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NAMESPACE
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executable file
·100 lines (99 loc) · 3.07 KB
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# Generated by roxygen2: do not edit by hand
export(.embed_mds)
export(calc_pairwise_mmds)
export(fit_sampleqc)
export(get_n_groups)
export(get_outliers)
export(list_known_metrics)
export(make_qc_dt)
export(make_sampleqc_report)
export(plot_alpha_js)
export(plot_alpha_js_likelihoods)
export(plot_beta_ks)
export(plot_embeddings)
export(plot_fit_over_biaxials)
export(plot_mmd_heatmap)
export(plot_outliers)
export(simulate_qcs)
import(BiocStyle)
import(patchwork)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpstart)
importFrom(BiocParallel,bpstop)
importFrom(MASS,cov.trob)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(assertthat,assert_that)
importFrom(assertthat,is.count)
importFrom(assertthat,is.flag)
importFrom(data.table,".N")
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,copy)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,melt)
importFrom(data.table,merge.data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,set)
importFrom(data.table,setcolorder)
importFrom(data.table,setkey)
importFrom(data.table,setnames)
importFrom(forcats,fct_reorder)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expand_limits)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_bin2d)
importFrom(ggplot2,geom_path)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_fill_brewer)
importFrom(ggplot2,scale_fill_distiller)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_linetype_manual)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(gtools,rdirichlet)
importFrom(igraph,as_adjacency_matrix)
importFrom(igraph,cluster_louvain)
importFrom(igraph,gorder)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,graph_from_edgelist)
importFrom(magrittr,"%>%")
importFrom(magrittr,set_colnames)
importFrom(magrittr,set_rownames)
importFrom(matrixStats,rowMins)
importFrom(mclust,mclustBIC)
importFrom(mclust,summaryMclustBIC)
importFrom(mixtools,ellipse)
importFrom(mvnfast,dmvt)
importFrom(mvtnorm,rmvnorm)
importFrom(mvtnorm,rmvt)
importFrom(patchwork,plot_layout)
importFrom(rmarkdown,render)
importFrom(scales,pretty_breaks)
importFrom(scales,rescale)
importFrom(stringr,str_match)
importFrom(uwot,umap)
useDynLib(SampleQC, .registration = TRUE)