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awesome-CRISPR

List of software/websites/databases/other stuff for genome engineering
https://github.com/davidliwei/awesome-CRISPR

Last synced: 1 day ago
JSON representation

  • Screening analysis

    • pinAPL-Py - [Python, webserver] – Python script and webtool for analyzing CRISPR screen dataset
    • BAGEL - [Python] - An algorithm is designed to identify negatively selected genes, by calculating a Bayes factor for each gene representing a confidence measure that the gene knockout results in a fitness defect. Bayesian analysis of gene knockout screens using pooled library CRISPR or RNAi.
    • casTLE - [Python] - Based on the empirical Bayesian framework to account for multiple sources of variability, including reagent efficacy and off-target effects.
    • CERES - [R] - An algorithm to estimate gene-dependency levels from CRISPR-Cas9 essentiality screens while accounting for this effect.
    • ENCoRE - [Java] - An efficient software for CRISPR screens identifies new players in extrinsic apoptosis.
    • gCrisprTools - [R] - An R/Bioconductor analysis suite facilitating quality assessment, target prioritization, and interpretation of arbitrarily complex competitive screening experiments.
    • MAGeCK-VISPR - [Python] - A comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.
    • MAGeCK - [Python] - Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) for prioritizing single-guide RNAs, genes and HiTSelectpathways in genome-scale CRISPR/Cas9 knockout screens. Paper: [Genome Biology 2014](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0554-4) **Recommended**
    • PBNPA - [R] - A Permutation-Based Non-Parametric Analysis (PBNPA) algorithm, which computes p-values at the gene level by permuting sgRNA labels, and thus it avoids restrictive distributional assumptions.
    • RIGER - [Gene-E extension] - RNAi Gene Enrichment Ranking (RIGER).
    • RSA - [perl, R, C#] - Redundant siRNA Activity (RSA) is a probability-based approach for the analysis of large-scale RNAi screens.
    • scMAGeCK - [Python, R] - A computational model to identify genes associated with multiple expression phenotypes from CRISPR screening coupled with single-cell RNA sequencing data. Paper: [Genome Biology 2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1928-4)
    • STARS - [Python] - A gene-ranking algorithm for genetic perturbation screens, computing a score for genes using the probability mass function of a binomial distribution. To analyze either shRNA or sgRNA based screening data.

  • Reviews

  • Summary (not a complete list)

  • Guide design

    • ATUM - [webserver] - A website to design gRNA(s) which efficiently engineer your target and minimize off-target effects using ATUM Scoring Algorithms.
    • BE-DICT - [Python, webserver] - An attention-based deep learning algorithm capable of predicting base editing outcomes. It is aimed to assist scientists in designing base editor experiments.
    • Breaking-Cas - [webserver] - A website of designing gRNAs based on multiple organisms.
    • Cas-Designer - [webserver] - A bulge-allowed quick guide-RNA designer for CRISPR/Cas derived RGENs.
    • Cas13design - [webserver] - This resource provides optimized guide RNAs to target transcripts in the human transcriptome, model organisms and viral RNA genomes.
    • CGAT - [python] - CGAT provides an extensive suite of tools designed to assist in the analysis of genome scale data from a range of standard file formats.
    • CHOPCHOPv3 - [webserver] - A web tool for selecting target sites for CRISPR/Cas9, CRISPR/Cpf1, CRISPR/Cas13 or NICKASE/TALEN-directed mutagenesis.
    • CRISpick - [webserver] - CRISPick, developed by the Broad Institute, ranks and picks candidate CRISPRko/a/i sgRNA sequences
    • CRISPOR - [webserver] - A program helps to design, evaluate and clone guide sequences for the CRISPR/Cas9 system.
    • crisprBase - [R] - Base functions and classes for CRISPR gRNA design for the Bioconductor project
    • crisprBowtie - [R] - A Bioconductor package for on- and off-target alignment of CRISPR guide RNAs with Bowtie.
    • crisprBwa - [R] - A Bioconductor package for on- and off-target alignment of CRISPR guide RNAs with BWA.
    • crisprDesign - [R] - A Bioconductor package for comprehensive design of CRISPR gRNAs across nucleases and base editors.
    • CRISPR LifePipe - [webserver] - A web application which allows designing gRNA and donor DNA sequences for CRISPR experiments.
    • CRISPR MultiTargeter - [webserver] - A web-based tool which automatically searches for CRISPR guide RNA targets. It can find highly similar or identical target sites in multiple genes, transcripts or design targets unique to particular genes or transcripts.
    • CRISPR-DO - [webserver] - A web application for designing and optimizing of guide sequences that target both coding and non-coding regions in spCas9 CRISPR system across human, mouse, zebrafish, fly and worm genomes. **Recommended**
    • CRISPR-DT - [webserver] - A web application that allows a user to upload DNA sequences, set specifications according to experimental goals, and recieve target candidates.
    • CRISPR-ERA - [webserver] - A Fast and Comprehensive Guide RNA Design Tool for Genome Editing, Repression and Activation.
    • CRISPR-FOCUS - [webserver] - A web-based platform to search and prioritize sgRNAs for CRISPR screening experiments. **Recommended**
    • CRISPR-Local - [software, webserver] - A local single-guide RNA (sgRNA) design tool for non-reference plant genomes
    • CRISPR-P - [webserver] - One of the most popular tools for sgRNA design in plants with minimal off-target effects.
    • CRISPR-RT - [webserver] - A web application for RNA-targeting prediction and visualization with the CRISPR-C2c2/Cas13a System.
    • CRISPRa/i - [webserver] - This tool ranks and picks CRISPRa/i sgRNA sequences candidates by the gene targets provided, while attempting to maximize on-target activity and minimizing off-target activity.
    • crisprScore - [R] - A Bioconductor package for on- and off-target scoring of guide RNAs.
    • CRISPRseek - [R] - A Bioconductor Package for identifying target-specific guide RNAs for CRISPR-Cas9 Genome-Editing Systems.
    • crisprVerse - A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies.
    • CRISPy-web - [webserver] - This tool allows researchers to interactively select a region of their genome of interest to scan for possible sgRNAs.
    • CROP-IT - [webserver] - A web tool assists biologists in designing CRISPR/CAS9 sgRNAs, by predicting the off-target sites and ranking them according to the chances of occurrence.
    • CT-Finder - [webserver] - A web service that allows a user to upload DNA sequences, set specifications according to experimental goals, and receive candidate guide RNA targets.
    • DeepCas13 - [webserver] - A deep learning method to predict the efficiency of Cas13d (CasRx) RNA knockdown system.
    • DeepHF - [webserver] - Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning.
    • E-CRISP: - [webserver] - An algorithm is available for twelve organisms and can be easily extended to design both sgRNA and pgRNA.
    • EuPaGDT - [webserver] - A web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens
    • GPP Web Portal - [webserver] - A web-based platform for generating matching sgRNA knockout (CRISPRko) designed for a mouse or human gene, transcript or target sequence.
    • GuideHOM - [Google Colab] - An algorithm to search and analyze on-target and off-target cleavage efficiency of gRNAs with additional information on prediction variance; Uncertainty-aware and interpretable evaluation of Cas9-gRNA and Cas12a-gRNA specificity for fully matched and partially mismatched targets with Deep Kernel Learning.
    • GUIDES - [webserrver] - A web application to design customized CRISPR knockout libraries as easily as possible without sacrificing control.
    • IDT - [webserver] - It can generate CRISPR-Cas9 guide RNAs targeting any sequence from any species.
    • Off-Spotter - [webserver] - A website identifies all genomic instances for the given combination of gRNA(s), PAM, number of mismatches, and seed.
    • PAVOOC - [webserver] - A web tool that design and control cutting-edge-scored sgRNAs in the blink of an eye.
    • pgRNADesign - [Python] - An algorithm to design paired gRNAs for knocking out long non-coding RNAs (lncRNAs).
    • Primeedit - [webserver] - This website designs pegRNAs and secondary sgRNAs for PE2, PE3 and PE3b prime editors for ClinVar human pathogenic variants.
    • sgRNA Scorerv2.0 - [python, webserver] - A software allows users to identify sgRNA sites for any PAM sequence of interest.
    • SSC - [webserver] - A sequence model for predicting sgRNA efficiency in CRISPR/Cas9 knockout experiments.
    • Synthego - [webserver] - A software chooses from over 120,000 genomes and over 8,300 species to easily design guide RNAs for gene knockout with minimal off-target effects.
    • BE-DICT - [Python, webserver] - An attention-based deep learning algorithm capable of predicting base editing outcomes. It is aimed to assist scientists in designing base editor experiments.
    • beditor - [python] - A Computational Workflow for Designing Libraries of sgRNAs for CRISPR-Mediated Base Editing.
    • CLD - [software] - CRISPR library designer (CLD), a software for multispecies design of single guide RNA libraries
    • Crackling - [software] - Crackling is a standalone pipeline that combines multiple scoring approaches and constant-time search algorithms to select safe and efficient CRISPR-Cas9 guide RNA from whole genomes
    • Crisflash - [software] - A software to generate CRISPR guide RNAs against genomes annotated with individual variation.
    • CRISPR Library Designer - [software] - A software for the multispecies design of sgRNA libraries.
    • CRISPR-ko - [webserver] - A tool ranks and picks sgRNA sequences candidates for the targets provided while attempting to maximize on-target activity and minimize off-target activity.
    • PrimeDesign - [webserver, software] - A flexible and comprehensive design tool for prime editing.
    • Protospacer Workbench - [software] - Protospacer Workbench offers an interface for finding, evaluating, and sharing Cas9 guide-RNA (gRNA) designs.
    • PrimeDesign - [webserver, software] - A flexible and comprehensive design tool for prime editing.
    • sgRNA Scorerv2.0 - [python, webserver] - A software allows users to identify sgRNA sites for any PAM sequence of interest.
    • Guide Picker - [webserver] - A meta-tool for designing CRISPR experiments by presenting ten different guide RNAs scoring functions in one simple graphical interface.

  • Off-target prediction algorithms

    • 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.
    • COSMID - [webserver] - A Web-based tool for identifying and validating CRISPR/Cas off-target sites. **Recommended**
    • CRISPRme - [webserver] - CRISPRme is a tool for comprehensive off-target assessment that considers effects of human genetic variants. [code](https://github.com/pinellolab/crisprme) **Recommended**
    • CRISPRTarget - [webserver] - A tool to explore the targets of CRISPR RNAs.
    • 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.
    • 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.

  • Genome editing outcomes and predictions

    • Cas-analyze - [webserver] - An online tool for assessing genome editing results using NGS data.
    • CRISPR-GA - [webserver] - A platform to assess the quality of gene editing using NGS data to quantify and characterize insertions, deletions, and homologous recombination.
    • CRISPResso2 - [Python, webserver] - A software pipeline for the analysis of targeted CRISPR-Cas9 sequencing data. This algorithm allows for the quantification of both non-homologous ends joining (NHEJ) and homologous directed repair (HDR) occurrences.
    • FORECasT - [Python, webserver] - A method to predict and view mutational profiles for individual gRNAs.
    • Lindel - [webserver] - A Logistic regression model for accurate indel prediction induced by Cas9 cleavage. [NAR 2019](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz487/5511473)
    • 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.
    • TIDE/TIDER - [webserver] - Quantifying non-templated and templated CRISPR/Cas9 editing results from Sanger sequencing.

  • Databases

    • CRISP-View - [webserver] - A comprehensive database of published CRISPR screening dataset. Datasets are uniformly processed using an integrated MAGeCK-VISPR pipeline with quality control (QC) evaluations. Users can browse, search and visualize cell lines, conditions, genes and associated sgRNAs across datasets.
    • DepMap - [webserver] - A comprehensive reference map of the Cancer Dependency Map project at the Broad Institute. Paper: [Cell 2017](https://www.ncbi.nlm.nih.gov/pubmed/28753430)
    • 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](https://www.ncbi.nlm.nih.gov/pubmed/28753431).
    • Project Score (Sanger DepMap) - [webserver] - Genome-scale CRISPR–Cas9 screens in 324 human cancer cell lines from 30 cancer types. Paper: [Nature 2019](https://www.ncbi.nlm.nih.gov/pubmed/30971826).
    • The Genome Targeting Catalogue - [webserver] - A public repository of experiments using CRISPR/Cas enzymes, manually curated from published literature, encompassing both targeted and genome-wide studies in 47 species.

  • CRISPR identification and diversity

    • CRF - [webserver, software] - Filter the invalid CRISPRs.
    • CRISPRCasTyper - [webserver] - Detect CRISPR-Cas genes and arrays, and predict the subtype based on both Cas genes and CRISPR repeat sequence.
    • CRISPRcompar - [webserver] - Compare the CRISPRs of two or several genomes.
    • CRISPRDetect - [webserver, software] - A tool to predict and analyze CRISPR arrays.
    • CRISPRDirection - [software] - Predict CRISPR orientation.
    • CRISPRleader - [software] - A tool predicts CRISPR arrays in the correct orientation, and annotates the CRISPR leader boundaries.
    • CRT - [software] - CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.
    • metaCRT - [software] - A software for de novo prediction of CRISPR.
    • Patscan - [webserver] - A pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input.
    • PILER-CR - [software] - A public domain software for finding CRISPR repeats.
    • CRISPRone - [webserver(database)] - A database provides annotation of CRISPR—Cas systems including: CRISPR arrays of repeat-spacer units and cas genes, and type of predicted system(s), and anti-repeats.
    • CRISPRstand - [webserver] - Predict repeat orientations to determine the crRNA-encoding strand at CRISPR loci.
    • CRISPRCasFinder - [software, webserver] - A program enables the easy detection of CRISPRs and cas genes in user-submitted sequence data.
Programming Languages
Perl 2 python 2 C 1 C++ 1 Python 1
Categories
Guide design 56 Screening analysis 13 CRISPR identification and diversity 13 Reviews 12 Off-target prediction algorithms 9 Genome editing outcomes and predictions 8 Databases 7 Summary (not a complete list) 4
Sub Categories
Keywords
crispr 2 specificity 1 issl 1 efficacy 1 crispr-design 1 crispr-analysis 1 bioinformatics 1 guide-rna-library 1 genome-wide-targeted-mutagenesis 1 base-editing 1