Package: CPSM
Type: Package
Title: CPSM: Cancer patient survival model
Version: 1.1.2
Authors@R: c(person("Harpreet", "Kaur", email = "hks04180@gmail.com", 
         role = c("aut", "cre"),
         comment = c(ORCID = "0000-0003-0421-8341")),
         person("Pijush", "Das", email = "topijush@gmail.com",
         role = c("aut")),
	 person("Kevin", "Camphausen", email = "camphauk@mail.nih.gov",
         role = c("aut")),
         person("Uma", "Shankavaram" , email = "uma@mail.nih.gov",
         role = c("aut")))
Description: 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.
License: GPL-3 | file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports: SummarizedExperiment, grDevices, reshape2 , survival ,
        survminer , ggplot2 , MTLR , glmnet , rms , preprocessCore ,
        Matrix , stats, Hmisc, ggfortify, randomForestSRC, caret, MASS,
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle
URL: https://github.com/hks5august/CPSM/
BugReports: https://github.com/hks5august/CPSM/issues
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: Normalization, Survival, GeneExpression,
        Preprocessing,FeatureExtraction, Software, Visualization
git_url: https://git.bioconductor.org/packages/CPSM
git_branch: devel
git_last_commit: 2044bc8
git_last_commit_date: 2025-05-01
Repository: Bioconductor 3.22
Date/Publication: 2025-05-04
NeedsCompilation: no
Packaged: 2025-05-04 20:47:37 UTC; biocbuild
Author: Harpreet Kaur [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0421-8341>),
  Pijush Das [aut],
  Kevin Camphausen [aut],
  Uma Shankavaram [aut]
Maintainer: Harpreet Kaur <hks04180@gmail.com>
Depends: R (>= 3.5.0)
