GR Metrics Calculator and Browser

This web application was developed as part of the NIH LINCS Consortium in a collaboration between Harvard Medical School's Sorger Lab and Laboratory of Systems Pharmacology (LSP) and the University of Cincinnati's Laboratory for Statistical Genomics and Systems Biology. The former (HMS) is one of the LINCS Data and Signature Generation Centers (DSGCs) and the latter (Cincinnati) is part of the BD2K-LINCS Data Coordination and Integration Center (DCIC). All of the web applications are implemented in R, using the Shiny framework for interactive applications.

For offline computation, analysis, and visualization, see the Bioconductor R package GRmetrics.

References

[1] Hafner M*, Niepel M*, Chung M, Sorger PK. (2016) Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs. Nat Methods, vol. 13, 521<80><93>7. doi: 10.1038/nmeth.3853.

[2] Hafner M, Niepel M, Sorger PK. (2017) Alternative drug sensitivity metrics improve preclinical cancer pharmacogenomics. Nat Biotech, vol. 35(6), 500-2. doi: 10.1038/nbt.3882.

[3] Clark N*, Hafner M*, Kouril M, Williams EH, Muhlich J, Pilarczyk M, Niepel M, Sorger PK, Medvedovic M. (2017) GRcalculator: an online tool for calculating and mining dose-response data. BMC Cancer. doi: 10.1186/s12885-017-3689-3

*These authors contributed equally to this work.

Website design and online tool development

Nick Clark¹, Marc Hafner², Michal Kouril¹, Mario Niepel², Elizabeth Williams², Jeremy Muhlich² and Mario Medvedovic¹

¹ LINCS-BD2K Data Coordination and Integration Center; ² HMS LINCS Center, Harvard Medical School

Related web-tools

LINCS data portal - A unified resource for accessing all LINCS dataset packages and entities.
http://lincsportal.ccs.miami.edu/dcic-portal/

iLINCS - A data analysis platform aimed at developing statistical methods and computational tools for integrative analysis of the data produced by the LINCS program.
http://www.ilincs.org/

BD2K-LINCS Project

HMS-LINCS Small Molecule Library
http://lincs.hms.harvard.edu/db/sm/

NIH LINCS Consortium
http://www.lincsproject.org/

HMS LINCS Center
http://lincs.hms.harvard.edu/

LINCS Data and Signature Generation Centers (DSGCs)
http://www.lincsproject.org/LINCS/centers/data-and-signature-generating-centers

BD2K-LINCS Data Coordination and Integration Center (DCIC)
http://lincs-dcic.org/

Harvard Medical School

Laboratory of Systems Pharmacology (LSP)
http://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/

Sorger Lab
http://sorger.med.harvard.edu/

University of Cincinnati

Laboratory for Statistical Genomics and Systems Biology
http://eh3.uc.edu/