| Tools for dsRNA reagent design and evaluation |
| E-RNAi |
Web-based design and evaluation of RNAi reagents |
http://www.nextrnai.org/ |
Arziman et al. (2005) |
| UP-TORR |
RNAi reagent reannotation |
http://www.flyrnai.org/up-torr/ |
Hu et al. (2013) |
| Next-RNAi |
High-throughput design of RNAi reagent libraries |
http://www.nextrnai.org/ |
Horn et al. (2010) |
| RSVP |
Browsing and evaluation of RNAi stock phenotypes |
https://fgr.hms.harvard.edu/rsvp |
Perkins et al. (2015) |
| Tools for RNAi screen analysis |
| cellHTS |
R/Biconductor package for the statistical analysis of cell based RNAi screens |
http://www.bioconductor.org/packages/release/bioc/html/cellHTS2.html |
Boutros et al. (2006) |
| webcellHTS |
Web based version of cellHTS |
http://web-cellhts2.dkfz.de/cellHTS-java/cellHTS2/ |
Pelz et al. (2010) |
| cytominr |
R/Biconductor package for the statistical analysis of cell based screens of vaious kinds with strong focus on single-cell data |
https://github.com/cytomining/cytominer |
NA |
| StratomineR HC |
Web based integrated analysis tool suite for high content screen analysis |
https://hcstratominer.umcutrecht.nl/ |
Omta et al. (2016) |
| HTSanalyzeR |
Network and enrichment analysis for high throughput RNAi screens |
http://www.bioconductor.org/packages/release/bioc/html/HTSanalyzeR.html |
Wang et al. (2011) |
| HTSvis |
Web-based visualization of large scale screening data sets |
http://htsvis.dkfz.de/ |
Scheeder et al. (2017) |
| Tools for analysis of image based screens |
| EBImage |
R/Bioconductor base image analysis and feature extraction |
https://bioconductor.org/packages/release/bioc/html/EBImage.html |
Pau et al. (2010) |
| imagHTS |
R/Bioconductor end-to-end pipeline for the analysis of image based high throughput RNAi screens |
https://bioconductor.org/packages/release/bioc/html/imageHTS.html |
Pau et al. (2013) |
| CellProfiler |
Python based GUIed image analysis and feature extraction |
http://cellprofiler.org/ |
Carpenter et al. (2006) |
| CellProfiler Analyst |
Python based machine learning package for management and analysis of image based screening data |
http://cellprofiler.org/cp-analyst/ |
Jones et al. (2008) |
| Phenotype and gene information databases |
| GenomeRNAi |
Database of RNAi screen phenotypes |
www.genomernai.org |
Schmidt et al. (2013) |
| FlyBase |
General purpose database for information on Drosophila alleles and genome function |
http://flybase.org/ |
St. Pierre et al. (2014) |
| Gene2Function |
Gene conservation database integrating several sources of ortholog, paralog and interlog data |
http://www.gene2function.org/ |
Hu et al. (2017) |
| RSVP |
Browsing and evaluation of RNAi stock phenotypes |
https://fgr.hms.harvard.edu/rsvp |
Perkins et al. (2015) |
| PubChem BioAssay |
Repository for reagent activities of drugs and gene perturbation agents |
https://pubchem.ncbi.nlm.nih.gov/ |
Wang et al. (2017) |
| Drosophila stock collections for in vivo screening |
| VDRC |
Query several genome wide RNAi stock collections |
http://stockcenter.vdrc.at/control/main |
NA |
| DRSC/TRiP |
Compendium of online and offline resources |
www.flyrnai.org |
Flockhart et al. (2012) |
| Bloomington |
Fly RNAi stock collection |
http://flystocks.bio.indiana.edu/ |
Cook et al. (2010) |
| Tools for sgRNA design and evaluation |
| E-CRISP |
Web-based design of sgRNA reagents |
http://www.e-crisp.org/E-CRISP/ |
Heigwer et al. (2014) |
| Find CRISPRs |
Web-based database of sgRNA reagents |
http://www.flyrnai.org/crispr/ |
Ren et al. (2013) |
| FlyCRISPR Target Finder |
Web-based design of sgRNA reagents |
http://tools.flycrispr.molbio.wisc.edu/targetFinder/ |
Gratz et al. (2014) |
| ChopChop |
Web-based design of sgRNA or TALEN reagents for a few different organisms |
http://chopchop.cbu.uib.no/index.php |
Montague et al. (2014) |
| CRISPOR |
Web-based design of sgRNA reagents comparing different scoring algorithms |
http://crispor.tefor.net/ |
Haeussler et al. (2016) |
| CRISPR Library-Designer |
High-throughput design of sgRNA libraries |
https://github.com/boutroslab/cld |
Heigwer et al. (2016) |
