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A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype. The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <doi:10.1126/science.1132939>). Please cite using <doi:10.1093/bioinformatics/btab011>.
| Version: | 0.1.9 |
| Depends: | R (≥ 2.10) |
| Imports: | BiocGenerics, GSVA, grDevices, graphics, igraph, parallel, pheatmap, rvest, stats, xml2, ChemmineR |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| Published: | 2024-04-17 |
| DOI: | 10.32614/CRAN.package.SubtypeDrug |
| Author: | Xudong Han, Junwei Han, Chonghui Liu |
| Maintainer: | Junwei Han <hanjunwei1981 at 163.com> |
| BugReports: | https://github.com/hanjunwei-lab/SubtypeDrug/issues |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | no |
| CRAN checks: | SubtypeDrug results |
| Reference manual: | SubtypeDrug.pdf |
| Vignettes: |
SubtypeDrug: a software package for prioritization of candidate cancer subtype-specific drugs |
| Package source: | SubtypeDrug_0.1.9.tar.gz |
| Windows binaries: | r-devel: SubtypeDrug_0.1.9.zip, r-release: SubtypeDrug_0.1.9.zip, r-oldrel: SubtypeDrug_0.1.9.zip |
| macOS binaries: | r-release (arm64): SubtypeDrug_0.1.9.tgz, r-oldrel (arm64): not available, r-release (x86_64): SubtypeDrug_0.1.9.tgz, r-oldrel (x86_64): not available |
| Old sources: | SubtypeDrug archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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