Package: Canek 0.2.5
Canek: Batch Correction of Single Cell Transcriptome Data
Non-linear/linear hybrid method for batch-effect correction that uses Mutual Nearest Neighbors (MNNs) to identify similar cells between datasets. Reference: Loza M. et al. (NAR Genomics and Bioinformatics, 2020) <doi:10.1093/nargab/lqac022>.
Authors:
Canek_0.2.5.tar.gz
Canek_0.2.5.zip(r-4.5)Canek_0.2.5.zip(r-4.4)Canek_0.2.5.zip(r-4.3)
Canek_0.2.5.tgz(r-4.4-any)Canek_0.2.5.tgz(r-4.3-any)
Canek_0.2.5.tar.gz(r-4.5-noble)Canek_0.2.5.tar.gz(r-4.4-noble)
Canek_0.2.5.tgz(r-4.4-emscripten)Canek_0.2.5.tgz(r-4.3-emscripten)
Canek.pdf |Canek.html✨
Canek/json (API)
NEWS
| # Install 'Canek' in R: |
| install.packages('Canek', repos = c('https://martinloza.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/martinloza/canek/issues
- SimBatches - Dataset with simulated single cell RNA-seq from 2 batches.
batch-effectsbioinformaticssingle-cell-rna-seqtranscriptomics
Last updated 10 months agofrom:26075598fe. Checks:OK: 6 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | OK | Oct 31 2024 |
| R-4.5-linux | WARNING | Oct 31 2024 |
| R-4.4-win | OK | Oct 31 2024 |
| R-4.4-mac | OK | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:CorrectBatchCorrectBatchesRunCanek
Dependencies:assortheadBHBiocGenericsBiocNeighborsBiocParallelblusterclasscliclustercodetoolscpp11DEoptimRdiptestflexmixFNNformatRfpcfutile.loggerfutile.optionsgenericsglueigraphirlbakernlablambda.rlatticelifecyclemagrittrMASSMatrixmatrixStatsmclustmodeltoolsnnetnumberspkgconfigprabclusRcpprlangrobustbaseS4Vectorssnowvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| CheckZeroCV | CheckZeroCV |
| CorrectBatch | CorrectBatch |
| CorrectBatches | CorrectBatches |
| Correction vector estimation | EkfBE |
| Title Fuzzy | Fuzzy |
| MeanBE | MeanBE |
| Correction vector estimation | MedianBE |
| Title PairsFiltering | PairsFiltering |
| RunCanek | RunCanek RunCanek.list RunCanek.Seurat RunCanek.SingleCellExperiment |
| Dataset with simulated single cell RNA-seq from 2 batches. | SimBatches |
