Single-cell RNA-seq batch effects correction methods interface

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Documentation for package ‘BatChef’ version 0.99.12

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

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adjusted_rand_index	Adjusted Rand Index (ARI)
average_silhouette_width	Average Silhouette Width (ASW)
batchCorrect	batchCorrect
batchCorrect-method	batchCorrect
BatChefParams-class	BatChefParams methods
batch_params	Batch effects strength
BBKNNParams-class	BatChefParams methods
capture_params	Capture parameters of the correction methods
clustInput	Convert into a SingleCellExperiment object for clustering
clustInput-method	Convert into a SingleCellExperiment object for clustering
CombatParams	BatChefParams methods
CombatParams-class	BatChefParams methods
combatRun	ComBat method
compute_lisi	Local Inverse Simpson Index (LISI)
compute_simpson_index	Compute the Local Inverse Simpson Index (LISI)
extract_features	Extract data characteristics
FastMNNParams	BatChefParams methods
FastMNNParams-class	BatChefParams methods
fastMNNPost	Convert fastMNN output
fastMNNPost-method	Convert fastMNN output
fastMNNRun	fastMNN method
HarmonyParams	BatChefParams methods
HarmonyParams-class	BatChefParams methods
harmonyPost	Convert Harmony output
harmonyPost-method	Convert Harmony output
harmonyRun	Harmony method
kl_gamma	Kullback-Leibler (KL) divergence) between two Gamma distributions
leiden_clustering	Leiden clustering
lib_size_params	Library size parameters
ligerInput	Convert to a LIGER compatible object
ligerInput-method	Convert to a LIGER compatible object
LigerParams	BatChefParams methods
LigerParams-class	BatChefParams methods
ligerPost	Convert the LIGER output
ligerPost-method	Convert the LIGER output
ligerRun	LIGER method
LimmaParams	BatChefParams methods
LimmaParams-class	BatChefParams methods
limmaRun	limma method
linearInput	Convert into a SingleCellExperiment object for linear model based methods
linearInput-method	Convert into a SingleCellExperiment object for linear model based methods
linearPost	Convert the output of linear models
linearPost-method	Convert the output of linear models
local_inverse_simpson_index	Median of Local Inverse Simposon Index (LISI)
log_transf	A shifted log transformation
merge_params	Parameters merging
metrics	Performance evaluation metrics.
normalized	Normalization
normalized_mutual_info	Normalized Mutual Information (NMI)
outlier_params	Highly expressed genes probability
params_btc_factors	Gamma parameters estimation of batch factors
prediction_plot	Prediction plot
ScanoramaParams-class	BatChefParams methods
sceInput	Convert into a SingleCellExperiment object
sceInput-method	Convert into a SingleCellExperiment object
ScMerge2Params	BatChefParams methods
ScMerge2Params-class	BatChefParams methods
scMerge2Post	Convert the scMerge2 output
scMerge2Post-method	Convert the scMerge2 output
scMerge2Run	scMerge2 method
SCVIParams-class	BatChefParams methods
seuratv3Input	Convert to a SeuratV3 compatible object
seuratv3Input-method	Convert to a SeuratV3 compatible object
SeuratV3Params	BatChefParams methods
SeuratV3Params-class	BatChefParams methods
seuratv3Post	Convert the SeuratV3 output
seuratv3Post-method	Convert the SeuratV3 output
seuratV3Run	Seurat V3 method
seuratv5Input	Convert to a SeuratV5 compatible object
seuratv5Input-method	Convert to a SeuratV5 compatible object
SeuratV5Params	BatChefParams methods
SeuratV5Params-class	BatChefParams methods
seuratv5Post	Convert the SeuratV5 output
seuratv5Post-method	Convert the SeuratV5 output
seuratV5Run	Seurat V5 method
simulate_data	Function to simulate data
suggested_method	Suggested method prediction
wasserstein_distance	Wasserstein distance
winsorization	Winsorization