Shunsuke-1994 / CaRTRIDGE

CaRTRIDGE

CaRTRIDGE

Code repository for "Programmable mammalian translational modulators by CRISPR-associated proteins"

Requirements

• python > 3.3
• viennarna
• numpy
• pandas/openpyxl
• matplotlib/seaborn
• scipy

Directories

CaRTRIDGE
├── LICENSE
├── README.md
├── datasets
│   ├── Crosstalk-ON.xlsx
│   ├── Orthogonal OFF-3.xlsx
│   └── gRNA list for MFE2.xlsx
├── notebooks
│   ├── calcMFE.ipynb
│   └── orthogonality_check.ipynb
└── outputs
    └── gRNA list for MFE2_RNAfold.xlsx

• datasets/Crosstalk-ON.xlsx : normalized fold change information of on-switches.
• datasets/Orthogonal OFF-3.xlsx : normalized fold change information of off-switches.
• datasets/gRNA list for MFE2.xlsx : sequences of switches used for MFE calculation.

Reference

Kawasaki, S., Ono, H., Hirosawa, M., Kuwabara, T., & Saito, H. (2021). Programmable mammalian translational modulators by CRISPR-associated proteins. bioRxiv.