Package: cypress
Type: Package
Title: Cell-Type-Specific Power Assessment
Version: 1.5.0
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
git_url: https://git.bioconductor.org/packages/cypress
git_branch: devel
git_last_commit: 7533a01
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-04 22:28:26 UTC; biocbuild
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 4.5.0; ; 2025-06-05 12:46:37 UTC; windows
