| 4dd6572b |
# Generated by roxygen2: do not edit by hand
|
| 3072d7b0 |
export(TreeHeatmap)
|
| b58fc74e |
export(aggDS)
|
| 0e883b38 |
export(buildTree)
|
| 264adc57 |
export(calcMediansByTreeMarker)
|
| 0e883b38 |
export(calcTreeCounts)
export(calcTreeMedians)
|
| 0599c93d |
export(edgerWrp)
|
| 7cd3da2f |
export(evalCand)
|
| e4078e98 |
export(fdr)
|
| 6c6c50ae |
export(findChild)
|
| 4decca33 |
export(findExcl)
|
| 0e883b38 |
export(getCand)
|
| 3072d7b0 |
export(getData)
|
| 6c6c50ae |
export(getLevel)
|
| 68598ae7 |
export(infoCand)
|
| 6c6c50ae |
export(isConnect)
|
| b58fc74e |
export(medianByClusterMarker)
|
| 68598ae7 |
export(nodeResult)
|
| 6c6c50ae |
export(parEstimate)
|
| 0599c93d |
export(runDA)
|
| b58fc74e |
export(runDS)
|
| 6c6c50ae |
export(selNode)
export(simData)
|
| 0599c93d |
export(topNodes)
|
| e4078e98 |
export(tpr)
|
| 6c6c50ae |
export(treeScore)
importFrom(S4Vectors,metadata)
|
| b58fc74e |
importFrom(SummarizedExperiment,SummarizedExperiment)
|
| d82c4244 |
importFrom(SummarizedExperiment,assay)
|
| e7cf279d |
importFrom(SummarizedExperiment,assayNames)
|
| 4dd6572b |
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
|
| 43b5095c |
importFrom(TreeSummarizedExperiment,TreeSummarizedExperiment)
|
| d82c4244 |
importFrom(TreeSummarizedExperiment,addLabel)
|
| 43b5095c |
importFrom(TreeSummarizedExperiment,aggTSE)
importFrom(TreeSummarizedExperiment,colLinks)
|
| e7cf279d |
importFrom(TreeSummarizedExperiment,colTree)
|
| 744f8889 |
importFrom(TreeSummarizedExperiment,convertNode)
importFrom(TreeSummarizedExperiment,findDescendant)
|
| b0b179f9 |
importFrom(TreeSummarizedExperiment,isLeaf)
|
| a5685d55 |
importFrom(TreeSummarizedExperiment,joinNode)
|
| 6c6c50ae |
importFrom(TreeSummarizedExperiment,matTree)
importFrom(TreeSummarizedExperiment,printNode)
|
| 39c278b0 |
importFrom(TreeSummarizedExperiment,rowLinks)
|
| 43b5095c |
importFrom(TreeSummarizedExperiment,rowTree)
|
| e7cf279d |
importFrom(TreeSummarizedExperiment,showNode)
|
| 0e883b38 |
importFrom(ape,as.phylo)
|
| 43b5095c |
importFrom(diffcyt,calcCounts)
|
| 0e883b38 |
importFrom(diffcyt,calcMediansByClusterMarker)
|
| 6c6c50ae |
importFrom(dirmult,dirmult)
importFrom(dirmult,rdirichlet)
|
| a5685d55 |
importFrom(dplyr,all_of)
|
| b58fc74e |
importFrom(dplyr,arrange)
|
| 3f93dc0a |
importFrom(dplyr,bind_cols)
|
| a5685d55 |
importFrom(dplyr,bind_rows)
|
| 43b5095c |
importFrom(dplyr,desc)
|
| 0e883b38 |
importFrom(dplyr,distinct)
|
| 6c6c50ae |
importFrom(dplyr,filter)
|
| b58fc74e |
importFrom(dplyr,group_by)
|
| 6c6c50ae |
importFrom(dplyr,mutate)
|
| 0e883b38 |
importFrom(dplyr,select)
|
| b58fc74e |
importFrom(dplyr,slice)
|
| 3072d7b0 |
importFrom(dplyr,summarise)
|
| b58fc74e |
importFrom(dplyr,summarize_all)
|
| 4dd6572b |
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
|
| 8fb4cb62 |
importFrom(edgeR,filterByExpr)
|
| 4dd6572b |
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
|
| eea8947e |
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
|
| 4dd6572b |
importFrom(edgeR,topTags)
|
| 3072d7b0 |
importFrom(ggnewscale,new_scale_color)
importFrom(ggplot2,aes)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_viridis_c)
importFrom(ggplot2,scale_fill_viridis_d)
importFrom(ggplot2,theme_void)
importFrom(ggtree,ggtree)
|
| 4dd6572b |
importFrom(methods,is)
|
| b0b179f9 |
importFrom(rlang,.data)
|
| 85eadd94 |
importFrom(stats,as.formula)
|
| 0e883b38 |
importFrom(stats,dist)
importFrom(stats,hclust)
|
| 264adc57 |
importFrom(stats,median)
|
| b58fc74e |
importFrom(stats,model.matrix)
|
| ac64df34 |
importFrom(stats,p.adjust)
|
| 6c6c50ae |
importFrom(stats,rmultinom)
importFrom(stats,rnbinom)
importFrom(stats,runif)
|
| b58fc74e |
importFrom(tibble,column_to_rownames)
|
| 3ce07bac |
importFrom(tidyr,pivot_longer)
|
| 6c6c50ae |
importFrom(utils,flush.console)
|
| 4dd6572b |
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
|
| 3072d7b0 |
importFrom(viridis,viridis)
|
