CPSM
This is the released version of CPSM; for the devel version, see CPSM.
CPSM: Cancer patient survival model
Bioconductor version: Release (3.23)
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("CPSM")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | FeatureExtraction, GeneExpression, Normalization, Preprocessing, Software, Survival, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL-3 | file LICENSE |
| Depends | R (>= 4.5) |
| Imports | SummarizedExperiment, grDevices, reshape2, survival, survminer, ggplot2, MTLR, glmnet, rms, preprocessCore, Matrix, stats, Hmisc, ggfortify, randomForestSRC, caret, SurvMetrics, 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_1.4.0.tar.gz |
| Windows Binary (x86_64) | CPSM_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | CPSM_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | CPSM_1.4.0.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 |