Single-Cell Batch Correction Methods

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Documentation for package ‘batchelor’ version 1.25.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

applyMultiSCE	Apply function over multiple SingleCellExperiments
batchCorrect	Batch correction methods
batchCorrect-method	Batch correction methods
batchelor-restrict	Using restriction
BatchelorParam-class	BatchelorParam methods
checkBatchConsistency	Check batch inputs
checkIfSCE	Check batch inputs
checkRestrictions	Check batch inputs
ClassicMnnParam	BatchelorParam methods
ClassicMnnParam-class	BatchelorParam methods
clusterAbundanceTest	Cluster-based correction diagnostics
clusterAbundanceVar	Cluster-based correction diagnostics
clusterMNN	Cluster-based MNN
convertPCsToSCE	Convert corrected PCs to a SingleCellExperiment
correctExperiments	Correct SingleCellExperiment objects
cosineNorm	Cosine normalization
diagnostics-cluster	Cluster-based correction diagnostics
divideIntoBatches	Divide into batches
fastMNN	Fast mutual nearest neighbors correction
FastMnnParam	BatchelorParam methods
FastMnnParam-class	BatchelorParam methods
intersectRows	Take the intersection of rows across batches
mnnCorrect	Mutual nearest neighbors correction
mnnDeltaVariance	Computes the variance of the paired MNN deltas
multiBatchNorm	Per-batch scaling normalization
multiBatchPCA	Multi-batch PCA
noCorrect	No correction
NoCorrectParam	BatchelorParam methods
NoCorrectParam-class	BatchelorParam methods
quickCorrect	Quickly perform batch correction
reducedMNN	MNN correction in reduced dimensions
regressBatches	Regress out batch effects
RegressParam	BatchelorParam methods
RegressParam-class	BatchelorParam methods
rescaleBatches	Scale counts across batches
RescaleParam	BatchelorParam methods
RescaleParam-class	BatchelorParam methods