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SherryDong committed Jan 11, 2021
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88 changes: 44 additions & 44 deletions DESCRIPTION
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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
3 changes: 3 additions & 0 deletions NAMESPACE
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Expand Up @@ -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)
Expand All @@ -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)
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