Package: PoweREST 0.1.0

Lan Shui

PoweREST: A Bootstrap-Based Power Estimation Tool for Spatial Transcriptomics

Power estimation and sample size calculation for 10X Visium Spatial Transcriptomics data to detect differential expressed genes between two conditions based on bootstrap resampling. See Shui et al. (2024) <doi:10.1101/2024.08.30.610564> for method details.

Authors:Lan Shui [aut, cre]

PoweREST_0.1.0.tar.gz
PoweREST_0.1.0.tar.gz(r-4.5-noble)PoweREST_0.1.0.tar.gz(r-4.4-noble)
PoweREST_0.1.0.tgz(r-4.4-emscripten)
PoweREST.pdf |PoweREST.html✨
PoweREST/json (API)

# Install 'PoweREST' in R:

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

Datasets:

power_example - An example of power results with multiple replicates number
result_example - An example of power results from PoweREST

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 5 scripts 144 downloads 11 exports 168 dependencies

Last updated 3 months agofrom:2ca025e0cf. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 09 2024
R-4.5-linux	OK	Dec 09 2024

Exports:%>%fit_powerest fit_XGBoost plotly_powerest PoweREST PoweREST_gene PoweREST_subset pred_powerest pred_XGBoost vis_powerest vis_XGBoost

Dependencies:abind askpass base64enc BH bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table decido deldir digest doParallel dotCall64 dplyr dqrng evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome foreach fs future future.apply generics ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr hms htmltools htmlwidgets httpuv httr ica igraph irlba isoband iterators jpeg jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval leiden lifecycle listenv lmtest magrittr MASS Matrix matrixStats memoise mgcv mime miniUI munsell nlme openssl parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip prettyunits progress progressr promises purrr R6 RANN rappdirs raster rayimage rayrender rayshader rayvertex RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppThread RcppTOML resample reshape2 reticulate rgl rlang rmarkdown ROCR rprojroot RSpectra Rtsne sass scales scam scattermore sctransform Seurat SeuratObject shiny sitmo sourcetools sp spacefillr spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys tensor terra terrainmeshr tibble tidyr tidyselect tiff tinytex utf8 uwot vctrs viridisLite withr xfun xgboost xtable yaml zoo

A simple workflow for PoweREST

Lan Shui

Rendered fromPoweREST.Rmdusingknitr::rmarkdownon Dec 09 2024.

Last update: 2024-09-10
Started: 2024-09-10

Citation

Readme and manuals

Help Manual

Help page	Topics
Fit the power surface	fit_powerest
Fit with XGBoost	fit_XGBoost
3D interactive visualization	plotly_powerest
An example of power results with multiple replicates number	power_example
Bootstrap resampling and power calculation upon ST data	PoweREST
Bootstrap resampling and power estimation for one single gene	PoweREST_gene
Bootstrap resampling and power calculation for a subset of genes	PoweREST_subset
Power value prediction	pred_powerest
Prediction results from XGBoost	pred_XGBoost
An example of power results from PoweREST	result_example
Visualization of the power surface	vis_powerest
Visualization of the power estimations from XGBoost	vis_XGBoost