Table 1.
Online tools and databases.
| Tool | Location | Comment |
|---|---|---|
| MAGeCK | https://sourceforge.net/p/mageck/wiki/Home/ | An open source computational tool for CRISPR screen analysis. |
| CRISPRanalyzeR | http://crispr-analyzer.dkfz.de | Web based tool for CRISPR screen analysis. |
| Addgene | https://www.addgene.org/crispr/ | A non-profit plasmid repository where many CRISPR relevant plasmids, and pooled gRNA libraries can be obtained. |
| The Human Protein Atlas | https://www.proteinatlas.org/humanproteome/proteinclasses | Database including protein class categorization (including drug targets), as well as extensive expression information from human cells and tissues. |
| Gene Ontology (GO) database | http://geneontology.org/ | Extensive categorization of genes into GO-terms. |
| Gene Set Enrichment Analysis (GSEA) | https://www.gsea-msigdb.org/gsea/index.jsp | Pathway analysis tool for RNAseq data. |
| g:GOSt of g:Profiler | https://biit.cs.ut.ee/gprofiler/gost | Pathway analysis tool based on lists of manually input genes. |
| Mouse Genome Informatics (MGI) Gene Ontology Browser | http://www.informatics.jax.org/vocab/gene_ontology/ | Simple tool to search GO-terms. |
| g:Converter of g:Profiler | https://biit.cs.ut.ee/gprofiler/convert | Tool that can be used to convert Gene Ids, and to extract genes from GO-terms, KEGG pathways etc. |
| Pathway Commons | https://www.pathwaycommons.org/ | Analyses lists of genes and shows interactions and enriched pathways. |
| GeneMANIA | https://genemania.org/ | Analyses lists of genes and shows interactions and enriched pathways (plugin for Cytoscape also exists). |
| Harmonizome | https://amp.pharm.mssm.edu/Harmonizome/ | Database that extracts information from multiple other sources and integrates it into a search feature |
| Geneshot | https://amp.pharm.mssm.edu/geneshot/ | Literature mining tools providing lists of genes linked to the search term(s). |
| Green Listed tool | http://greenlisted.cmm.ki.se/ | Rapid gRNA design tool for custom CRISPR screens. Can also be used to extract non-targeting and intergenic control gRNAs (select Zhang/GeCKOv2 or Wang/Lander/Sabatini and press “Detailed Information”). |
| Depmap portal | https://depmap.org/portal | Cancer dependencies analytical and visualization tools, which e.g. can be used to identify essential genes. |
| g:Orth of g:Profiler | https://biit.cs.ut.ee/gprofiler/orth | Translates gene identifiers between organisms. |
| MGI batch query | http://www.informatics.jax.org/batch | Tool that can identify alternative names of genes. |
| Drug Gene Interaction | http://www.dgidb.org/druggable_gene_categories | Database of drug targets. |
| Probe Miner | https://probeminer.icr.ac.uk/#/ | Database of small molecule drugs and their targets. |