From 8a38a4f559acbbeae0ed16a3fa7430cdb2a9e59b Mon Sep 17 00:00:00 2001 From: SherryDong Date: Mon, 11 Jan 2021 15:23:34 +0800 Subject: [PATCH] fix version --- DESCRIPTION | 88 +++++++++++++++++++++++----------------------- NAMESPACE | 3 ++ NetBID_manual.pdf | Bin 512126 -> 512126 bytes 3 files changed, 47 insertions(+), 44 deletions(-) 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 43109586fb52f38fa0473142b70e7effa37e5554..ab9df6eaf4995b8d8c279cca78bd4ea9d092c651 100644 GIT binary patch delta 1102 zcmV-U1hM=6pdbFAAFy28!rs=y-t`q8dCpc>KYt9EM=@fIM&4@UQA!ZOsmExHSR8n(%=>3@J0*C+ z*H3&araq1Em)f2o?g*ry*jUe}T`u+;e?w!GyeP z7Zg*{7&!ZLawbJ7qpUIH6BeR`F<8VXAhfl$n#SSeSc#X&_yS2Ilmr31>D`Zd_g!=y z$|n(ulc;AS$wZpmO&6k=#yuV6=6jPcrJwvqUW=@acE*pQmb`3tpUREUqFi?gRh#y? z&~i$n$+yO1q3bSDfBjaf4o%&0wC)Vz_zOJ3y$wewL5xV+M?w)sfs?8|K47}xvNZ4$ z`u&}YiKQq?&Quk+rpgB#;RhVVf6G$yvRQQ*XqF3AZZG~41($id{N?%3;e&=Ub(v*%j^9sNNb#rd?)3nG7{l?L?_e(;=*Y*G}pDOC`FaGBm6hPjnxJ?8#{8VG|WMs zTf~k@ib7b9vfs>a=G(j|Y>h&hLj;A@OYDzlRf~GZE30r4G(LRb3NHAav5tVyA)V`c z__hk7$p>qjz!(@!XHm;-_Gr->gHn#ir(lL3L-N`p8~E^c2tdPZeah5H;iWaJ&;~=Zn$ner$uCD$E${7)#gBc))86W|N z86X0O86X3P86X6Q86X9R86XC?86XEgDFrn$GBPojT}cNX1vN4LpC=wI6fdeFf~F(GB8C%HZwIsI7Tu=LpV4! 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