Adding RaggedExperiment, basecallQC, CATALYST, GenomicScores, IMAS, s…

…emisup, ImpulseDE2, methylInheritance, biotmle, biotmleData, BLMA, TCGAWorkflow, metavizr

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metavizr@128350 bc3139a8-67e5-0310-9ffc-ced21a209358

.Rbuildignore

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+.gitignore
+inst/www
+work
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+.DS_Store
+.Rproj.user
+.Rhistory
+.RData
+*.Rproj

DESCRIPTION

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+Package: metavizr
+Type: Package
+Version: 0.99.8
+Author: c( person("Hector", "Corrada Bravo",
+        email="hcorrada@gmail.com", role=c("cre","aut", "main")),
+        person("Florin", "Chelaru", email="florin.chelaru@gmail.com",
+        role=c("aut")), person("Justin", "Wagner",
+        email="jwagner@cs.umd.edu", role=c("aut")), person("Jayaram",
+        "Kancherla", email="jayaram.kancherla@gmail.com",
+        role=c("aut")), person("Joseph", "Paulson",
+        email="jpaulson@jimmy.harvard.edu", role=c("aut")))
+Maintainer: Hector Corrada Bravo <hcorrada@gmail.com>
+License: Artistic-2.0
+Title: R Interface to the metaviz web app for interactive metagenomics
+        data analysis and visualization
+Description: This package provides Websocket communication to the
+        metaviz web app (http://metaviz.cbcb.umd.edu) for interactive
+        visualization of metagenomics data. Objects in R/bioc
+        interactive sessions can be displayed in plots and data can be
+        explored using a facetzoom visualization. Fundamental
+        Bioconductor data structures are supported (e.g., MRexperiment
+        objects), while providing an easy mechanism to support other
+        data structures. Visualizations (using d3.js) can be easily
+        added to the web app as well.
+VignetteBuilder: knitr
+Depends: R (>= 3.3), metagenomeSeq (>= 1.17.1), methods, data.table,
+        phyloseq, Biobase
+Imports: epivizr, epivizrData, epivizrServer, epivizrStandalone, vegan,
+        GenomeInfoDb
+Suggests: knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s,
+        testthat, gss
+Collate: 'metavizControl.R' 'startMetaviz.R' 'utils.R'
+        'EpivizMetagenomicsData-class.R' 'register-methods.R'
+        'validateMRExperiment.R' 'MetavizApp-class.R'
+        'MetavizGraph-class.R'
+biocViews: Visualization, Infrastructure, GUI, Metagenomics
+RoxygenNote: 6.0.1

LICENSE

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+YEAR: 2012-2016
+COPYRIGHT HOLDER: Hector Corrada Bravo <hcorrada@gmail.com> 

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(generateSelection)
+export(metavizControl)
+export(startMetaviz)
+export(startMetavizStandalone)
+export(validateObject)
+exportClasses(EpivizMetagenomicsData)
+exportClasses(MetavizApp)
+import(GenomeInfoDb)
+import(data.table)
+import(epivizr)
+import(epivizrStandalone)
+import(metagenomeSeq)
+import(methods)
+importClassesFrom(epivizr,EpivizApp)
+importClassesFrom(epivizrData,EpivizData)
+importClassesFrom(epivizrData,EpivizDataMgr)
+importClassesFrom(epivizrData,EpivizMeasurement)
+importClassesFrom(epivizrServer,EpivizServer)
+importClassesFrom(phyloseq,phyloseq)
+importFrom(Biobase,fData)
+importFrom(phyloseq,phyloseq_to_metagenomeSeq)
+importFrom(vegan,diversity)
+importMethodsFrom(epivizrData,register)