awesome-crispr

Bradford et al. -

Doench -

Esposito et al. -

[Perl] - AmpliconDIVider contains the scripts used to identify deletion and insertion variants (DIVs) in DNA amplicons.

[Perl] - A batch analysis of Next-Generation Sequencing data for genome editing assessment.

[webserver] - An online tool for assessing genome editing results using NGS data.

[Python, R] - A workflow to analyze CRISPR-Cas-induced indel mutations in targeted/amplicon DNA sequencing. Can work with single/multiplexed sgRNAs per region(s).

[Perl, R] - A CRISPR NGS data analysis and visualization pipeline.

[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.

[webserver] - A website to design gRNA(s) which efficiently engineer your target and minimize off-target effects using ATUM Scoring Algorithms.

[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.

[python] - A Computational Workflow for Designing Libraries of sgRNAs for CRISPR-Mediated Base Editing.

[webserver] - A website that can design optimal CRISPR gRNAs by analyzing target location, specificity, and efficiency.

[webserver] - A website of designing gRNAs based on multiple organisms.

[webserver] - This resource provides optimized guide RNAs to target transcripts in the human transcriptome, model organisms and viral RNA genomes.

[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.

[R] - A pipeline for end-to-end analysis of pooled CRISPR/Cas9 screening data. Including in-depth analysis of screening quality and sgRNA phenotypes.

[Python] - Based on the empirical Bayesian framework to account for multiple sources of variability, including reagent efficacy and off-target effects.

[R] - An algorithm to estimate gene-dependency levels from CRISPR-Cas9 essentiality screens while accounting for this effect.

[R] - A hierarchical mixture model for CRISPR pooled screens

[R] - A software provides functions for hit gene identification and quantification of sgRNA abundances for CRISPR pooled screen data analysis using Beta-Binomial test.

[webserver] - An open repository of CRISPR screens compiled through comprehensive curation efforts. Paper:

[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.

[webserver] - A comprehensive reference map of the Cancer Dependency Map project at the Broad Institute. Paper:

[webserver] - A database for high-throughput CRISPR/Cas9 screening experiments.

[webserver] - A database of pooled in-vitro CRISPR knockout library essentiality screens.

[webserver] - A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening. Paper:

[Python] - An algorithm for identifying specific Cas9 targets in genomes.

[webserver] - An algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases.

[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.

[webserver] - An algorithm to predict CRISPR/Cas9 target.

[webserver] - A web tool for selecting target sites for CRISPR/Cas9, CRISPR/Cpf1.

[webserver] - A Web-based tool for identifying and validating CRISPR/Cas off-target sites.

[software] - A program that searches through raw metagenomic reads for CRISPR.

[webserver, software] - Filter the invalid CRISPRs.

[software, webserver] - A program enables the easy detection of CRISPRs and cas genes in user-submitted sequence data.

[webserver] - Detect CRISPR-Cas genes and arrays, and predict the subtype based on both Cas genes and CRISPR repeat sequence.

[webserver] - Compare the CRISPRs of two or several genomes.

[webserver, software] - A tool to predict and analyze CRISPR arrays.