# Generated by roxygen2 (4.0.0): do not edit by hand

import(Biobase)
import(HSMMSingleCell)

importClassesFrom(methods, character, matrix, oldClass)

importMethodsFrom(BiocGenerics, as.data.frame, as.vector, cbind,
                  clusterEvalQ, colnames, do.call, lapply, mapply,
                  ncol, nrow, parCapply, parRapply, paste, rbind,
                  rownames, sort, unique, unlist)

importMethodsFrom(VGAM, lrtest, predict)

importFrom(cluster, pam)

importFrom(combinat, permn)

importFrom(fastICA, ica.R.def, ica.R.par)

importFrom(limma, removeBatchEffect)

importFrom(ggplot2, aes, aes_string, element_blank, element_line,
           element_rect, element_text, facet_wrap, geom_jitter,
           geom_line, geom_path, geom_point, geom_rect, geom_segment,
           ggplot, mean_cl_boot, scale_color_hue, scale_fill_gradient,
           scale_fill_gradient2, scale_x_continuous,
           scale_y_continuous, scale_y_log10, stat_density2d,
           stat_summary, qplot, theme, xlab, ylab)

importFrom(grid, unit)

importFrom(igraph, delete.vertices, E, ecount, edge, get.diameter,
           get.edgelist, get.shortest.paths, graph.adjacency,
           graph.empty, graph.neighborhood, induced.subgraph,
           minimum.spanning.tree, subcomponent, V, "V<-", vertex)

importFrom(irlba, irlba)

importFrom(matrixStats, rowSds)

importFrom(methods, is, new, validObject)

importFrom(parallel, makeCluster, stopCluster)

importFrom(plyr, ., arrange, ddply, rename)

importFrom(reshape2, melt)

importFrom(stats, as.dist, as.formula, cor, dist, hclust, p.adjust,
           rnorm, runif)

importFrom(utils, head, tail)

importFrom(VGAM, tobit, vgam)

exportClasses( "CellDataSet" )

export( 
   newCellDataSet,
   detectGenes,
   reduceDimension,
   reducedDimS,
   "reducedDimS<-",
   reducedDimW,
   "reducedDimW<-",
   reducedDimA,
   "reducedDimA<-",
   minSpanningTree,
   "minSpanningTree<-",
   cellPairwiseDistances,
   "cellPairwiseDistances<-",
   setOrderingFilter,
   orderCells,
   plot_spanning_tree,
   plot_genes_in_pseudotime,
   plot_genes_jitter,
   plot_genes_positive_cells,
   plot_clusters,
   differentialGeneTest,
   fitModel,
   compareModels,
   responseMatrix,
   clusterGenes,
   selectNegentropyGenes
)
