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commit 04b5c965b59f5d6ffcb49f60893ad681e77e98e6 Merge: bc79824 d1f6047 Author: Dylan Aïssi <[email protected]> Date: Fri Nov 18 21:51:41 2016 +0100 Merge tag 'upstream/1.2.0' Upstream version 1.2.0 DESCRIPTION | 20 + NAMESPACE | 1 + R/cle.LS.R | 3898 + R/msea.kda.onestep.R | 69 + build/vignette.rds | Bin 0 -> 233 bytes data/job_kda_analyze.RData | Bin 0 -> 403488 bytes inst/NEWS | 2 + inst/doc/Mergeomics.R | 274 + inst/doc/Mergeomics.Rnw | 642 + inst/doc/Mergeomics.pdf | Bin 0 -> 265347 bytes inst/extdata/Significant_pathways.info.txt | 17 + inst/extdata/Significant_pathways.txt | 2351 + inst/extdata/coexpr.info.txt | 21 + .../genes.hdlc_040kb_ld70.human_eliminated.txt | 132706 +++++++++++++++ .../marker.hdlc_040kb_ld70.human_eliminated.txt | 76867 +++++++++ inst/extdata/mergedModules.info.txt | 16 + inst/extdata/mergedModules.txt | 2320 + inst/extdata/modules.mousecoexpr.liver.human.txt | 2907 + inst/extdata/msea2kda.nodes.txt | 14879 ++ inst/extdata/network.mouseliver.mouse.txt | 156853 ++++++++++++++++++ inst/extdata/symbols.txt | 20956 +++ inst/unitTests/test_kda.analyze.R | 38 + inst/unitTests/test_ssea.analyze.R | 29 + man/MSEA.KDA.onestep.Rd | 94 + man/Mergeomics-package.Rd | 70 + man/job.kda.Rd | 19 + man/kda.analyze.Rd | 97 + man/kda.analyze.exec.Rd | 102 + man/kda.analyze.simulate.Rd | 138 + man/kda.analyze.test.Rd | 127 + man/kda.configure.Rd | 98 + man/kda.finish.Rd | 78 + man/kda.finish.estimate.Rd | 54 + man/kda.finish.save.Rd | 61 + man/kda.finish.summarize.Rd | 65 + man/kda.finish.trim.Rd | 58 + man/kda.prepare.Rd | 105 + man/kda.prepare.overlap.Rd | 86 + man/kda.prepare.screen.Rd | 94 + man/kda.start.Rd | 96 + man/kda.start.edges.Rd | 68 + man/kda.start.identify.Rd | 54 + man/kda.start.modules.Rd | 70 + man/kda2cytoscape.Rd | 101 + man/kda2cytoscape.colorize.Rd | 58 + man/kda2cytoscape.colormap.Rd | 37 + man/kda2cytoscape.drivers.Rd | 75 + man/kda2cytoscape.edges.Rd | 79 + man/kda2cytoscape.exec.Rd | 103 + man/kda2cytoscape.identify.Rd | 59 + man/kda2himmeli.Rd | 84 + man/kda2himmeli.colorize.Rd | 59 + man/kda2himmeli.colormap.Rd | 37 + man/kda2himmeli.drivers.Rd | 77 + man/kda2himmeli.edges.Rd | 81 + man/kda2himmeli.exec.Rd | 115 + man/kda2himmeli.identify.Rd | 59 + man/ssea.analyze.Rd | 113 + man/ssea.analyze.observe.Rd | 101 + man/ssea.analyze.randgenes.Rd | 118 + man/ssea.analyze.randloci.Rd | 119 + man/ssea.analyze.simulate.Rd | 113 + man/ssea.analyze.statistic.Rd | 45 + man/ssea.control.Rd | 97 + man/ssea.finish.Rd | 112 + man/ssea.finish.details.Rd | 102 + man/ssea.finish.fdr.Rd | 102 + man/ssea.finish.genes.Rd | 102 + man/ssea.meta.Rd | 98 + man/ssea.prepare.Rd | 118 + man/ssea.prepare.counts.Rd | 107 + man/ssea.prepare.structure.Rd | 105 + man/ssea.start.Rd | 110 + man/ssea.start.configure.Rd | 108 + man/ssea.start.identify.Rd | 51 + man/ssea.start.relabel.Rd | 114 + man/ssea2kda.Rd | 133 + man/ssea2kda.analyze.Rd | 133 + man/ssea2kda.import.Rd | 93 + man/tool.aggregate.Rd | 50 + man/tool.cluster.Rd | 59 + man/tool.cluster.static.Rd | 42 + man/tool.coalesce.Rd | 64 + man/tool.coalesce.exec.Rd | 55 + man/tool.coalesce.find.Rd | 58 + man/tool.coalesce.merge.Rd | 62 + man/tool.fdr.Rd | 36 + man/tool.fdr.bh.Rd | 32 + man/tool.fdr.empirical.Rd | 33 + man/tool.graph.Rd | 75 + man/tool.graph.degree.Rd | 94 + man/tool.graph.list.Rd | 81 + man/tool.metap.Rd | 43 + man/tool.normalize.Rd | 49 + man/tool.normalize.quality.Rd | 41 + man/tool.overlap.Rd | 46 + man/tool.read.Rd | 35 + man/tool.save.Rd | 34 + man/tool.subgraph.Rd | 51 + man/tool.subgraph.find.Rd | 53 + man/tool.subgraph.search.Rd | 59 + man/tool.subgraph.stats.Rd | 73 + man/tool.translate.Rd | 37 + man/tool.unify.Rd | 29 + tests/runTests.R | 1 + vignettes/Mergeomics.Rnw | 642 + vignettes/top5KDs.png | Bin 0 -> 148067 bytes 107 files changed, 421752 insertions(+) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-mergeomics.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
