BatChef-package	BatChef-package
adjusted_rand_index	adjusted_rand_index
average_silhouette_width	average_silhouette_width
batchCorrect	batchCorrect
batchCorrect,CombatParams-method	batchCorrect
batchCorrect,FastMNNParams-method	batchCorrect
batchCorrect,HarmonyParams-method	batchCorrect
batchCorrect,LigerParams-method	batchCorrect
batchCorrect,LimmaParams-method	batchCorrect
batchCorrect,ScMerge2Params-method	batchCorrect
batchCorrect,SeuratV3Params-method	batchCorrect
batchCorrect,SeuratV5Params-method	batchCorrect
BatChef	BatChef-package
BatChefParams-class	BatChefParams
batch_params	batch_params
BBKNNParams-class	BatChefParams
capture_params	capture_params
clustInput	clustInput
clustInput,AnnDataR6,AnnDataR6-method	clustInput
clustInput,AnnDataR6-method	clustInput
clustInput,Seurat,Seurat-method	clustInput
clustInput,Seurat-method	clustInput
clustInput,SingleCellExperiment,SingleCellExperiment-method	clustInput
clustInput,SingleCellExperiment-method	clustInput
CombatParams	BatChefParams
CombatParams-class	BatChefParams
combatRun	combatRun
compute_lisi	compute_lisi
compute_simpson_index	compute_simpson_index
extract_features	extract_features
FastMNNParams	BatChefParams
FastMNNParams-class	BatChefParams
fastMNNPost	fastMNNPost
fastMNNPost,AnnDataR6,AnnDataR6-method	fastMNNPost
fastMNNPost,AnnDataR6-method	fastMNNPost
fastMNNPost,Seurat,Seurat-method	fastMNNPost
fastMNNPost,Seurat-method	fastMNNPost
fastMNNPost,SingleCellExperiment,SingleCellExperiment-method	fastMNNPost
fastMNNPost,SingleCellExperiment-method	fastMNNPost
fastMNNRun	fastMNNRun
HarmonyParams	BatChefParams
HarmonyParams-class	BatChefParams
harmonyPost	harmonyPost
harmonyPost,AnnDataR6,AnnDataR6-method	harmonyPost
harmonyPost,AnnDataR6-method	harmonyPost
harmonyPost,Seurat,Seurat-method	harmonyPost
harmonyPost,Seurat-method	harmonyPost
harmonyPost,SingleCellExperiment,SingleCellExperiment-method	harmonyPost
harmonyPost,SingleCellExperiment-method	harmonyPost
harmonyRun	harmonyRun
kl_gamma	kl_gamma
leiden_clustering	leiden_clustering
lib_size_params	lib_size_params
ligerInput	ligerInput
ligerInput,AnnDataR6,AnnDataR6-method	ligerInput
ligerInput,AnnDataR6-method	ligerInput
ligerInput,Seurat,Seurat-method	ligerInput
ligerInput,Seurat-method	ligerInput
ligerInput,SingleCellExperiment,SingleCellExperiment-method	ligerInput
ligerInput,SingleCellExperiment-method	ligerInput
LigerParams	BatChefParams
LigerParams-class	BatChefParams
ligerPost	ligerPost
ligerPost,AnnDataR6,AnnDataR6-method	ligerPost
ligerPost,AnnDataR6-method	ligerPost
ligerPost,Seurat,Seurat-method	ligerPost
ligerPost,Seurat-method	ligerPost
ligerPost,SingleCellExperiment,SingleCellExperiment-method	ligerPost
ligerPost,SingleCellExperiment-method	ligerPost
ligerRun	ligerRun
LimmaParams	BatChefParams
LimmaParams-class	BatChefParams
limmaRun	limmaRun
linearInput	linearInput
linearInput,AnnDataR6,AnnDataR6-method	linearInput
linearInput,AnnDataR6-method	linearInput
linearInput,Seurat,Seurat-method	linearInput
linearInput,Seurat-method	linearInput
linearInput,SingleCellExperiment,SingleCellExperiment-method	linearInput
linearInput,SingleCellExperiment-method	linearInput
linearPost	linearPost
linearPost,AnnDataR6,AnnDataR6-method	linearPost
linearPost,AnnDataR6-method	linearPost
linearPost,Seurat,Seurat-method	linearPost
linearPost,Seurat-method	linearPost
linearPost,SingleCellExperiment,SingleCellExperiment-method	linearPost
linearPost,SingleCellExperiment-method	linearPost
local_inverse_simpson_index	local_inverse_simpson_index
log_transf	log_transf
merge_params	merge_params
metrics	metrics
normalized	normalized
normalized_mutual_info	normalized_mutual_info
outlier_params	outlier_params
params_btc_factors	params_btc_factors
prediction_plot	prediction_plot
ScanoramaParams-class	BatChefParams
sceInput	sceInput
sceInput,AnnDataR6,AnnDataR6-method	sceInput
sceInput,AnnDataR6-method	sceInput
sceInput,Seurat,Seurat-method	sceInput
sceInput,Seurat-method	sceInput
sceInput,SingleCellExperiment,SingleCellExperiment-method	sceInput
sceInput,SingleCellExperiment-method	sceInput
ScMerge2Params	BatChefParams
ScMerge2Params-class	BatChefParams
scMerge2Post	scMerge2Post
scMerge2Post,AnnDataR6,AnnDataR6-method	scMerge2Post
scMerge2Post,AnnDataR6-method	scMerge2Post
scMerge2Post,Seurat,Seurat-method	scMerge2Post
scMerge2Post,Seurat-method	scMerge2Post
scMerge2Post,SingleCellExperiment,SingleCellExperiment-method	scMerge2Post
scMerge2Post,SingleCellExperiment-method	scMerge2Post
scMerge2Run	scMerge2Run
SCVIParams-class	BatChefParams
seuratv3Input	seuratv3Input
seuratv3Input,AnnDataR6,AnnDataR6-method	seuratv3Input
seuratv3Input,AnnDataR6-method	seuratv3Input
seuratv3Input,Seurat,Seurat-method	seuratv3Input
seuratv3Input,Seurat-method	seuratv3Input
seuratv3Input,SingleCellExperiment,SingleCellExperiment-method	seuratv3Input
seuratv3Input,SingleCellExperiment-method	seuratv3Input
SeuratV3Params	BatChefParams
SeuratV3Params-class	BatChefParams
seuratv3Post	seuratv3Post
seuratv3Post,AnnDataR6,AnnDataR6-method	seuratv3Post
seuratv3Post,AnnDataR6-method	seuratv3Post
seuratv3Post,Seurat,Seurat-method	seuratv3Post
seuratv3Post,Seurat-method	seuratv3Post
seuratv3Post,SingleCellExperiment,SingleCellExperiment-method	seuratv3Post
seuratv3Post,SingleCellExperiment-method	seuratv3Post
seuratV3Run	seuratV3Run
seuratv5Input	seuratv5Input
seuratv5Input,AnnDataR6,AnnDataR6-method	seuratv5Input
seuratv5Input,AnnDataR6-method	seuratv5Input
seuratv5Input,Seurat,Seurat-method	seuratv5Input
seuratv5Input,Seurat-method	seuratv5Input
seuratv5Input,SingleCellExperiment,SingleCellExperiment-method	seuratv5Input
seuratv5Input,SingleCellExperiment-method	seuratv5Input
SeuratV5Params	BatChefParams
SeuratV5Params-class	BatChefParams
seuratv5Post	seuratv5Post
seuratv5Post,AnnDataR6,AnnDataR6-method	seuratv5Post
seuratv5Post,AnnDataR6-method	seuratv5Post
seuratv5Post,Seurat,Seurat-method	seuratv5Post
seuratv5Post,Seurat-method	seuratv5Post
seuratv5Post,SingleCellExperiment,SingleCellExperiment-method	seuratv5Post
seuratv5Post,SingleCellExperiment-method	seuratv5Post
seuratV5Run	seuratV5Run
simulate_data	simulate_data
suggested_method	suggested_method
wasserstein_distance	wasserstein_distance
winsorization	winsorization
