Introduction | Related work and scope | Installation | Aggregate single-cell counts | Construct an auditable example | Review the design before fitting | Fit and inspect the ledger | Output dictionary | Inspect figures | Report missing coverage, design failure and valid effects together | Reproduce a real single-nucleus example | Read the donor-deletion results | Method and data references | Session information
Package: scDonorAudit 0.99.9
Fuhao Jiang
scDonorAudit: Audit Donor Influence in Single-Cell Pseudobulk Analyses
Audits sample and donor design for two-condition single-cell pseudobulk differential expression analyses. Fits an edgeR quasi-likelihood model to each cell type and repeats the analysis after omitting each donor. Links planned donor omissions to design checks, fit outcomes and observed gene-effect changes. Provides descriptive summaries of donor-deletion sensitivity together with the coverage of valid effects.
Authors:
scDonorAudit_0.99.9.tar.gz
scDonorAudit_0.99.9.zip(r-4.7-any)scDonorAudit_0.99.9.zip(r-4.6-any)scDonorAudit_0.99.9.zip(r-4.5-any)
scDonorAudit_0.99.9.tgz(r-4.6-any)scDonorAudit_0.99.9.tgz(r-4.5-any)
scDonorAudit_0.99.9.tar.gz(r-4.7-any)scDonorAudit_0.99.9.tar.gz(r-4.6-any)
scDonorAudit_0.99.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scDonorAudit/json (API)
| # Install 'scDonorAudit' in R: |
| install.packages('scDonorAudit', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/emr-27/scdonoraudit/issues
singlecellrnaseqgeneexpressiondifferentialexpressionqualitycontrolsoftware
Last updated from:ae6e56ac8d. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 165 | ||
| linux-devel | OK | 315 | ||
| source / vignettes | OK | 297 | ||
| linux-release | OK | 326 | ||
| macos-release | OK | 232 | ||
| macos-oldrel | OK | 212 | ||
| windows-devel | OK | 259 | ||
| windows-release | OK | 266 | ||
| windows-oldrel | OK | 217 | ||
| wasm-release | OK | 113 |
Exports:assessDonorInfluenceauditDesignplotInfluencepreparePseudobulksummarizeInfluence
Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArrayedgeRfarvergenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsR6RColorBrewerrlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraystatmodSummarizedExperimentvctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Assess the influence of omitting each donor | assessDonorInfluence |
| Audit a two-condition donor design | auditDesign |
| Plot donor coverage or gene-level influence | plotInfluence |
| Prepare donor-aware pseudobulk counts | preparePseudobulk |
| Audit donor omission in two-condition pseudobulk analyses | scDonorAudit-package scDonorAudit |
| Summarize observed donor influence on each gene | summarizeInfluence |