Initial commit

Author: notllikethat

DESCRIPTION

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+Package: ShinyGATOM
+Title: Shiny GATOM
+Version: 0.0.0.9000
+Authors@R: 
+    person("Mariia", "Emelianova", , "[email protected]", role = c("aut", "cre"))
+Description: A web-service for integrated network analysis of transcriptional and metabolic data.
+License: file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.2
+Imports: 
+    BioNet,
+    data.table,
+    devtools,
+    igraph,
+    logging,
+    markdown,
+    mwcsr,
+    parallel,
+    pryr,
+    RCurl,
+    shiny

LICENCE

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+The MIT License (MIT)
+
+Copyright (c) 2015 Alexey Sergushichev
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Makefile

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+all: www/d3.v3.min.js
+
+www/d3.v3.min.js:
+	wget http://d3js.org/d3.v3.min.js -O www/d3.v3.min.js

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+import("BioNet")
+import(RCurl)
+import(data.table)
+import(gatom)
+import(igraph)
+import(markdown)
+import(mwcsr)
+import(parallel)
+import(pryr)
+import(shiny)

R/app.R

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+uploaderPath <- "/mnt/data/upload"
+
+## PATHS
+path.to.kegg.network <- "/home/masha/Research/RCode/RShiny/data/network.kegg.rds"
+path.to.rhea.network <- "/home/masha/Research/RCode/RShiny/data/network.rhea.rds"
+path.to.met.kegg.db <- "/home/masha/Research/RCode/RShiny/data/met.kegg.db.rds"
+path.to.met.rhea.db <- "/home/masha/Research/RCode/RShiny/data/met.rhea.db.rds"
+path.to.org.Mm.eg.gatom.anno <- "/home/masha/Research/RCode/RShiny/data/org.Mm.eg.gatom.anno.rda"
+path.to.org.Hs.eg.gatom.anno <- "/home/masha/Research/RCode/RShiny/data/org.Hs.eg.gatom.anno.rda"
+
+example.gene.de.path <- "/home/masha/Research/RCode/RShiny/data/Ctrl.vs.MandLPSandIFNg.gene.de.tsv"
+example.met.de.path <- "/home/masha/Research/RCode/RShiny/data/Ctrl.vs.MandLPSandIFNg.met.de.tsv"