Package: cypress 1.9.0

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_1.9.0.tar.gz
cypress_1.9.0.zip(r-4.7)cypress_1.9.0.zip(r-4.6)cypress_1.9.0.zip(r-4.5)
cypress_1.9.0.tgz(r-4.6-any)cypress_1.9.0.tgz(r-4.5-any)
cypress_1.9.0.tar.gz(r-4.7-any)cypress_1.9.0.tar.gz(r-4.6-any)
cypress_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cypress/json (API)

# Install 'cypress' in R:

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

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

Datasets:

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

On BioConductor:cypress-1.9.0(bioc 3.24)cypress-1.8.0(bioc 3.23)

software geneexpression dataimport rnaseq sequencing

4.00 score 1 stars 2 scripts 9 exports 128 dependencies

Last updated from:b8b699f3d2. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	198
linux-devel-x86_64	OK	719
source / vignettes	OK	467
linux-release-x86_64	OK	689
macos-release-arm64	OK	398
macos-oldrel-arm64	OK	423
windows-devel	OK	759
windows-release	OK	707
windows-oldrel	OK	703
wasm-release	OK	200

Exports:getcypress plotFDC plotPower plotTDR quickPower setcypress show simFromData simFromParam

Dependencies:abind admisc annotate AnnotationDbi askpass backports BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob cachem CDM checkmate class cli codetools config corpcor cpp11 crayon curl data.table DBI DelayedArray DESeq2 doParallel dplyr e1071 edgeR EpiDISH farver fastmap forcats foreach formatR futile.logger futile.options gdata genefilter generics GenomicRanges GGally ggplot2 ggstats glue gmodels gtable gtools hms httr IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfdr locfit magrittr MASS Matrix matrixcalc MatrixGenerics matrixStats memoise mime mvtnorm nloptr nnls openssl patchwork pbapply pbv pillar pkgconfig png polycor pracma preprocessCore prettyunits progress PROPER proxy purrr quadprog R6 RColorBrewer Rcpp RcppArmadillo rlang RSQLite rsvd S4Arrays S4Vectors S7 scales Seqinfo sirt snow SparseArray statmod stringi stringr SummarizedExperiment survival sys TAM TCA tibble tidyr tidyselect TOAST utf8 vctrs viridisLite withr XML xtable XVector yaml

cypress Package User's Guide

Rendered fromcypress.Rmdusingknitr::rmarkdown

Last update: 2024-05-27
Started: 2023-12-24

Help page	Topics
cypress: cell-type-specific power assessment	cypress-package cypress
Simulation parameters estimated from ASD study	asd_noprop_param asd_param quickParaASD
Power calculation results From ASD data	asdPower asd_nopropPower quickPowerASD
SimFromData example raw input data	ASD_prop ASD_prop_se
Classes for cypress Package	AllClasses cypress-class cypress_out-class est_out-class
Get a slot from cypress output	cypress-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 figure	plotFDC
plotPower: Generate statistical power results figure	plotPower
plotTDR: Generate TDR results figure	plotTDR
Obtain pre-calculated results from three available datasets	quickPower
Power calculation results on input data	simFromData
Power calculation results on pre-calculated parameters	simFromParam

Package: cypress 1.9.0

cypress: Cell-Type-Specific Power Assessment

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)