Package: cypress 1.1.1

Shilin Yu

cypress: Cell-Type-Specific Power Assessment

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.

Authors:Shilin Yu [aut, cre], Guanqun Meng [aut], Wen Tang [aut]

cypress_1.1.1.tar.gz
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cypress_1.1.1.tgz(r-4.4-any)cypress_1.1.1.tgz(r-4.3-any)
cypress_1.1.1.tar.gz(r-4.5-noble)cypress_1.1.1.tar.gz(r-4.4-noble)
cypress_1.1.1.tgz(r-4.4-emscripten)cypress_1.1.1.tgz(r-4.3-emscripten)
cypress.pdf |cypress.html✨
cypress/json (API)
NEWS

# Install 'cypress' in R:
install.packages('cypress', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/renlyly/cypress/issues

Datasets:
  • ASD_prop - SimFromData example raw input data
  • GSE60424Power - Power calculation results from immune-related disease
  • GSE60424_param - Simulation parameters estimated from immune-related disease
  • asd_nopropPower - Power calculation results From ASD data
  • asd_noprop_param - Simulation parameters estimated from ASD study
  • ibd_propPower - Power calculation results from pediatric inflammatory bowel disease
  • ibd_prop_param - Simulation parameters estimated from pediatric inflammatory bowel disease

On BioConductor:cypress-1.1.1(bioc 3.20)cypress-1.0.0(bioc 3.19)

bioconductor-package

9 exports 1.45 score 129 dependencies

Last updated 1 months agofrom:dd1c0e1351

Exports:getcypressplotFDCplotPowerplotTDRquickPowersetcypressshowsimFromDatasimFromParam

Dependencies:abindadmiscaskpassbackportsBHBiobaseBiocGenericsBiocParallelbitbit64broombroom.helpersCDMcheckmateclassclicliprcodetoolscolorspaceconfigcorpcorcpp11crayoncurldata.tableDelayedArrayDESeq2doParalleldplyre1071edgeREpiDISHfansifarverforcatsforeachformatRfutile.loggerfutile.optionsgdatagenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGGallyggplot2ggstatsgluegmodelsgtablegtoolshavenhmshttrIRangesisobanditeratorsjsonlitelabelinglabelledlambda.rlatticelifecyclelimmalocfdrlocfitmagrittrMASSMatrixmatrixcalcMatrixGenericsmatrixStatsmgcvmimemunsellmvtnormnlmenloptrnnlsopensslpatchworkpbapplypbvpillarpkgconfigplyrpolycorpracmapreprocessCoreprettyunitsprogressPROPERproxypurrrquadprogR6RColorBrewerRcppRcppArmadilloreadrrlangrsvdS4ArraysS4VectorsscalessirtsnowSparseArraystatmodstringistringrSummarizedExperimentsysTAMTCAtibbletidyrtidyselectTOASTtzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVectoryamlzlibbioc

Readme and manuals

Help Manual

Help pageTopics
cypress: cell-type-specific power assessmentcypress-package cypress
Simulation parameters estimated from ASD studyasd_noprop_param asd_param quickParaASD
Power calculation results From ASD dataasdPower asd_nopropPower quickPowerASD
SimFromData example raw input dataASD_prop ASD_prop_se
Classes for cypress PackageAllClasses cypress-class cypress_out-class est_out-class
Get a slot from cypress outputcypress-methods getcypress getcypress,cypress_out-method getcypress,design_in-method getcypress,est_out-method setcypress setcypress,cypress_out-method setcypress,design_in-method setcypress,est_out-method show,cypress_out-method show,est_out-method
Simulation parameters estimated from immune-related disease (IAD) study (GSE60424)GSE60424_param quickParaGSE60424
Power calculation results from immune-related disease (IAD) study (GSE60424)GSE60424Power iad_param quickPowerGSE60424
Simulation parameters estimated from pediatric inflammatory bowel disease (IBD) study (GSE57945)ibd_param ibd_prop_param quickParaIBD
Power calculation results from pediatric inflammatory bowel disease (IBD) study (GSE57945)ibdPower ibd_propPower quickPowerIBD
plotFDC: Generate FDC results figureplotFDC
plotPower: Generate statistical power results figureplotPower
plotTDR: Generate TDR results figureplotTDR
Obtain pre-calculated results from three available datasetsquickPower
Power calculation results on input datasimFromData
Power calculation results on pre-calculated parameterssimFromParam