolio site or pinned GitHub README linking to 2–3 projects
  • Tailor CV to 3 real job ads in the sector and submit applications
  • Practice 5 mock technical interviews with sector-specific case studies
Citation · documentation
Nature Protocols — CRISPR collection
Nature Portfolio
Why: Exact sector match (CRISPR & Gene Editing)
Dataset · dataset
DepMap (CRISPR essentiality)
Broad Institute
Why: Exact sector match (CRISPR & Gene Editing)

Curated learning resources

Verified, canonical resources from the official providers in this sector. The AI roadmap builder draws from this same library when it personalizes your roadmap.

Courses

Coursera · Genome Editing (Hopkins / Harvard variants)
Coursera
Python for Everybody
Coursera · Univ. of Michigan
LinkedIn Learning paths
LinkedIn

Trainings

Innovative Genomics Institute training
IGI · UC Berkeley
Software Carpentry lessons
The Carpentries
Kaggle Learn
Kaggle

Documentations

Addgene — CRISPR reagents & protocols
Addgene
Nature Protocols — CRISPR collection
Nature Portfolio
Git & GitHub fundamentals
GitHub Docs

Tools

CRISPOR — guide RNA design
Tefor / UCSC
MAGeCK — CRISPR screen analysis
Liu Lab
CRISPResso2 — edit quantification
Pinello Lab
Benchling CRISPR design
Benchling

Datasets

DepMap (CRISPR essentiality)
Broad Institute
ENCODE sgRNA library resources
ENCODE

Books

R for Data Science (2e)
Hadley Wickham et al.

Typical career paths

CRISPR Scientist

Designs and runs CRISPR experiments — gRNA design, editing validation, screen analysis.

Genome Editing Bioinformatician

Builds pipelines for guide design, screen analysis (MAGeCK) and amplicon-level edit quantification (CRISPResso2).

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