bioc-issue-bot
commented
5 months ago Hi @renlyly
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: cypress
Type: Package
Title: Cell-Type-Specific Power Assessment
Version: 0.99.0
Date: 2023-12-21
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(>= 4.3.0)
Imports: stats, abind, sirt, lubridate, MASS, TOAST, e1071, tibble,
parallel, preprocessCore, SummarizedExperiment, TCA, PROPER, methods,dplyr,
utils, RColorBrewer, Biobase, graphics, edgeR, BiocParallel
Suggests: knitr, rmarkdown, MatrixGenerics, htmltools, RUnit, BiocGenerics
Collate: AllClasses.R CIBERSORT.R csRNA_seq_sim.R cypress_design.R
cypress_wrapper.R cypressEmbedded.R metrics.R show_methods.R PlotTDR.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 an 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 the
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
lshep
renlyly
HelenaLC
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