List of software/websites/databases/reviews for CRISPR gene editing.
This collection is inspired by awesome-CRISPR.
- On-target prediction algorithms
- Off-target prediction algorithms
- Genome editing outcome predictions
- Databases
- Reviews
- 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.
- 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.
- 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.
- 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.
- 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.
- 2018 - Doench - Am I ready for CRISPR? A user's guide to genetic screens.