Load Packages | Prepare data | Compute power values through Bootstrapping | Instead of using default Wilcoxon test | PoweREST_gene | PoweREST_subset | Fit the power surface using smoothing splines | Visualize the power surface | Create interactive visualization result | Fit local power surface with XGBoost | Visualize the local power surface
Package: PoweREST 0.1.2
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. (2025) <doi:10.1371/journal.pcbi.1013293> for method details.
Authors:
PoweREST_0.1.2.tar.gz
PoweREST_0.1.2.tar.gz(r-4.7-any)PoweREST_0.1.2.tar.gz(r-4.6-any)
PoweREST_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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.
Last updated from:d72671c9ea. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 199 | ||
| source / vignettes | OK | 295 | ||
| linux-release-x86_64 | OK | 192 | ||
| wasm-release | OK | 202 |
Exports:%>%fit_powerestfit_XGBoostplotly_powerestPoweRESTPoweREST_genePoweREST_subsetpred_powerestpred_XGBoostvis_powerestvis_XGBoost
Dependencies:clicpp11data.tabledplyrfarvergenericsggplot2gluegtableisobandjsonlitelabelinglatticelifecyclemagrittrMatrixmgcvnlmepillarpkgconfigR6RColorBrewerresamplerlangS7scalesscamtibbletidyselectutf8vctrsviridisLitewithrxgboost
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 |