Panos Balomenos authored on 25/11/2020 16:59:35
| ... | ... |
@@ -1,18 +1,11 @@ |
| 1 | 1 |
import( 'locfit' ) |
| 2 |
-importFrom( 'DESeq', |
|
| 3 |
- 'newCountDataSet', |
|
| 4 |
- 'estimateSizeFactors', |
|
| 5 |
- 'estimateDispersions', |
|
| 6 |
- 'nbinomTest', |
|
| 7 |
- 'getVarianceStabilizedData') |
|
| 2 |
+ |
|
| 8 | 3 |
importFrom( 'DESeq2', |
| 9 | 4 |
'DESeqDataSetFromMatrix', |
| 10 | 5 |
'estimateSizeFactors', |
| 11 | 6 |
'estimateDispersions', |
| 12 | 7 |
'nbinomWaldTest', |
| 13 | 8 |
'results') |
| 14 |
- |
|
| 15 |
- |
|
| 16 | 9 |
importFrom( 'limma', |
| 17 | 10 |
'voom', |
| 18 | 11 |
'lmFit', |
| ... | ... |
@@ -136,7 +129,8 @@ importFrom( 'methods', |
| 136 | 129 |
'setGeneric', |
| 137 | 130 |
'setMethod', |
| 138 | 131 |
'signature', |
| 139 |
- 'new') |
|
| 132 |
+ 'new', |
|
| 133 |
+ 'is') |
|
| 140 | 134 |
export( 'DEsubs', |
| 141 | 135 |
'geneVisualization', |
| 142 | 136 |
'organismVisualization', |
Panos Balomenos authored on 31/08/2018 20:52:52
Panos Balomenos authored on 03/08/2018 18:18:53
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEsubs@131540 bc3139a8-67e5-0310-9ffc-ced21a209358
Panos Balomenos authored on 24/07/2017 20:43:17
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEsubs@122029 bc3139a8-67e5-0310-9ffc-ced21a209358
Martin Morgan authored on 07/10/2016 08:32:34
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,144 @@ |
| 1 |
+import( 'locfit' ) |
|
| 2 |
+importFrom( 'DESeq', |
|
| 3 |
+ 'newCountDataSet', |
|
| 4 |
+ 'estimateSizeFactors', |
|
| 5 |
+ 'estimateDispersions', |
|
| 6 |
+ 'nbinomTest', |
|
| 7 |
+ 'getVarianceStabilizedData') |
|
| 8 |
+importFrom( 'DESeq2', |
|
| 9 |
+ 'DESeqDataSetFromMatrix', |
|
| 10 |
+ 'estimateSizeFactors', |
|
| 11 |
+ 'estimateDispersions', |
|
| 12 |
+ 'nbinomWaldTest', |
|
| 13 |
+ 'results') |
|
| 14 |
+importFrom( 'samr', |
|
| 15 |
+ 'SAMseq' ) |
|
| 16 |
+importFrom( 'limma', |
|
| 17 |
+ 'voom', |
|
| 18 |
+ 'lmFit', |
|
| 19 |
+ 'eBayes' ) |
|
| 20 |
+importFrom( 'EBSeq', |
|
| 21 |
+ 'MedianNorm', |
|
| 22 |
+ 'EBTest', |
|
| 23 |
+ 'GetPPMat') |
|
| 24 |
+importFrom( 'NBPSeq', |
|
| 25 |
+ 'nbp.test') |
|
| 26 |
+importFrom( 'edgeR', |
|
| 27 |
+ 'DGEList', |
|
| 28 |
+ 'exactTest', |
|
| 29 |
+ 'calcNormFactors', |
|
| 30 |
+ 'estimateCommonDisp', |
|
| 31 |
+ 'estimateTagwiseDisp') |
|
| 32 |
+importFrom( 'graph', |
|
| 33 |
+ 'ugraph') |
|
| 34 |
+importFrom( 'RBGL', |
|
| 35 |
+ 'kCliques') |
|
| 36 |
+importFrom( 'igraph', |
|
| 37 |
+ 'as_graphnel', |
|
| 38 |
+ 'graph_from_edgelist', |
|
| 39 |
+ 'as_data_frame', |
|
| 40 |
+ 'closeness', |
|
| 41 |
+ 'hub_score', |
|
| 42 |
+ 'decompose', |
|
| 43 |
+ 'cluster_walktrap', |
|
| 44 |
+ 'cluster_edge_betweenness', |
|
| 45 |
+ 'cluster_fast_greedy', |
|
| 46 |
+ 'cluster_leading_eigen', |
|
| 47 |
+ 'cluster_infomap', |
|
| 48 |
+ 'cluster_louvain', |
|
| 49 |
+ 'cliques', |
|
| 50 |
+ 'max_cliques', |
|
| 51 |
+ 'coreness', |
|
| 52 |
+ 'components', |
|
| 53 |
+ 'as.undirected', |
|
| 54 |
+ 'betweenness', |
|
| 55 |
+ 'eccentricity', |
|
| 56 |
+ 'articulation_points', |
|
| 57 |
+ 'page_rank', |
|
| 58 |
+ 'degree', |
|
| 59 |
+ 'dfs', |
|
| 60 |
+ 'ego', |
|
| 61 |
+ 'get.edgelist', |
|
| 62 |
+ 'get.adjacency', |
|
| 63 |
+ 'graph.adjacency', |
|
| 64 |
+ 'graph.adjlist', |
|
| 65 |
+ 'V', |
|
| 66 |
+ 'E', |
|
| 67 |
+ 'all_simple_paths', |
|
| 68 |
+ 'graph.data.frame', |
|
| 69 |
+ 'simplify', |
|
| 70 |
+ 'V<-', |
|
| 71 |
+ 'E<-', |
|
| 72 |
+ 'layout.davidson.harel', |
|
| 73 |
+ 'write.graph') |
|
| 74 |
+importFrom( 'Matrix', |
|
| 75 |
+ 'triu') |
|
| 76 |
+importFrom( 'circlize', |
|
| 77 |
+ 'circos.par', |
|
| 78 |
+ 'chordDiagram', |
|
| 79 |
+ 'get.all.sector.index', |
|
| 80 |
+ 'get.cell.meta.data', |
|
| 81 |
+ 'circos.text', |
|
| 82 |
+ 'circos.clear') |
|
| 83 |
+importFrom( 'grDevices', |
|
| 84 |
+ 'pdf', |
|
| 85 |
+ 'png', |
|
| 86 |
+ 'svg', |
|
| 87 |
+ 'rainbow', |
|
| 88 |
+ 'dev.off', |
|
| 89 |
+ 'colorRampPalette', |
|
| 90 |
+ 'dev.copy2pdf') |
|
| 91 |
+importFrom( 'graphics', |
|
| 92 |
+ 'par', |
|
| 93 |
+ 'barplot', |
|
| 94 |
+ 'text', |
|
| 95 |
+ 'plot') |
|
| 96 |
+importFrom( 'stats', |
|
| 97 |
+ 'deviance', |
|
| 98 |
+ 'glm', |
|
| 99 |
+ 'hatvalues', |
|
| 100 |
+ 'pchisq', |
|
| 101 |
+ 'pf', |
|
| 102 |
+ 'poisson', |
|
| 103 |
+ 'qchisq', |
|
| 104 |
+ 'qf', |
|
| 105 |
+ 'residuals', |
|
| 106 |
+ 'p.adjust', |
|
| 107 |
+ 'phyper', |
|
| 108 |
+ 'model.matrix', |
|
| 109 |
+ 'cor', |
|
| 110 |
+ 'predict') |
|
| 111 |
+importFrom( 'pheatmap', |
|
| 112 |
+ 'pheatmap') |
|
| 113 |
+importFrom( 'utils', |
|
| 114 |
+ 'browseURL', |
|
| 115 |
+ 'head', |
|
| 116 |
+ 'write.table', |
|
| 117 |
+ 'read.table', |
|
| 118 |
+ 'capture.output') |
|
| 119 |
+importFrom( 'ggplot2', |
|
| 120 |
+ 'qplot', |
|
| 121 |
+ 'theme_classic', |
|
| 122 |
+ 'geom_point', |
|
| 123 |
+ 'scale_colour_gradientn', |
|
| 124 |
+ 'labs', |
|
| 125 |
+ 'cut_number', |
|
| 126 |
+ 'theme', |
|
| 127 |
+ 'element_text') |
|
| 128 |
+importFrom( 'jsonlite', |
|
| 129 |
+ 'toJSON') |
|
| 130 |
+importFrom( 'tools', |
|
| 131 |
+ 'file_ext') |
|
| 132 |
+importFrom( 'methods', |
|
| 133 |
+ 'representation', |
|
| 134 |
+ 'setClass', |
|
| 135 |
+ 'setGeneric', |
|
| 136 |
+ 'setMethod', |
|
| 137 |
+ 'signature', |
|
| 138 |
+ 'new') |
|
| 139 |
+export( 'DEsubs', |
|
| 140 |
+ 'geneVisualization', |
|
| 141 |
+ 'organismVisualization', |
|
| 142 |
+ 'subpathwayToGraph', |
|
| 143 |
+ 'subpathwayVisualization', |
|
| 144 |
+ 'subpathwayTypes' ) |