CPSM
This is the development version of CPSM; for the stable release version, see CPSM.
CPSM: Cancer patient survival model
Bioconductor version: Development (3.22)
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]
Maintainer: Harpreet Kaur <hks04180 at gmail.com>
citation("CPSM")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("CPSM")
For older versions of R, please refer to the appropriate Bioconductor release.
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 | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Normalization, Prediction, Preprocessing, Software, Survival, Visualization |
| Version | 1.1.1 |
| In Bioconductor since | BioC 3.21 (R-4.5) (< 6 months) |
| License | GPL-3 | file LICENSE |
| Depends | R (>= 3.5.0) |
| Imports | SummarizedExperiment, grDevices, reshape2, survival, survminer, ggplot2, MTLR, glmnet, rms, preprocessCore, Matrix, svglite, stats, Hmisc, ROCR, ggfortify, randomForestSRC, caret, MASS |
| System Requirements | |
| URL | https://github.com/hks5august/CPSM/ |
| Bug Reports | https://github.com/hks5august/CPSM/issues |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CPSM_1.1.1.tar.gz |
| Windows Binary (x86_64) | CPSM_1.1.1.zip |
| macOS Binary (x86_64) | CPSM_1.1.1.tgz |
| macOS Binary (arm64) | CPSM_1.1.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CPSM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CPSM |
| Bioc Package Browser | https://code.bioconductor.org/browse/CPSM/ |
| Package Short Url | https://bioconductor.org/packages/CPSM/ |
| Package Downloads Report | Download Stats |