Package: batchelor 1.21.0
batchelor: Single-Cell Batch Correction Methods
Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression values. Functions are also provided to perform global rescaling to remove differences in depth between batches, and to perform a principal components analysis that is robust to differences in the numbers of cells across batches.
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batchelor.pdf |batchelor.html✨
batchelor/json (API)
NEWS
# Install 'batchelor' in R: |
install.packages('batchelor', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:batchelor-1.21.0(bioc 3.20)batchelor-1.20.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:8b03562f60
Exports:applyMultiSCEbatchCorrectcheckBatchConsistencycheckIfSCEcheckRestrictionsClassicMnnParamclusterAbundanceTestclusterAbundanceVarclusterMNNconvertPCsToSCEcorrectExperimentscosineNormdivideIntoBatchesfastMNNFastMnnParamfindMutualNNintersectRowsmnnCorrectmnnDeltaVariancemultiBatchNormmultiBatchPCAnoCorrectNoCorrectParamquickCorrectreducedMNNregressBatchesRegressParamrescaleBatchesRescaleParam
Dependencies:abindaskpassbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularclicodetoolscpp11crayoncurlDelayedArrayDelayedMatrixStatsformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrigraphIRangesirlbajsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpkgconfigR6RcppRcppHNSWResidualMatrixrlangrsvdS4ArraysS4VectorsScaledMatrixscuttleSingleCellExperimentsnowSparseArraysparseMatrixStatsSummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc
Correcting batch effects in single-cell RNA-seq data
Rendered fromcorrection.Rmd
usingknitr::rmarkdown
on Jun 17 2024.Last update: 2021-04-07
Started: 2019-02-11
Extending dispatch to more batch correction methods
Rendered fromextension.Rmd
usingknitr::rmarkdown
on Jun 17 2024.Last update: 2019-11-02
Started: 2019-02-11
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Apply function over multiple SingleCellExperiments | applyMultiSCE |
Batch correction methods | batchCorrect batchCorrect,ClassicMnnParam-method batchCorrect,FastMnnParam-method batchCorrect,NoCorrectParam-method batchCorrect,RegressParam-method batchCorrect,RescaleParam-method |
Using restriction | batchelor-restrict |
BatchelorParam methods | BatchelorParam-class ClassicMnnParam ClassicMnnParam-class FastMnnParam FastMnnParam-class NoCorrectParam NoCorrectParam-class RegressParam RegressParam-class RescaleParam RescaleParam-class |
Check batch inputs | checkBatchConsistency checkIfSCE checkRestrictions |
Cluster-based MNN | clusterMNN |
Convert corrected PCs to a SingleCellExperiment | convertPCsToSCE |
Correct SingleCellExperiment objects | correctExperiments |
Cosine normalization | cosineNorm |
Cluster-based correction diagnostics | clusterAbundanceTest clusterAbundanceVar diagnostics-cluster |
Divide into batches | divideIntoBatches |
Fast mutual nearest neighbors correction | fastMNN |
Take the intersection of rows across batches | intersectRows |
Mutual nearest neighbors correction | mnnCorrect |
Computes the variance of the paired MNN deltas | mnnDeltaVariance |
Per-batch scaling normalization | multiBatchNorm |
Multi-batch PCA | multiBatchPCA |
No correction | noCorrect |
Quickly perform batch correction | quickCorrect |
MNN correction in reduced dimensions | reducedMNN |
Regress out batch effects | regressBatches |
Scale counts across batches | rescaleBatches |