# Generated by roxygen2: do not edit by hand

export(CombatParams)
export(FastMNNParams)
export(HarmonyParams)
export(LigerParams)
export(LimmaParams)
export(ScMerge2Params)
export(SeuratV3Params)
export(SeuratV5Params)
export(adjusted_rand_index)
export(average_silhouette_width)
export(batchCorrect)
export(combatRun)
export(compute_lisi)
export(fastMNNRun)
export(harmonyRun)
export(leiden_clustering)
export(ligerRun)
export(limmaRun)
export(local_inverse_simpson_index)
export(metrics)
export(normalized_mutual_info)
export(scMerge2Run)
export(seuratV3Run)
export(seuratV5Run)
export(simulate_data)
export(suggested_method)
export(wasserstein_distance)
exportClasses(BBKNNParams)
exportClasses(BatChefParams)
exportClasses(CombatParams)
exportClasses(FastMNNParams)
exportClasses(HarmonyParams)
exportClasses(LigerParams)
exportClasses(LimmaParams)
exportClasses(SCVIParams)
exportClasses(ScMerge2Params)
exportClasses(ScanoramaParams)
exportClasses(SeuratV3Params)
exportClasses(SeuratV5Params)
import(Matrix)
import(Rcpp)
import(e1071)
import(methods)
importClassesFrom(S4Vectors,SimpleList)
importFrom(RANN,nn2)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,metadata)
importFrom(Seurat,"VariableFeatures<-")
importFrom(Seurat,CreateAssayObject)
importFrom(Seurat,CreateDimReducObject)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,DefaultAssay)
importFrom(Seurat,Embeddings)
importFrom(Seurat,FindIntegrationAnchors)
importFrom(Seurat,GetAssayData)
importFrom(Seurat,IntegrateData)
importFrom(Seurat,IntegrateLayers)
importFrom(Seurat,Reductions)
importFrom(Seurat,ScaleData)
importFrom(Seurat,SplitObject)
importFrom(Seurat,VariableFeatures)
importFrom(Seurat,as.Seurat)
importFrom(Seurat,as.SingleCellExperiment)
importFrom(SeuratObject,CreateAssay5Object)
importFrom(SeuratObject,Embeddings)
importFrom(SeuratObject,JoinLayers)
importFrom(SeuratObject,LayerData)
importFrom(SingleCellExperiment,"altExp<-")
importFrom(SingleCellExperiment,"logcounts<-")
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,"reducedDims<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,logcounts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,rowData)
importFrom(SparseArray,colSums)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(anndata,AnnData)
importFrom(aricode,NMI)
importFrom(batchelor,fastMNN)
importFrom(bluster,makeSNNGraph)
importFrom(cluster,silhouette)
importFrom(fitdistrplus,fitdist)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_sf)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grDevices,chull)
importFrom(harmony,RunHarmony)
importFrom(leidenAlg,leiden.community)
importFrom(limma,removeBatchEffect)
importFrom(mclust,adjustedRandIndex)
importFrom(methods,new)
importFrom(parallel,mclapply)
importFrom(purrr,keep)
importFrom(reticulate,r_to_py)
importFrom(rliger,createLiger)
importFrom(rliger,getMatrix)
importFrom(rliger,normalize)
importFrom(rliger,quantileNorm)
importFrom(rliger,runIntegration)
importFrom(rliger,scaleNotCenter)
importFrom(scCustomize,Convert_Assay)
importFrom(scMerge,scMerge2)
importFrom(scrapper,centerSizeFactors)
importFrom(scrapper,chooseRnaHvgs.se)
importFrom(scrapper,normalizeRnaCounts.se)
importFrom(scrapper,runPca.se)
importFrom(sf,st_as_sf)
importFrom(sf,st_collection_extract)
importFrom(sf,st_intersection)
importFrom(sf,st_intersects)
importFrom(sf,st_join)
importFrom(sf,st_nearest_feature)
importFrom(sf,st_polygon)
importFrom(sf,st_sf)
importFrom(sf,st_sfc)
importFrom(sf,st_union)
importFrom(sf,st_voronoi)
importFrom(splatter,newSplatParams)
importFrom(splatter,splatSimulateGroups)
importFrom(stats,dist)
importFrom(stats,median)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(sva,ComBat_seq)
importFrom(transport,pp)
importFrom(transport,wasserstein)
importFrom(utils,combn)
importFrom(zellkonverter,AnnData2SCE)
importFrom(zellkonverter,SCE2AnnData)
useDynLib(BatChef)
