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bioc
PharmacoGx:Analysis of Large-Scale Pharmacogenomic Data
Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.
Maintained by Benjamin Haibe-Kains. Last updated 3 months ago.
geneexpressionpharmacogeneticspharmacogenomicssoftwareclassificationdatasetspharmacogenomicpharmacogxcpp
68 stars 11.39 score 442 scripts 3 dependentsbioc
CoreGx:Classes and Functions to Serve as the Basis for Other 'Gx' Packages
A collection of functions and classes which serve as the foundation for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future 'Gx' suite programs. Major features include a 'CoreSet' class, from which 'RadioSet' and 'PharmacoSet' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) <doi:10.1093/bioinformatics/btv723>. Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
softwarepharmacogenomicsclassificationsurvival
6.36 score 63 scripts 6 dependentsbioc
ToxicoGx:Analysis of Large-Scale Toxico-Genomic Data
Contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation, visualization and statistical analysis of toxicogenomic data.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
geneexpressionpharmacogeneticspharmacogenomicssoftware
4.36 score 23 scripts