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/usr/lib/R/site-library/Mergeomics/help/AnIndex is in r-bioc-mergeomics 1.6.0-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

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Mergeomics-package	Mergeomics-package
job.kda	job.kda
kda.analyze	kda.analyze
kda.analyze.exec	kda.analyze.exec
kda.analyze.simulate	kda.analyze.simulate
kda.analyze.test	kda.analyze.test
kda.configure	kda.configure
kda.finish	kda.finish
kda.finish.estimate	kda.finish.estimate
kda.finish.save	kda.finish.save
kda.finish.summarize	kda.finish.summarize
kda.finish.trim	kda.finish.trim
kda.prepare	kda.prepare
kda.prepare.overlap	kda.prepare.overlap
kda.prepare.screen	kda.prepare.screen
kda.start	kda.start
kda.start.edges	kda.start.edges
kda.start.identify	kda.start.identify
kda.start.modules	kda.start.modules
kda2cytoscape	kda2cytoscape
kda2cytoscape.colorize	kda2cytoscape.colorize
kda2cytoscape.colormap	kda2cytoscape.colormap
kda2cytoscape.drivers	kda2cytoscape.drivers
kda2cytoscape.edges	kda2cytoscape.edges
kda2cytoscape.exec	kda2cytoscape.exec
kda2cytoscape.identify	kda2cytoscape.identify
kda2himmeli	kda2himmeli
kda2himmeli.colorize	kda2himmeli.colorize
kda2himmeli.colormap	kda2himmeli.colormap
kda2himmeli.drivers	kda2himmeli.drivers
kda2himmeli.edges	kda2himmeli.edges
kda2himmeli.exec	kda2himmeli.exec
kda2himmeli.identify	kda2himmeli.identify
Mergeomics	Mergeomics-package
MSEA.KDA.onestep	MSEA.KDA.onestep
ssea.analyze	ssea.analyze
ssea.analyze.observe	ssea.analyze.observe
ssea.analyze.randgenes	ssea.analyze.randgenes
ssea.analyze.randloci	ssea.analyze.randloci
ssea.analyze.simulate	ssea.analyze.simulate
ssea.analyze.statistic	ssea.analyze.statistic
ssea.control	ssea.control
ssea.finish	ssea.finish
ssea.finish.details	ssea.finish.details
ssea.finish.fdr	ssea.finish.fdr
ssea.finish.genes	ssea.finish.genes
ssea.meta	ssea.meta
ssea.prepare	ssea.prepare
ssea.prepare.counts	ssea.prepare.counts
ssea.prepare.structure	ssea.prepare.structure
ssea.start	ssea.start
ssea.start.configure	ssea.start.configure
ssea.start.identify	ssea.start.identify
ssea.start.relabel	ssea.start.relabel
ssea2kda	ssea2kda
ssea2kda.analyze	ssea2kda.analyze
ssea2kda.import	ssea2kda.import
tool.aggregate	tool.aggregate
tool.cluster	tool.cluster
tool.cluster.static	tool.cluster.static
tool.coalesce	tool.coalesce
tool.coalesce.exec	tool.coalesce.exec
tool.coalesce.find	tool.coalesce.find
tool.coalesce.merge	tool.coalesce.merge
tool.fdr	tool.fdr
tool.fdr.bh	tool.fdr.bh
tool.fdr.empirical	tool.fdr.empirical
tool.graph	tool.graph
tool.graph.degree	tool.graph.degree
tool.graph.list	tool.graph.list
tool.metap	tool.metap
tool.normalize	tool.normalize
tool.normalize.quality	tool.normalize.quality
tool.overlap	tool.overlap
tool.read	tool.read
tool.save	tool.save
tool.subgraph	tool.subgraph
tool.subgraph.find	tool.subgraph.find
tool.subgraph.search	tool.subgraph.search
tool.subgraph.stats	tool.subgraph.stats
tool.translate	tool.translate
tool.unify	tool.unify