Table 2.
Selected LINCS Software Tools
| Tool | Summary | Website |
|---|---|---|
| iLINCS | Transcriptomics and proteomics dataset analysis tools for a biologist audience | http://www.ilincs.org/ |
| piLINCS | Facilitates proteomics data access, integrated with iLINCS | http://www.pilincs.org |
| GR Calculator, GR Metrics, GR Browser | Access and visualize LINCS dose-response data, upload user data for analysis | http://www.grcalculator.org/grbrowser/ |
| LINCS Proteomics Data Portal | Proteomics data access and analysis, integrated with iLINCS | http://lincsproteomics.org |
| L1000CDS2 | LINCS perturbation search engine that returns signatures that either reverse or mimic a user input signature | http://amp.pharm.mssm.edu/L1000CDS2/ |
| HMS Breast Cancer Browser | Access to LINCS data relevant to breast cancer | http://www.cancerbrowser.org/ |
| CLUE Platform | A collection of apps that query, visualize, analyze LINCS transcriptomics and proteomics data | https://clue.io/ |
| OMICS Integrator | Identify candidate molecular pathways underlying integrated ‘omics data | http://fraenkel-nsf.csbi.mit.edu/omicsintegrator/ |
| Enrichr | Gene set search engine | http://amp.pharm.mssm.edu/Enrichr |
| Harmonizome | Omics integration tool | http://amp.pharm.mssm.edu/Harmonizome/ |
| Slicr | L1000 signature store | http://amp.pharm.mssm.edu/Slicr |
| LINCS Canvas Browser | L1000 visualization | http://www.maayanlab.net/LINCS/LCB/ |
| SEP-L1000 | Side effect predictions for LINCS small molecules | http://maayanlab.net/SEP-L1000 |