Skip to main content

Table 1 Description of the 14 batch-effect correction methods

From: A benchmark of batch-effect correction methods for single-cell RNA sequencing data

ToolsProgramming languageBatch-effect-corrected outputMethodsReference package version
Seurat 2 (CCA, MultiCCA)RNormalized canonical components (CCs)Canonical correlation analysis and dynamic time warpingButler et al. [4], Seurat package version 2.3.4
Seurat 3 (Integration)RNormalized gene expression matrixCanonical correlation analysis and mutual nearest neighbors-anchorsStuart et al. [12], Seurat package version 3.0.1
HarmonyRNormalized feature reduction vectors (Harmony)Iterative clustering in dimensionally reduced spaceKorsunsky et al. [13], Harmony version 0.99.9
MNN CorrectRNormalized gene expression matrixMutual nearest neighbor in gene expression spaceHaghverdi et al. [5], Scran package version 1.12.0
fastMNNRNormalized principal componentsMutual nearest neighbor in dimensionally reduced spaceHaghverdi et al. [5], Lun ATL [7], Scran package version 1.12.0
ComBatRNormalized gene expression matrixAdjusts for known batches using an empirical Bayesian frameworkJohnson et al. [1]
limmaRNormalized gene expression matrixLinear model/empirical Bayes modelSmyth et al. [2], limma version 3.38.3
scGenPythonNormalized gene expression matrixVariational auto-encoders neural network model and latent spaceLotfollahi et al. [16], 2019, scGen version 1.0.0
ScanoramaPython/RNormalized gene expression matrixMutual nearest neighbor and panoramic stitchingHie et al. [9], Scanorama version 1.4.
MND-ResNetPythonNormalized principal componentsResidual neural network for calibrationShaham et al. [15] updated code to Python 3
ZINB-WaVERNormalized feature reduction vectors (ZINB-WaVE)/normalized gene expression matrixZero-inflated negative binomial model, extension of RUV modelRisso et al. [6], ZINB-WaVE version 1.6.0
scMergeRNormalized gene expression matrixStably expressed genes (scSEGs) and RUVIII modelLin et al. [18], scMerge version 1.1.3
LIGERRNormalized feature reduction vectors (LIGER)Integrative non-negative matrix factorization (iNMF) and joint clustering + quantile alignmentWelch et al. [14], liger version 1.0
BBKNNPython/RConnectivity graph and normalized dimension reduction vectors (UMAP)Batch balanced k-nearest neighborsPolański et al. [10], bioRxiv. BBKNN version 1.3.2