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Division Signaling and Functional Genomics


 

 

 

Bioinformatic Tools

 

We develop database and computational tools for the design and analysis of high-throughput screening experiments.

GenomeCRISPR Database

GenomeCRISPR is a database for high-throughput screening experiments performed by using the CRISPR/Cas9 system. A dynamic web interface guides users through the process of finding information about published CRISPR screens. The database holds detailed data about observed hits and phenotypes. Moreover, it provides knowledge about performance of individual single guide RNAs (sgRNAs) used under various experimental conditions.

GenomeCRISPR can be accessed at genomecrispr.org

Please cite the following paper when using GenomeCRISPR: Rauscher, B., Heigwer, F., Breinig, M., Winter, J., Boutros, M. (2017). GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens. Nucleic Acids Res 45:D679-D86 Fulltext

GenomeRNAi Database

GenomeRNAi is a database with phenotype information from high-throughput RNAi experiments in human cells and Drosophila (cell-based or in vivo). The GenomeRNAi website features search and browse functionalities, a “frequent hitter” page, download options, and a dynamic genome browser based on a DAS server. It is well integrated with external resources. The website also provides details about RNAi reagents and associated mapping information, as well as an assessment of their specificity and efficiency. Direct submissions by data producers are welcome!

GenomeRNAi can be accessed at www.genomernai.org

Please cite the following paper when using GenomeRNAi: Schmidt, EE., Pelz, O., Buhlmann, S., Kerr, G., Horn, T., Boutros, M. (2013). GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update. Nucleic Acids Research 2013 Jan 1;41(D1):D1021-6. doi: 10.1093/nar/gks1170. Fulltext

E-CRISP

We developed E-CRISP to design CRISPR constructs and provide the possibility to alter various design parameters systematically. Currently E-CRISP is available for several different organisms, including mouse, rat, fish, fly, worm, Arabidopsis, yeast, human, frog, rice, medaka and more. E-CRISP identifies and evaluates potential CRISPR targets by a combination of options including specificity (should target one locus only), nucleotide composition, experimental purpose and genomic context (targeting a gene, specifying an exon, location in CpG island) among others.

E-CRISP can be accessed at www.e-crisp.org

Please cite the following paper when using E-CRISP: Heigwer, F., Kerr, G., Boutros, M. E-CRISP: fast CRISPR target site identification. Nature Methods 11, 122-123 (2014). doi:10.1038/nmeth.2812 Fulltext

CRISPR Library Designer (CLD)

CRISPR library designer (CLD) is an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting non-coding regions. It predicts a high fraction of functional sgRNAs.

CLD is publicly available at github.com/boutroslab/cld

Please cite the following paper when using CLD: Heigwer F, Zhan T, Breinig M, Winter J, Brügemann D, Leible S, Boutros M. (2016). CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries. Genome Biology 17:55. doi:10.1186/s13059-016-0915-2 Fulltext

caRpools

caRpools is an R package for exploratory data analysis of pooled CRISPR/Cas9 screens. It provides a user-friendly pipeline for end-to-end analysis of high-throughput CRISPR screening data. As an output, it generates standardized PDF and HTML reports including an in-depth analysis of screening quality, candidate hit calling using multiple, independent algorithms, in-depth analysis of sgRNA phenotypes, XLS output for storage and follow-up analysis, and annotation of candidate genes using biomaRt. After completion of a configuration file, caRpools runs the complete analysis workflow, including NGS data extraction and mapping.

caRpools can be accessed at github.com/boutroslab/caRpools

Please cite the following paper when using caRpools: Winter, J., Breinig, M., Heigwer, F., Brueggemann, D., Leible, S., Pelz, O., Zhan, T., Boutros, M. (2015). caRpools: An R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens. Bioinformatics 32:632-4. doi:10.1093/bioinformatics/btv617 Fulltext

E-RNAi

E-RNAi is a web application to design optimized RNAi reagents. It integrates genomic context information with predicted specificity and efficiency parameters.

E-RNAi can be accessed at e-rnai.org

Please cite the following paper when using E-RNAi: Horn, T., Boutros, M. (2010). E-RNAi: a web application for the multi-species design of RNAi reagents - 2010 update. Nucleic Acids Research 38:W332-339. Fulltext

NEXT-RNAi

NEXT-RNAi is a software for the design and evaluation of genome-wide RNAi libraries. It performs all steps from the prediction of specific and efficient RNAi target sites to the visualization of designed reagents in their genomic context.

NEXT-RNAi can be accessed at www.nextrnai.org and is available for download at GitHub.

Please cite the following paper when using NEXT-RNAi: Horn, T., Sandmann, T., Boutros., M. (2010). Design and evaluation of genome-wide libraries for RNAi screens. Genome Biology 11:R61. Fulltext

cellHTS

cellHTS is a software package implemented in Bioconductor/R to analyze cell-based high-throughput RNAi screens. The cellHTS2 package is an updated version of the cellHTS package, offering improved functionality for the analysis and integration of multi-channel screens and multiple screens.

More information on cellHTS can be found at: www.dkfz.de/signaling/cellHTS

Please cite the following paper when using cellHTS: Boutros, M., Bras, L., Huber, W. (2006). Analysis of cell-based RNAi screens. Genome Biology, 7:R66. Fulltext

web cellHTS

A prototype of a web-application that provides a user-friendly interface to cellHTS and a step-by-step tutorial how to use cellHTS for the analysis of high-throughput screening experiments. web cellHTS is available as open source and can be downloaded for local installation.

web cellHTS is accessible at web-cellhts2.dkfz.de and available for download at GitHub.

Please cite the following paper when using web cellHTS: Pelz., O., Gilsdorf, M., Boutros, M. (2010). web cellHTS2: A web application for the analysis of high-throughput screening data. BMC Bioinformatics 11:185. Fulltext

E-TALEN

E-TALEN is a new web service to design TALENs for introducing knock-out mutations, endogenous tagging or targeted excision repair. The tool can be used to design TALENs against a single target or up to 50 target genes in parallel. E-TALEN guides the user through an end-to-end de-novo design process for specific sequences or genomic loci. It can also be used to evaluate existing TALEN designs.

E-TALEN can be accessed at www.e-talen.org

Please cite the following paper when using E-TALEN: Heigwer, F., Kerr, G., Walther, N., Glaeser, K., Pelz, O., Breinig, M., Boutros, M. (2013). E-TALEN: a web tool to design TALENs for genome engineering. Nucleic Acids Research 1-7 (2013). doi:10.1093/nar/gkt789 Fulltext

 

Booking Calendar

A reservation management system for booking of lab equipment. Available for download at GitHub.


Please contact us with any suggestions or comments at b110-office (at) dkfz.de