Installation | Getting Started | Preprocessing | Running SAVER | Using SAVER estimates | Additional Settings | Normalization | Predicting certain genes | Using other predictions | Creating your own parallel backend | Combining SAVER objects | Sampling example | Correlation example
Package: SAVER 1.1.3
SAVER: Single-Cell RNA-Seq Gene Expression Recovery
An implementation of a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data. See Huang M, et al (2018) <doi:10.1038/s41592-018-0033-z> for more details.
Authors:
SAVER_1.1.3.tar.gz
SAVER_1.1.3.zip(r-4.7)SAVER_1.1.3.zip(r-4.6)SAVER_1.1.3.zip(r-4.5)
SAVER_1.1.3.tgz(r-4.6-any)SAVER_1.1.3.tgz(r-4.5-any)
SAVER_1.1.3.tar.gz(r-4.7-any)SAVER_1.1.3.tar.gz(r-4.6-any)
SAVER_1.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SAVER/json (API)
| # Install 'SAVER' in R: |
| install.packages('SAVER', repos = c('https://mohuangx.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mohuangx/saver/issues
Datasets:
- linnarsson - Mouse brain single-cell RNA-seq dataset
- linnarsson_saver - SAVER recovered mouse brain single-cell RNA-seq dataset
Last updated from:f28d719c1b. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 135 | ||
| source / vignettes | OK | 152 | ||
| linux-release-x86_64 | OK | 119 | ||
| macos-release-arm64 | OK | 180 | ||
| macos-oldrel-arm64 | OK | 136 | ||
| windows-devel | OK | 83 | ||
| windows-release | OK | 76 | ||
| windows-oldrel | OK | 119 | ||
| wasm-release | OK | 132 |
Exports:calc.acalc.bcalc.estimatecalc.estimate.meancalc.estimate.nullcalc.kcalc.loglik.acalc.loglik.bcalc.loglik.kcalc.maxcorcalc.postcombine.savercor.cellscor.genesexpr.predictget.musample.saversaversaver.fitsaver.fit.meansaver.fit.null
Dependencies:codetoolsdoParallelforeachglmnetiteratorslatticeMatrixRcppRcppEigenshapesurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SAVER: Single-cell Analysis Via Expression Recovery | SAVER-package |
| Optimizes variance | calc.a calc.b calc.k |
| Calculate estimate | calc.estimate calc.estimate.mean calc.estimate.null |
| Calculates marginal likelihood | calc.loglik.a calc.loglik.b calc.loglik.k |
| Calculate maximum correlation | calc.maxcor |
| Calculates SAVER posterior | calc.post |
| Combines SAVER | combine.saver |
| Calculates gene-to-gene and cell-to-cell SAVER correlation | cor.cells cor.genes |
| Calculates SAVER prediction. | expr.predict |
| Output prior predictions | get.mu |
| Mouse brain single-cell RNA-seq dataset | linnarsson |
| SAVER recovered mouse brain single-cell RNA-seq dataset | linnarsson_saver |
| Samples from SAVER | sample.saver |
| Runs SAVER | saver |
| Fits SAVER | saver.fit saver.fit.mean saver.fit.null |
