Package: CPSM
Type: Package
Title: CPSM: Cancer patient survival model 
Version: 1.3.1
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
Depends: R (>= 4.5)
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
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
