Package: cypress
Type: Package
Title: Cell-Type-Specific Power Assessment
Version: 1.7.0
Date: 2024-05-27
Authors@R: c( person("Shilin", "Yu", role=c("aut", "cre"),email=
  "sy597@georgetown.edu",comment=c(ORCID="0000-0002-5494-1960")),
            person("Guanqun", "Meng", role="aut",email="gxm324@case.edu"),
            person("Wen", "Tang", role="aut",email="wxt175@case.edu"))
License: GPL-2 | GPL-3
Depends: R(>= 4.4.0)
Imports: stats, abind, sirt, MASS,TOAST, tibble, parallel,
        preprocessCore, SummarizedExperiment, TCA, PROPER,
        methods,dplyr, utils, RColorBrewer, graphics, edgeR,
        BiocParallel, checkmate, mvtnorm, DESeq2, rlang, e1071
Suggests: knitr, rmarkdown, MatrixGenerics, htmltools, RUnit,
        BiocGenerics, BiocManager, BiocStyle, Biobase
Collate: AllClasses.R AllGenerics.R CIBERSORT.R csRNA_seq_sim.R
        cypress_design.R cypress_wrapper.R cypressEmbedded.R metrics.R
        cypress-methods.R PlotTDR.R DE_arg.R TOAST_implement.R user.R
        util_datasim.R util_EST.R PlotFDC.R PlotPower.R
biocViews: Software, GeneExpression, DataImport, RNASeq, Sequencing
Description: CYPRESS is a cell-type-specific power tool. This package
        aims to perform power analysis for the cell-type-specific data.
        It calculates FDR, FDC, and power, under various study design
        parameters, including but not limited to sample size, and
        effect size. It takes the input of a SummarizeExperimental(SE)
        object with observed mixture data (feature by sample matrix),
        and the cell-type mixture proportions (sample by cell-type
        matrix). It can solve the cell-type mixture proportions from
        the reference free panel from TOAST and conduct tests to
        identify cell-type-specific differential expression (csDE)
        genes.
Encoding: UTF-8
LazyData: FALSE
VignetteBuilder: knitr
URL: https://github.com/renlyly/cypress
BugReports: https://github.com/renlyly/cypress/issues
Config/pak/sysreqs: cmake libicu-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:29:05 UTC
RemoteUrl: https://github.com/bioc/cypress
RemoteRef: HEAD
RemoteSha: 40f21f4c715de3dbf4dbc743092d17a2b549ec59
NeedsCompilation: no
Packaged: 2025-11-02 14:50:42 UTC; root
Author: Shilin Yu [aut, cre] (ORCID: <https://orcid.org/0000-0002-5494-1960>),
  Guanqun Meng [aut],
  Wen Tang [aut]
Maintainer: Shilin Yu <sy597@georgetown.edu>
Built: R 4.6.0; ; 2025-11-02 14:53:01 UTC; windows
