Package: CPSM
Type: Package
Title: CPSM: Cancer patient survival model
Version: 1.2.0
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", "ctb")))
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,
        SurvMetrics, 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
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libjpeg-dev
        libpng-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:34:56 UTC
RemoteUrl: https://github.com/bioc/CPSM
RemoteRef: RELEASE_3_22
RemoteSha: 5c19f2fe6b5f34f58f9bbf9567f990e1c59d2836
NeedsCompilation: no
Packaged: 2026-01-24 21:09:49 UTC; root
Author: Harpreet Kaur [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0421-8341>),
  Pijush Das [aut],
  Kevin Camphausen [aut],
  Uma Shankavaram [aut, ctb]
Maintainer: Harpreet Kaur <hks04180@gmail.com>
Depends: R (>= 3.5.0)
Built: R 4.5.2; ; 2026-01-24 21:12:02 UTC; windows
