:: DESCRIPTION
CaRpools is an R package forexploratory data analysis of pooled CRISPR/Cas9 screens.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
caRpools: An R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens.
Winter J, Breinig M, Heigwer F, Brügemann D, Leible S, Pelz O, Zhan T, Boutros M.
Bioinformatics. 2015 Oct 27. pii: btv617.
:: DESCRIPTION
CRISPRCloud2 is a user-friendly cloud-based analysis platform for the deconvolution of CRISPR(Clustered Regularly Interspaced Short Palindromic Repeats) pooled screening data.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Jeong HH, Kim SY, Rousseaux MWC, Zoghbi HY, Liu Z.
CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution.
Bioinformatics. 2017 Sep 15;33(18):2963-2965. doi: 10.1093/bioinformatics/btx335. PMID: 28541456; PMCID: PMC5870715.
:: DESCRIPTION
WU-CRISPR is the Washington University gRNA designer for CRISPR/Cas9 knockouts.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system.
Wong N, Liu W, Wang X.
Genome Biol. 2015 Nov 2;16(1):218. doi: 10.1186/s13059-015-0784-0.
:: DESCRIPTION
Off-Spotteris a tool that when presented with a candidate gRNA and a PAM, quickly and exhaustively identifies all genomic sites that are identical or nearly-identical to the gRNA and also satisfy the PAM constraint.
::DEVELOPER
the Computational Medicine Center at the Sidney Kimmel Medical College of Thomas Jefferson University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
“Off-Spotter: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs“,
Venetia Pliatsika and Isidore Rigoutsos.
Biol. Direct. 2015;10 :4. doi: 10.1186/s13062-015-0035-z.
:: DESCRIPTION
CRISPR-DO is a web application for the Design and Optimization of guide sequences in several genomes (human, mouse, fly, worm and zebrafish). CRISPR-DO integrates an sgRNA efficiency prediction model (Xu, et al., 2015) and an off-target scoring function (Hsu, et al., 2013), which allow the users to evaluate the “goodness” of an sgRNA in both sensitivity and specificity.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
CRISPR-DO for genome-wide CRISPR design and optimization.
Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS.
Bioinformatics. 2016 Jul 10. pii: btw476.
:: DESCRIPTION
COSMID (CRISPR Off-target Sites with Mismatches, Insertions, and Deletions) is a web-based tool that searches genomes for potential off-target sites (http://crispr.bme.gatech.edu).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Cradick TJ, Qiu P, Lee CM, Fine EJ, Bao G.
COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites.
Mol Ther Nucleic Acids. 2014 Dec 2;3(12):e214. doi: 10.1038/mtna.2014.64. PMID: 25462530; PMCID: PMC4272406.
:: DESCRIPTION
CT-Finder is a web service that allows a user to upload DNA sequences, set specifications according to experimental goals, and receive candidate guide RNA targets.
CRISPR-DT is a web application that allows a user to upload DNA sequences, set specifications according to experimental goals, and recieve target candidates. Optimal candidates are suggested through consideration of predicted target efficiency and off-target effect. A visualization of on- and off-target matches against the chosen reference genome is provided in JBrowse.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhu H, Liang C.
CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity.
Bioinformatics. 2019 Aug 15;35(16):2783-2789. doi: 10.1093/bioinformatics/bty1061. PMID: 30615056.
CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization.
Zhu H, Misel L, Graham M, Robinson ML, Liang C.
Sci Rep. 2016 May 23;6:25516. doi: 10.1038/srep25516.
:: DESCRIPTION
MAGeCKFlute is designed to support downstream analysis, utilizing the gene summary data provided through MAGeCK or MAGeCK-VISPR. Quality control, normalization, and screen hit identification for CRISPR screen data are performed in pipeline. Identified hits within the pipeline are categorized based on experimental design, and are subsequently interpreted by functional enrichment analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nat Protoc. 2019 Mar;14(3):756-780. doi: 10.1038/s41596-018-0113-7.
Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute.
Wang B, et al.
:: DESCRIPTION
SSC is a tool for predicting sgRNA efficiency from spacer sequences. It supports the applications of optimizing sgRNA libraries in CRISPR/Cas9 knockout or CRISPR/dCas9 inhibition/activation screens.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Res. 2015 Aug;25(8):1147-57. doi: 10.1101/gr.191452.115. Epub 2015 Jun 10.
Sequence determinants of improved CRISPR sgRNA design.
Xu H, Xiao T, Chen CH, Li W, Meyer CA, Wu Q, Wu D, Cong L, Zhang F, Liu JS, Brown M, Liu XS.
:: DESCRIPTION
CRISPRone is an online server providing annotation of CRISPR—Cas systems including the array, cas genes, type (and subtype) of the predicted systems, etc.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2017 Feb 6;18(1):92. doi: 10.1186/s12859-017-1512-4.
Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements.
Zhang Q, Ye Y.