CRISPR-design

List of software/websites/databases/reviews for CRISPR gene editing.

This collection is inspired by awesome-CRISPR.

Overview

Contents

• On-target prediction algorithms
• Off-target prediction algorithms
• Genome editing outcome predictions
• Databases
• Reviews

On-target prediction algorithms (Machine Learning based)

• SSC - [webserver] - A sequence model for predicting sgRNA efficiency in CRISPR/Cas9 knockout experiments.
• CRISPRscan - [webserver] - A novel algorithm to predict gRNA efficiency in zebrafish.
• WU-CRISPR - [webserver] - A web tool to design gRNA for CRISPR/Cas9 Knockout system (replaced by sgDesigner).
• CRISPOR - [webserver] - A program that helps to design, evaluate and clone guide sequences for the CRISPR/Cas9 system.
• Azimuth - [Python, webserver, webserver] - Predictive Modelling of CRISPR/Cas9 guide efficiency based on Gradient-Boosted Regression Trees.
• TSAM - [Python, MATLAB, webserver] - Two-Step-Averaging-Method (TSAM) by averaging the predicted efficiency scores of a boosting algorithm and those by a support vector machine (SVM).
• sgDesigner - [Perl/Python, webserver] - A stacking model framework using XGBoost, SVM and Logistic Regression as classifiers.

On-target prediction algorithms (Deep Learning based)

• DeepCRISPR - [Python, webserver] - A deep learning based prediction model for sgRNA on-target knockout efficacy and genome-wide off-target cleavage profile prediction.
• DeepCas9 - [R] - DeepCas9 can be used to make CRISPR sgRNAs activity predictions based on CNNs and a one-hot representation of DNA sequences.
• DeepSpCas9 - [Python, webserver] - A CNN-based tool that was trained on a dataset of ~12k gRNAs and showed a high generalization performance.
• DeepHF - [Python, webserver] - A BiLSTM neural network trained on ~50k gRNAs together with hand-crafted biological features. Supports various types of SpCas9 nucleases (SpCas9_U6, SpCas9_T7, eSpCas9(1.1), and SpCas9-HF1).
• CRISPRLearner - [Python] - A deep learning based system to predict CRISPR/Cas9 on target cleavage efficiency with 10 different model weights.
• CNN-SVR - [Python] - A merged CNN as the front-end for extracting gRNA and epigenetic features as well as an SVR as the back-end for regression and predicting gRNA cleavage efficiency.
• C-RNNCrispr - [Python] - A hybrid CNN and BGRU framework for predicting CRISPR/Cas9 guide RNA on-target activity.
• CRISPR-ONT - [Python] - An attention-based CNN framework to predict CRISPR/Cas9 sgRNA on-target activity.
• AttCRISPR - [Python] - A spacetime interpretable model for prediction of sgRNA on-target activity.

Off-target prediction algorithms

• CasFinder - [Python] - An algorithm for identifying specific Cas9 targets in genomes.
• CasOT - [webserver] - A tool to find potential off-target sites in any given genome or user-provided sequence, with user-specified types of the protospacer adjacent motif, and the number of mismatches allowed in the seed and non-seed regions.
• Cas-OFFinder - [webserver] - An algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases.
• CCtop - [webserver] - An algorithm to predict CRISPR/Cas9 target.
• CHOPCHOP - [webserver] - A web tool for selecting target sites for CRISPR/Cas9, CRISPR/Cpf1.
• CRISPR RGEN Tools - [webserver] - An algorithm can identify of RGEN off-target sites without limitation by the number of mismatches and allow variations in PAM sequences recognized by Cas9. Meanwhile, it can search for RGEN targets with low potential off-target effects and high knock-out efficiencies in the exon region.
• CRISPRTarget - [webserver] - A tool to explore the targets of CRISPR RNAs.
• flyCRISPR - [webserver] - Specificity for Drosophila to find CRISPR target sites and evaluate each identified CRISPR target.
• Geneious CRISPR Site Finder - [software] - It searches for off-target binding sites against a database of sequences.
• GT-Scan - [webserver] - A flexible web-based tool that ranks all potential targets in a user-selected region of a genome in terms of how many off-targets they have.
• GT-Scan2 - [R] - It is Chromatin- and Transcription-aware target site optimization tool for CRISPR/CAS9.
• sgRNAcas9 - [software] - A software package that can be applied to search rapidly for CRISPR target sites, and analyze the potential off-target cleavage sites of CRISPR-Cas9 simultaneously.
• WGE - [webserver] - A algorithm shows CRISPR sites (paired or single) in and around genes and scores the pairs for potential off-target sites, and browse individual and paired CRISPR sites across human, mouse.

Genome editing outcome predictions

• FORECasT - [Python, webserver] - A method to predict and view mutational profiles for individual gRNAs.
• inDelphi - [webserver] - A computational model that predicts the heterogeneous (100+ unique) mixture of indels resulting from microhomology-mediated end-joining (MMEJ) and non-homologous end-joining (NHEJ) at a CRISPR-induced cut. inDelphi synthesizes known biological mechanisms of DNA repair with machine learning and achieves strong accuracy.
• Lindel - [webserver] - A Logistic regression model for accurate indel prediction induced by Cas9 cleavage. NAR 2019
• Microhomology-Predictor - [webserver] - A web tool can simply predict the mutation patterns caused by microhomology-mediated end joining (MMEJ) and estimate how frequently unwanted in-frame deletions would happen.
• SPROUT - [webserver] - A machine learning algorithm to predict the repair outcome of a CRISPR-CAS9 knockout experiment. Trained in primary human T cells, SPROUT may facilitate design of SpCas9 guide RNAs in therapeutically important primary human cells.

Databases

• BioGRID ORCS - [webserver] - An open repository of CRISPR screens compiled through comprehensive curation efforts. Paper: Nucleic Acids Research 2019
• DepMap - [webserver] - A comprehensive reference map of the Cancer Dependency Map project at the Broad Institute. Paper: Cell 2017
• GenomeCRISPR - [webserver] - A database for high-throughput CRISPR/Cas9 screening experiments.
• PICKLES - [webserver] - A database of pooled in-vitro CRISPR knockout library essentiality screens.
• Project Drive - [webserver] - A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening. Paper: Cell 2017.
• Project Score (Sanger DepMap) - [webserver] - Genome-scale CRISPR–Cas9 screens in 324 human cancer cell lines from 30 cancer types. Paper: Nature 2019.

Reviews

• 2018 - Doench - Am I ready for CRISPR? A user's guide to genetic screens.