CPSM
CPSM: Cancer patient survival model
Bioconductor version: 3.23 · Package version: 1.4.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
CPSM provides a comprehensive computational pipeline for predicting survival probability and risk groups in cancer patients. The package includes steps for data preprocessing, training/test split, and normalization. It enables feature selection using univariate survival analysis and computes a LASSO-based prognostic index (PI) score. CPSM supports the development of predictive models using various feature sets and offers a suite of visualization tools, including survival curves based on predicted probabilities, barplots for predicted mean and median survival times, KM plots overlaid with individual survival predictions, and nomograms for estimating 1-, 3-, 5-, and 10-year survival probabilities. This makes CPSM a versatile tool for survival analysis in cancer research.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CPSM")Details
| Maintainer | Harpreet Kaur <hks04180@gmail.com> |
| Author | Harpreet Kaur [aut, cre] (ORCID: <https://orcid.org/0000-0003-0421-8341>), Pijush Das [aut], Kevin Camphausen [aut], Uma Shankavaram [aut, ctb] |
| License | GPL-3 | file LICENSE |
| URL | https://github.com/hks5august/CPSM/ |
| Bug Reports | https://github.com/hks5august/CPSM/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | FeatureExtraction, GeneExpression, Normalization, Preprocessing, Software, Survival, Visualization |
| Package Short Url | https://bioconductor.org/packages/CPSM/ |
Citation
From within R, enter citation("CPSM"):
Harpreet Kaur, Pijush Das, Kevin Camphausen, Uma Shankavaram. CPSM: CPSM: Cancer patient survival model. doi:10.18129/B9.bioc.CPSM, R package version 1.4.0, https://bioconductor.org/packages/CPSM.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | CPSM_1.4.0.tar.gz |
| Windows binary (x86_64) | CPSM_1.4.0.zip |
| macOS binary (arm64) | CPSM_1.4.0.tgz |
| macOS binary (x86_64) | CPSM_1.4.0.tgz |
Dependencies
Depends: R (>= 4.5)
Imports: SummarizedExperiment, grDevices, reshape2, survival, survminer, ggplot2, MTLR, glmnet, rms, preprocessCore, Matrix, stats, Hmisc, ggfortify, randomForestSRC, caret, SurvMetrics, MASS
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle