diff --git a/DESCRIPTION b/DESCRIPTION index de79ba5..333927c 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,44 +1,44 @@ -Package: NetBID2 -Type: Package -Title: Network-based Bayesian Inference of Drivers, version 2 -Version: 0.1.2 -Authors@R: person('Xinran', 'Dong', email = 'xinran.dong@stjude.org', role = c('aut', 'cre')) -Maintainer@R: person('Xinran', 'Dong', email = 'xinran.dong@stjude.org') -Description: An integrative systems biology algorithm to infer drivers of phenotype based on data-driven context-specific network and Bayesian inference. -License: GPL (>= 2) -Encoding: UTF-8 -LazyData: true -Depends: - R (>= 3.6.0), - Matrix (>= 1.2-17), - SummarizedExperiment (>= 1.14.0), - lme4 (>= 1.1-21), - Biobase (>= 2.38.0), - GEOquery (>= 2.46.15), - limma (>= 3.34.9), - impute (>= 1.52.0), - tximport (>= 1.6.0), - DESeq2 (>= 1.20.0), - ConsensusClusterPlus (>= 1.38.0), - aricode (>= 0.1.1), - igraph (>= 1.1.2), - RColorBrewer (>= 1.1-2), - plot3D (>= 1.1.1), - plotrix (>= 3.7-3), - umap (>= 0.2.0.0), - ComplexHeatmap (>= 1.17.1), - ordinal (>= 2019.4-25), - MCMCglmm (>= 2.26), - arm (>= 1.10-1), - reshape (>= 0.8.7), - biomaRt (>= 2.34.2), - GSVA (>= 1.22.4), - msigdbr (>= 6.2.1), - openxlsx (>= 4.1.0), - rmarkdown (>= 1.11), - kableExtra (>= 1.1.0), - rhdf5 (>= 2.28.0), - plotly (>= 4.9.0) -Imports: -Suggests: -RoxygenNote: 6.1.1 +Package: NetBID2 +Type: Package +Title: Network-based Bayesian Inference of Drivers, version 2 +Version: 2.0.3 +Authors@R: person('Xinran', 'Dong', email = 'xinran.dong@foxmail.com', role = c('aut', 'cre')) +Maintainer@R: person('Xinran', 'Dong', email = 'xinran.dong@foxmail.com') +Description: An integrative systems biology algorithm to infer drivers of phenotype based on data-driven context-specific network and Bayesian inference. +License: GPL (>= 2) +Encoding: UTF-8 +LazyData: true +Depends: + R (>= 3.6.0), + Matrix (>= 1.2-17), + SummarizedExperiment (>= 1.14.0), + lme4 (>= 1.1-21), + Biobase (>= 2.38.0), + GEOquery (>= 2.46.15), + limma (>= 3.34.9), + impute (>= 1.52.0), + tximport (>= 1.6.0), + DESeq2 (>= 1.20.0), + ConsensusClusterPlus (>= 1.38.0), + aricode (>= 0.1.1), + igraph (>= 1.1.2), + RColorBrewer (>= 1.1-2), + plot3D (>= 1.1.1), + plotrix (>= 3.7-3), + umap (>= 0.2.0.0), + ComplexHeatmap (>= 1.17.1), + ordinal (>= 2019.4-25), + MCMCglmm (>= 2.26), + arm (>= 1.10-1), + reshape (>= 0.8.7), + biomaRt (>= 2.34.2), + GSVA (>= 1.22.4), + msigdbr (>= 6.2.1), + openxlsx (>= 4.1.0), + rmarkdown (>= 1.11), + kableExtra (>= 1.1.0), + rhdf5 (>= 2.28.0), + plotly (>= 4.9.0) +Imports: +Suggests: +RoxygenNote: 7.1.1 diff --git a/NAMESPACE b/NAMESPACE index 5ed631c..3a3edbf 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -35,10 +35,12 @@ export(draw.funcEnrich.bar) export(draw.funcEnrich.cluster) export(draw.heatmap) export(draw.network.QC) +export(draw.oncoprint) export(draw.targetNet) export(draw.targetNet.TWO) export(draw.volcanoPlot) export(funcEnrich.Fisher) +export(funcEnrich.GSEA) export(generate.eset) export(generate.masterTable) export(get.SJAracne.network) @@ -64,6 +66,7 @@ export(merge_eset) export(merge_gs) export(merge_target_list) export(out2excel) +export(processDriverProfile) export(test.targetNet.overlap) export(update_SJAracne.network) export(update_eset.feature) diff --git a/NetBID_manual.pdf b/NetBID_manual.pdf index 4310958..ab9df6e 100644 Binary files a/NetBID_manual.pdf and b/NetBID_manual.pdf differ