CPSM
This is the development version of CPSM; for the stable release version, see CPSM.
All Bioconductor versions of CPSM
3.24 (devel), 3.23 (release), 3.22, 3.21
CPSM: Cancer patient survival model
Bioconductor version: 3.24 · Package version: 1.5.0
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.
Author: Harpreet Kaur [aut, cre] 
, Pijush Das [aut], Kevin Camphausen [aut], Uma Shankavaram [aut, ctb]
Maintainer: Harpreet Kaur <hks04180 at gmail.com>
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 1.5.0, https://bioconductor.org/packages/CPSM.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("CPSM")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.5.0 |
| License | GPL-3 | file LICENSE |
| URL | https://github.com/hks5august/CPSM/ |
| Bug Reports | https://github.com/hks5august/CPSM/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1 year) |
| Downloads rank | 2033 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | FeatureExtraction, GeneExpression, Normalization, Preprocessing, Software, Survival, Visualization |
| Package Short Url | https://bioconductor.org/packages/CPSM/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CPSM")| CPSM: Cancer patient survival model | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | CPSM_1.5.0.tar.gz |
| Windows binary (x86_64) | CPSM_1.5.0.zip |
| macOS binary (arm64) | CPSM_1.5.0.tgz |
| macOS binary (x86_64) | CPSM_1.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CPSM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CPSM |
| Package Downloads Report | Download Stats |
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