CRISPR Library Creation Tool

Computational Genomics Internship at Stanford
Project Details

The emergence of CRISPR technology has made targeted genome editing more efficient and more widespread. The CRISPR/Cas9 system uses a CRISPR RNA guide to lead a Cas9 protein to a specific sequence in the genome. This technology allows for site-specific genome cleavage, which then can lead to insertions, deletions, or substitutions at the target site. I developed an R package to sample genomic regions and provide all possible guides based on user-inputted filters of cell-type, chromatin state, and gene ontology of interest.

The tool was designed for any given genome dataset. I worked with the Bassik Lab in Stanford's genetic department to create a CRISPR library to repress enhancers in K562, a human leukemic cell line. I had weekly meetings with their team to see what additional filters I could add and other ways I could modify my tool to make it more useful to them.

  • Kundaje Lab Stanford Dept. of Genetics and Computer Science
  • Date: June - August 2014

R Coding & Analysis

Data visualization & statistical analysis of big data. Used principal component analysis. Created R package made available on Github.

Cluster Computing

Needed extensive computing resources to process large genomic datasets.


Used ENCODE/Roadmap dataset to understand correlation between gene expression and cell lines. Accessed gene ontology information from GOrilla.


Researched the novel genome editing tool in depth soon after its inception.

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