1. Introduction | 2. Citation | 3. Installation | 4. Input | 5. Test data | 6. Usage | 6.1 Imputation using scRecover | 6.1.1 With read counts matrix input | 6.1.2 With SingleCellExperiment input | 6.2 Estimate dropout gene number in a cell | 7. Output | 8. Parallelization | 8.1 For Unix and Mac users | 8.2 For Windows users | 9. Evaluation of scRecover | 9.1 On downsampling data | 9.1.1 Accuracy of dropout prediction | 9.1.2 Predicted dropout number | 9.2 On 10X data | 9.3 On SMART-seq data | 10. Help | 11. Author | 12. Session info
Package: scRecover 1.28.0
Zhun Miao
scRecover: scRecover for imputation of single-cell RNA-seq data
scRecover is an R package for imputation of single-cell RNA-seq (scRNA-seq) data. It will detect and impute dropout values in a scRNA-seq raw read counts matrix while keeping the real zeros unchanged, since there are both dropout zeros and real zeros in scRNA-seq data. By combination with scImpute, SAVER and MAGIC, scRecover not only detects dropout and real zeros at higher accuracy, but also improve the downstream clustering and visualization results.
Authors:
scRecover_1.28.0.tar.gz
scRecover_1.28.0.zip(r-4.7)scRecover_1.28.0.zip(r-4.6)scRecover_1.28.0.zip(r-4.5)
scRecover_1.28.0.tgz(r-4.6-any)scRecover_1.28.0.tgz(r-4.5-any)
scRecover_1.28.0.tar.gz(r-4.7-any)scRecover_1.28.0.tar.gz(r-4.6-any)
scRecover_1.28.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scRecover/json (API)
| # Install 'scRecover' in R: |
| install.packages('scRecover', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/miaozhun/screcover/issues
Datasets:
On BioConductor:scRecover-1.29.0(bioc 3.24)scRecover-1.28.0(bioc 3.23)
geneexpressionsinglecellrnaseqtranscriptomicssequencingpreprocessingsoftware
Last updated from:815f862bd4 (on RELEASE_3_23). Checks:1 ERROR, 2 NOTE, 2 OK, 5 FAIL. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 167 | ||
| linux-devel-x86_64 | NOTE | 263 | ||
| source / vignettes | OK | 271 | ||
| linux-release-x86_64 | NOTE | 281 | ||
| macos-release-arm64 | FAIL | 76 | ||
| macos-oldrel-arm64 | FAIL | 74 | ||
| windows-devel | FAIL | 88 | ||
| windows-release | FAIL | 73 | ||
| windows-oldrel | FAIL | 73 | ||
| wasm-release | OK | 119 |
Exports:countsSamplingestDropoutNumnormalizationscRecover
Dependencies:bbmlebdsmatrixBHBiocParallelcodetoolscpp11doParallelforeachformatRfutile.loggerfutile.optionsgamlssgamlss.datagamlss.distglmnetiteratorskernlablambda.rlatticeMASSMatrixmvtnormnlmenumDerivpenalizedpolynompreseqRpsclRcppRcppArmadilloRcppEigenrsvdSAVERshapesnowsurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| countsSampling: Downsampling the read counts in a cell | countsSampling |
| estDropoutNum: Estimate dropout gene number in a cell | estDropoutNum |
| normalization: Normalization for single-cell RNA-seq data | normalization |
| scRecover: Imputation for single-cell RNA-seq data | scRecover |
| scRecoverTest: A test dataset for scRecover | counts labels oneCell scRecoverTest |