Package: cypress 1.3.0

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_1.3.0.tar.gz
cypress_1.3.0.zip(r-4.5)cypress_1.3.0.zip(r-4.4)cypress_1.1.1.zip(r-4.3)
cypress_1.3.0.tgz(r-4.4-any)cypress_1.1.1.tgz(r-4.3-any)
cypress_1.3.0.tar.gz(r-4.5-noble)cypress_1.3.0.tar.gz(r-4.4-noble)
cypress_1.3.0.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-1.3.0(bioc 3.21)cypress-1.2.0(bioc 3.20)

softwaregeneexpressiondataimportrnaseqsequencing

3.88 score 1 stars 2 scripts 156 downloads 9 exports 119 dependencies

Last updated 23 days agofrom:f8d19ceea7. Checks:ERROR: 2 WARNING: 5. Indexed: yes.

TargetResultDate
Doc / VignettesFAILOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxERROROct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGSep 25 2024
R-4.3-macWARNINGSep 25 2024

Exports:getcypressplotFDCplotPowerplotTDRquickPowersetcypressshowsimFromDatasimFromParam

Dependencies:abindadmiscaskpassbackportsBHBiobaseBiocGenericsBiocParallelCDMcheckmateclassclicodetoolscolorspaceconfigcorpcorcpp11crayoncurldata.tableDelayedArrayDESeq2doParalleldplyre1071edgeREpiDISHfansifarverforcatsforeachformatRfutile.loggerfutile.optionsgdatagenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGGallyggplot2ggstatsgluegmodelsgtablegtoolshmshttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelimmalocfdrlocfitmagrittrMASSMatrixmatrixcalcMatrixGenericsmatrixStatsmgcvmimemunsellmvtnormnlmenloptrnnlsopensslpatchworkpbapplypbvpillarpkgconfigplyrpolycorpracmapreprocessCoreprettyunitsprogressPROPERproxypurrrquadprogR6RColorBrewerRcppRcppArmadillorlangrsvdS4ArraysS4VectorsscalessirtsnowSparseArraystatmodstringistringrSummarizedExperimentsysTAMTCAtibbletidyrtidyselectTOASTUCSC.utilsutf8vctrsviridisLitewithrXVectoryamlzlibbioc

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