# Single-Cell Batch Correction Methods

## Documentation for package ‘batchelor’ version 1.8.1

- 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