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executable file
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# Generated by roxygen2: do not edit by hand
S3method(print,SplineOmics)
export(cluster_genes_multiomics)
export(cluster_hits)
export(compare_results)
export(create_clustering_report)
export(create_limma_report)
export(create_ora_report)
export(create_pvc_report)
export(create_splineomics)
export(download_enrichr_databases)
export(explore_data)
export(extract_data)
export(extract_gene_sets)
export(find_pvc)
export(plot_umap_clusters)
export(preprocess_rna_seq_data)
export(run_limma_splines)
export(run_ora)
export(update_splineomics)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,SnowParam)
importFrom(BiocParallel,bpstart)
importFrom(BiocParallel,bpstop)
importFrom(BiocParallel,register)
importFrom(ClusterR,MiniBatchKmeans)
importFrom(ClusterR,predict_KMeans)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,ht_opt)
importFrom(RhpcBLASctl,blas_set_num_threads)
importFrom(base64enc,base64encode)
importFrom(base64enc,dataURI)
importFrom(car,leveneTest)
importFrom(checkmate,assert)
importFrom(checkmate,assert_choice)
importFrom(checkmate,assert_number)
importFrom(checkmate,assert_string)
importFrom(dplyr,anti_join)
importFrom(dplyr,any_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,c_across)
importFrom(dplyr,case_when)
importFrom(dplyr,coalesce)
importFrom(dplyr,distinct)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,last_col)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,relocate)
importFrom(dplyr,rename)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,slice_head)
importFrom(dplyr,summarize)
importFrom(dplyr,transmute)
importFrom(dplyr,ungroup)
importFrom(ggplot2,aes)
importFrom(ggplot2,after_stat)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_blank)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_colorbar)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_brewer)
importFrom(ggplot2,scale_color_gradient)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_size_area)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grid,gpar)
importFrom(grid,grid.draw)
importFrom(grid,grid.newpage)
importFrom(grid,unit)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,plotMDS)
importFrom(limma,removeBatchEffect)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(methods,is)
importFrom(pbapply,pbapply)
importFrom(pbapply,pblapply)
importFrom(progress,progress_bar)
importFrom(purrr,discard)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map_chr)
importFrom(purrr,partial)
importFrom(reformulas,findbars)
importFrom(reformulas,nobars)
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,abort)
importFrom(rlang,sym)
importFrom(rstudioapi,getSourceEditorContext)
importFrom(rstudioapi,isAvailable)
importFrom(scales,hue_pal)
importFrom(scales,oob_squish)
importFrom(splines,bs)
importFrom(splines,ns)
importFrom(stats,acf)
importFrom(stats,aggregate)
importFrom(stats,as.formula)
importFrom(stats,cmdscale)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,hatvalues)
importFrom(stats,kmeans)
importFrom(stats,lm)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,relevel)
importFrom(stats,residuals)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,var)
importFrom(svglite,svglite)
importFrom(tibble,as_tibble)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,separate)
importFrom(tools,file_path_sans_ext)
importFrom(utils,capture.output)
importFrom(utils,combn)
importFrom(utils,head)
importFrom(utils,sessionInfo)
importFrom(utils,write.table)
importFrom(variancePartition,dream)
importFrom(variancePartition,voomWithDreamWeights)
importFrom(writexl,write_xlsx)
importFrom(zip,zip)