CPSM
This is the development version of CPSM; to use it, please install the devel version of Bioconductor.
CPSM: Cancer patient survival model
Bioconductor version: Development (3.21)
The CPSM package provides a comprehensive computational pipeline for predicting the survival probability of cancer patients. It offers a series of steps including data processing, splitting data into training and test subsets, and normalization of data. The package enables the selection of significant features based on univariate survival analysis and generates a LASSO prognostic index score. It supports the development of predictive models for survival probability using various features and provides visualization tools to draw survival curves based on predicted survival probabilities. Additionally, SPM includes functionalities for generating bar plots that depict the predicted mean and median survival times of patients, making it a versatile tool for survival analysis in cancer research.
Author: Harpreet Kaur [aut, cre] (ORCID:
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 |
Details
| biocViews | GeneExpression, Normalization, Software, Survival |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| License | GPL-3 | file LICENSE |
| Depends | R (>= 3.5.0) |
| Imports | SummarizedExperiment, grDevices, reshape2, survival, survminer, ggplot2, MTLR, pec, glmnet, rms, preprocessCore, survivalROC, Matrix, svglite, stats, Hmisc, ROCR, ggfortify, 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_0.99.7.tar.gz |
| Windows Binary (x86_64) | CPSM_0.99.7.zip |
| macOS Binary (x86_64) | CPSM_0.99.7.tgz |
| macOS Binary (arm64) | CPSM_0.99.7.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 |