DeepPrime

Deep learning-based model that can predict the prime editing efficiency for all possible pegRNAs for a given target sequence

Published Paper Publication
DeepPrime

GenET Usage

GenET (Genome Editing Toolkit) is a library of various python functions for the purpose of analyzing and evaluating data from genome editing experiments. GenET is still in its early stages of development and continue to improve and expand. Currently planned functions include guideRNA design, saturation library design, deep sequenced data analysis, and guide RNA activity prediction.

View on GitHub

System requirement

GenET can be run on either Mac or Linux system. GenET is currently available on Linux or Mac based systems as one of the dependent tools, ViennaRNA package, is limited to these operating systems. Windows users must establish a docker or virtual OS environment to use this tool.

Installation

The latest GenET is version 0.15.0 (04-25-2024)

# Create virtual env for genet.
# python 3.10 was tested.
> $ conda create -n genet python=3.10
> $ conda activate genet
# install genet package in your env.
> $ pip install genet

How to use DeepPrime by GenET

Please see Github for more details.

> from genet.predict import DeepPrime
> results = DeepPrime(input_sequence).predict('PE2max')