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CRISPR-Cas9 knockout screen data analysis bioinformatics software tools

Genetic screens by CRISPR/Cas9-mediated genome engineering have become a powerful tool for functional genomics. However, there is currently a lack of end-to-end software pipelines to analyze CRISPR/Cas9 screens based on next generation…
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CREATE
Web

CREATE CRISPR-enabled trackable genome engineering

Links each guide RNA to homologous repair cassettes that both edit loci and…

Links each guide RNA to homologous repair cassettes that both edit loci and function as barcodes to track genotype-phenotype relationships. CREATE combines automated design of CREATE cassettes…

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MAGeCK
Desktop

MAGeCK Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout

Identifies positively and negatively selected sgRNAs and genes in genome-scale…

Identifies positively and negatively selected sgRNAs and genes in genome-scale CRISPR/Cas9 knockout experiments. MAGeCK consists of four steps: read count normalization, mean-variance modeling, sgRNA…

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MAGeCK-VISPR
Desktop

MAGeCK-VISPR

Overcomes the computational challenges of Clustered Regularly Interspaced Short…

Overcomes the computational challenges of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) screens. MAGeCK-VISPR is a package that (i) defines a set of quality control (QC)…

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PBNPA
Desktop

PBNPA Permutation-Based Non-Parametric Analysis

Allows analysis of clustered regularly-interspaced short palindromic repeats…

Allows analysis of clustered regularly-interspaced short palindromic repeats (CRISPR) data. PBNPA is a method that mitigates the three major drawbacks of existing CRISPR methods. It avoids…

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caRpools
Desktop

caRpools CRISPR-AnalyzeR for pooled screens

An R package for exploratory data analysis that provides a complete workflow to…

An R package for exploratory data analysis that provides a complete workflow to analyze CRISPR/Cas9 screens. To further support the analysis of large-scale screens, caRpools integrates screening…

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ScreenBEAM
Desktop

ScreenBEAM Screening Bayesian Evaluation and Analysis Method

A hierarchical modelling algorithm within Bayesian framework for meta-analysis…

A hierarchical modelling algorithm within Bayesian framework for meta-analysis of large-scale FG screens. This novel multi-probe approach performs more robustly than previously established analysis…

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PinAPL-Py
Web
Desktop

PinAPL-Py Platform-INdependent Analysis of PooLed screens using PYthon

Allows users to proceed alignment, quality control, enrichment/depletion…

Allows users to proceed alignment, quality control, enrichment/depletion analysis and gene ranking. PinAPL-Py is optimized for transparency and user-friendly operation. It facilitates standardized,…

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CRISPRAnalyzeR
Desktop

CRISPRAnalyzeR

Analyzes, documents and explores pooled CRISR/Cas9 screens using a unified…

Analyzes, documents and explores pooled CRISR/Cas9 screens using a unified single workflow. CRISPRAnalyzeR integrates metainformation from 26 external data resources, providing a wide array of…

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CRISPRcloud
Web

CRISPRcloud

Intends to analyze raw next generation sequencing (NGS) files earned from…

Intends to analyze raw next generation sequencing (NGS) files earned from pooled screening experiments. CRISPRcloud allows users to deposit raw sequencing files confidentially, extract and cluster…

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BAGEL
Desktop

BAGEL Bayesian Analysis of Gene EssentiaLity

Allows to analyze gene knockout screens. BAGEL is an adaptation of the Bayesian…

Allows to analyze gene knockout screens. BAGEL is an adaptation of the Bayesian classifier. It estimates the distribution of fold changes of all gRNA targeting all genes in either the essential or…

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HiTSelect
Desktop

HiTSelect

A comprehensive analysis pipeline for rigorously selecting screen hits and…

A comprehensive analysis pipeline for rigorously selecting screen hits and identifying functionally relevant genes and pathways by addressing off-target effects, controlling for variance in both gene…

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CRISPulator
Desktop

CRISPulator

Simulates the impact of screen parameters on the robustness of screen results.…

Simulates the impact of screen parameters on the robustness of screen results. CRISPulator facilitates the design of pooled genetic screens by enabling the exploration of a large space of…

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SAVE
Web

SAVE Screening Analysis Visual Explorer

Serves as a useful web-based analysis pipeline for reanalysis of pooled CRISPR…

Serves as a useful web-based analysis pipeline for reanalysis of pooled CRISPR screening datasets. SAVE serves a dual purpose of extracting, clustering and analyzing raw next generation sequencing…

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grID
Dataset

grID gRNA Identification

Provides a universal CRISPR annotation system. grID is an extensive compilation…

Provides a universal CRISPR annotation system. grID is an extensive compilation of gRNA properties including sequence and variations, thermodynamic parameters, off-target analyses, and alternative…

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sgRSEA
Desktop

sgRSEA single-guide RNA Set Enrichment Analysis

Identifies essential genes from genetic screening data using CRISPR (clustered…

Identifies essential genes from genetic screening data using CRISPR (clustered regularly interspaced short palindromic repeats) and Cas9 (CRISPR-associated nuclease 9) system. sgRSEA computes sgRNA…

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