1. NoRCE
  2. NAMESPACE
Browse code

update

guldenolgun authored on 20/10/2022 00:42:15
Showing 1 changed files
NAMESPACE
History View file @ 4bfec3e
... ... 
@@ -44,6 +44,7 @@ import(stringr)
44 44 
 import(zlibbioc)
45 45 
 importFrom(AnnotationDbi,Term)
46 46 
 importFrom(AnnotationDbi,mappedkeys)
47 
+importFrom(GenomeInfoDb,seqlevels)
47 48 
 importFrom(GenomicFeatures,as.list)
48 49 
 importFrom(GenomicFeatures,intronsByTranscript)
49 50 
 importFrom(GenomicRanges,GRanges)
Browse code

update

guldenolgun authored on 13/10/2022 02:53:46
Showing 1 changed files
NAMESPACE
History View file @ 6e6299b
... ... 
@@ -40,6 +40,7 @@ import(GO.db)
40 40 
 import(GenomicFeatures)
41 41 
 import(dbplyr)
42 42 
 import(readr)
43 
+import(stringr)
43 44 
 import(zlibbioc)
44 45 
 importFrom(AnnotationDbi,Term)
45 46 
 importFrom(AnnotationDbi,mappedkeys)
Browse code

update

guldenolgun authored on 26/08/2021 22:04:00
Showing 1 changed files
NAMESPACE
History View file @ bcb2948
... ... 
@@ -4,6 +4,7 @@ export(KeggEnrichment)
4 4 
 export(WikiEnrichment)
5 5 
 export(assembly)
6 6 
 export(calculateCorr)
7 
+export(convertGMT)
7 8 
 export(convertGeneID)
8 9 
 export(corrbased)
9 10 
 export(corrbasedMrna)
Browse code

update

guldenolgun authored on 14/01/2020 16:56:30
Showing 1 changed files
NAMESPACE
History View file @ 07160d7
... ... 
@@ -29,7 +29,6 @@ export(mirnaGOEnricher)
29 29 
 export(mirnaPathwayEnricher)
30 30 
 export(mirnaRegionGOEnricher)
31 31 
 export(mirnaRegionPathwayEnricher)
32 
-export(pathwayEnrichment)
33 32 
 export(predictmiTargets)
34 33 
 export(reactomeEnrichment)
35 34 
 export(setParameters)
Browse code

update

guldenolgun authored on 05/11/2019 17:09:21
Showing 1 changed files
NAMESPACE
History View file @ c7b54d1
... ... 
@@ -87,6 +87,7 @@ importFrom(rtracklayer,"genome<-")
87 87 
 importFrom(rtracklayer,browserSession)
88 88 
 importFrom(rtracklayer,genome)
89 89 
 importFrom(rtracklayer,getTable)
90 
+importFrom(rtracklayer,import)
90 91 
 importFrom(rtracklayer,ucscTableQuery)
91 92 
 importFrom(stats,chisq.test)
92 93 
 importFrom(stats,cor)
Browse code

update

guldenolgun authored on 24/10/2019 23:10:02
Showing 1 changed files
NAMESPACE
History View file @ 2d0bb60
... ... 
@@ -40,6 +40,7 @@ import(GO.db)
40 40 
 import(GenomicFeatures)
41 41 
 import(dbplyr)
42 42 
 import(readr)
43 
+import(zlibbioc)
43 44 
 importFrom(AnnotationDbi,Term)
44 45 
 importFrom(AnnotationDbi,mappedkeys)
45 46 
 importFrom(GenomicFeatures,as.list)
Browse code

update

guldenolgun authored on 24/10/2019 21:58:11
Showing 1 changed files
NAMESPACE
History View file @ 8a80d4a
... ... 
@@ -59,6 +59,8 @@ importFrom(GenomicRanges,split)
59 59 
 importFrom(GenomicRanges,start)
60 60 
 importFrom(GenomicRanges,strand)
61 61 
 importFrom(GenomicRanges,width)
62 
+importFrom(IRanges,IRanges)
63 
+importFrom(IRanges,subsetByOverlaps)
62 64 
 importFrom(biomaRt,getBM)
63 65 
 importFrom(biomaRt,useEnsembl)
64 66 
 importFrom(biomaRt,useMart)
Browse code

update

guldenolgun authored on 24/10/2019 21:12:53
Showing 1 changed files
NAMESPACE
History View file @ 3ffe39b
... ... 
@@ -38,11 +38,10 @@ export(writeEnrichment)
38 38 
 exportClasses(NoRCE)
39 39 
 import(GO.db)
40 40 
 import(GenomicFeatures)
41 
+import(dbplyr)
41 42 
 import(readr)
42 
-import(tidyr)
43 43 
 importFrom(AnnotationDbi,Term)
44 44 
 importFrom(AnnotationDbi,mappedkeys)
45 
-importFrom(DBI,dbConnect)
46 45 
 importFrom(GenomicFeatures,as.list)
47 46 
 importFrom(GenomicFeatures,intronsByTranscript)
48 47 
 importFrom(GenomicRanges,GRanges)
... ... 
@@ -60,20 +59,10 @@ importFrom(GenomicRanges,split)
60 59 
 importFrom(GenomicRanges,start)
61 60 
 importFrom(GenomicRanges,strand)
62 61 
 importFrom(GenomicRanges,width)
63 
-importFrom(KEGGREST,keggGet)
64 
-importFrom(RCurl,postForm)
65 
-importFrom(RSQLite,SQLite)
66 62 
 importFrom(biomaRt,getBM)
67 63 
 importFrom(biomaRt,useEnsembl)
68 64 
 importFrom(biomaRt,useMart)
69 
-importFrom(cRegulome,get_mir)
70 
-importFrom(dplyr,arrange)
71 
-importFrom(dplyr,collect)
72 
-importFrom(dplyr,count)
73 
-importFrom(dplyr,filter)
74 
-importFrom(dplyr,mutate)
75 
-importFrom(dplyr,select)
76 
-importFrom(dplyr,tbl)
65 
+importFrom(dplyr,"%>%")
77 66 
 importFrom(ggplot2,aes)
78 67 
 importFrom(ggplot2,element_text)
79 68 
 importFrom(ggplot2,geom_point)
... ... 
@@ -81,9 +70,6 @@ importFrom(ggplot2,ggplot)
81 70 
 importFrom(ggplot2,labs)
82 71 
 importFrom(ggplot2,theme)
83 72 
 importFrom(ggplot2,theme_bw)
84 
-importFrom(grDevices,adjustcolor)
85 
-importFrom(grDevices,colorRampPalette)
86 
-importFrom(graphics,plot)
87 73 
 importFrom(igraph,"E<-")
88 74 
 importFrom(igraph,"V<-")
89 75 
 importFrom(igraph,E)
... ... 
@@ -93,12 +79,6 @@ importFrom(igraph,degree)
93 79 
 importFrom(igraph,graph_from_data_frame)
94 80 
 importFrom(igraph,layout_with_fr)
95 81 
 importFrom(igraph,norm_coords)
96 
-importFrom(png,readPNG)
97 
-importFrom(png,writePNG)
98 
-importFrom(psych,corr.test)
99 
-importFrom(rWikiPathways,downloadPathwayArchive)
100 
-importFrom(reactome.db,reactomePATHID2EXTID)
101 
-importFrom(reactome.db,reactomePATHID2NAME)
102 82 
 importFrom(reshape2,melt)
103 83 
 importFrom(rtracklayer,"genome<-")
104 84 
 importFrom(rtracklayer,browserSession)
... ... 
@@ -116,7 +96,6 @@ importFrom(stats,phyper)
116 96 
 importFrom(stats,reorder)
117 97 
 importFrom(stats,setNames)
118 98 
 importFrom(stats,var)
119 
-importFrom(tidyr,gather)
120 99 
 importFrom(utils,browseURL)
121 100 
 importFrom(utils,installed.packages)
122 101 
 importFrom(utils,read.table)
Browse code

update

guldenolgun authored on 22/10/2019 23:21:10
Showing 1 changed files
NAMESPACE
History View file @ 709da6e
... ... 
@@ -38,20 +38,6 @@ export(writeEnrichment)
38 38 
 exportClasses(NoRCE)
39 39 
 import(GO.db)
40 40 
 import(GenomicFeatures)
41 
-import(TxDb.Celegans.UCSC.ce11.refGene)
42 
-import(TxDb.Dmelanogaster.UCSC.dm6.ensGene)
43 
-import(TxDb.Drerio.UCSC.danRer10.refGene)
44 
-import(TxDb.Hsapiens.UCSC.hg19.knownGene)
45 
-import(TxDb.Hsapiens.UCSC.hg38.knownGene)
46 
-import(TxDb.Mmusculus.UCSC.mm10.knownGene)
47 
-import(TxDb.Rnorvegicus.UCSC.rn6.refGene)
48 
-import(org.Ce.eg.db)
49 
-import(org.Dm.eg.db)
50 
-import(org.Dr.eg.db)
51 
-import(org.Hs.eg.db)
52 
-import(org.Mm.eg.db)
53 
-import(org.Rn.eg.db)
54 
-import(org.Sc.sgd.db)
55 41 
 import(readr)
56 42 
 import(tidyr)
57 43 
 importFrom(AnnotationDbi,Term)
Browse code

update

guldenolgun authored on 20/10/2019 12:04:41
Showing 1 changed files
NAMESPACE
History View file @ 4575151
... ... 
@@ -2,6 +2,7 @@
2 2
3 3 
 export(KeggEnrichment)
4 4 
 export(WikiEnrichment)
5 
+export(assembly)
5 6 
 export(calculateCorr)
6 7 
 export(convertGeneID)
7 8 
 export(corrbased)
... ... 
@@ -31,8 +32,7 @@ export(mirnaRegionPathwayEnricher)
31 32 
 export(pathwayEnrichment)
32 33 
 export(predictmiTargets)
33 34 
 export(reactomeEnrichment)
34 
-export(readGMT)
35 
-export(readbed)
35 
+export(setParameters)
36 36 
 export(topEnrichment)
37 37 
 export(writeEnrichment)
38 38 
 exportClasses(NoRCE)
... ... 
@@ -80,6 +80,7 @@ importFrom(RSQLite,SQLite)
80 80 
 importFrom(biomaRt,getBM)
81 81 
 importFrom(biomaRt,useEnsembl)
82 82 
 importFrom(biomaRt,useMart)
83 
+importFrom(cRegulome,get_mir)
83 84 
 importFrom(dplyr,arrange)
84 85 
 importFrom(dplyr,collect)
85 86 
 importFrom(dplyr,count)
... ... 
@@ -112,7 +113,6 @@ importFrom(psych,corr.test)
112 113 
 importFrom(rWikiPathways,downloadPathwayArchive)
113 114 
 importFrom(reactome.db,reactomePATHID2EXTID)
114 115 
 importFrom(reactome.db,reactomePATHID2NAME)
115 
-importFrom(readr,read_table)
116 116 
 importFrom(reshape2,melt)
117 117 
 importFrom(rtracklayer,"genome<-")
118 118 
 importFrom(rtracklayer,browserSession)
Browse code

update

guldenolgun authored on 24/08/2019 15:33:04
Showing 1 changed files
NAMESPACE
History View file @ 2c28c16
... ... 
@@ -54,6 +54,7 @@ import(org.Rn.eg.db)
54 54 
 import(org.Sc.sgd.db)
55 55 
 import(readr)
56 56 
 import(tidyr)
57 
+importFrom(AnnotationDbi,Term)
57 58 
 importFrom(AnnotationDbi,mappedkeys)
58 59 
 importFrom(DBI,dbConnect)
59 60 
 importFrom(GenomicFeatures,as.list)
... ... 
@@ -113,6 +114,7 @@ importFrom(reactome.db,reactomePATHID2EXTID)
113 114 
 importFrom(reactome.db,reactomePATHID2NAME)
114 115 
 importFrom(readr,read_table)
115 116 
 importFrom(reshape2,melt)
117 
+importFrom(rtracklayer,"genome<-")
116 118 
 importFrom(rtracklayer,browserSession)
117 119 
 importFrom(rtracklayer,genome)
118 120 
 importFrom(rtracklayer,getTable)
Browse code

update

guldenolgun authored on 24/08/2019 10:33:59
Showing 1 changed files
NAMESPACE
History View file @ de989ae
... ... 
@@ -36,7 +36,6 @@ export(readbed)
36 36 
 export(topEnrichment)
37 37 
 export(writeEnrichment)
38 38 
 exportClasses(NoRCE)
39 
-import(AnnotateDbi)
40 39 
 import(GO.db)
41 40 
 import(GenomicFeatures)
42 41 
 import(TxDb.Celegans.UCSC.ce11.refGene)
Browse code

update

guldenolgun authored on 24/08/2019 09:32:35
Showing 1 changed files
NAMESPACE
History View file @ 91e2fe2
... ... 
@@ -36,9 +36,26 @@ export(readbed)
36 36 
 export(topEnrichment)
37 37 
 export(writeEnrichment)
38 38 
 exportClasses(NoRCE)
39 
+import(AnnotateDbi)
40 
+import(GO.db)
39 41 
 import(GenomicFeatures)
42 
+import(TxDb.Celegans.UCSC.ce11.refGene)
43 
+import(TxDb.Dmelanogaster.UCSC.dm6.ensGene)
44 
+import(TxDb.Drerio.UCSC.danRer10.refGene)
45 
+import(TxDb.Hsapiens.UCSC.hg19.knownGene)
46 
+import(TxDb.Hsapiens.UCSC.hg38.knownGene)
47 
+import(TxDb.Mmusculus.UCSC.mm10.knownGene)
48 
+import(TxDb.Rnorvegicus.UCSC.rn6.refGene)
49 
+import(org.Ce.eg.db)
50 
+import(org.Dm.eg.db)
51 
+import(org.Dr.eg.db)
52 
+import(org.Hs.eg.db)
53 
+import(org.Mm.eg.db)
54 
+import(org.Rn.eg.db)
55 
+import(org.Sc.sgd.db)
40 56 
 import(readr)
41 57 
 import(tidyr)
58 
+importFrom(AnnotationDbi,mappedkeys)
42 59 
 importFrom(DBI,dbConnect)
43 60 
 importFrom(GenomicFeatures,as.list)
44 61 
 importFrom(GenomicFeatures,intronsByTranscript)
... ... 
@@ -97,6 +114,10 @@ importFrom(reactome.db,reactomePATHID2EXTID)
97 114 
 importFrom(reactome.db,reactomePATHID2NAME)
98 115 
 importFrom(readr,read_table)
99 116 
 importFrom(reshape2,melt)
117 
+importFrom(rtracklayer,browserSession)
118 
+importFrom(rtracklayer,genome)
119 
+importFrom(rtracklayer,getTable)
120 
+importFrom(rtracklayer,ucscTableQuery)
100 121 
 importFrom(stats,chisq.test)
101 122 
 importFrom(stats,cor)
102 123 
 importFrom(stats,cor.test)
... ... 
@@ -110,5 +131,6 @@ importFrom(stats,setNames)
110 131 
 importFrom(stats,var)
111 132 
 importFrom(tidyr,gather)
112 133 
 importFrom(utils,browseURL)
134 
+importFrom(utils,installed.packages)
113 135 
 importFrom(utils,read.table)
114 136 
 importFrom(utils,write.table)
Browse code

update

guldenolgun authored on 23/08/2019 19:59:51
Showing 1 changed files
NAMESPACE
History View file @ 29b9715
... ... 
@@ -60,13 +60,6 @@ importFrom(GenomicRanges,width)
60 60 
 importFrom(KEGGREST,keggGet)
61 61 
 importFrom(RCurl,postForm)
62 62 
 importFrom(RSQLite,SQLite)
63 
-importFrom(TxDb.Celegans.UCSC.ce11.refGene,TxDb.Celegans.UCSC.ce11.refGene)
64 
-importFrom(TxDb.Dmelanogaster.UCSC.dm6.ensGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene)
65 
-importFrom(TxDb.Drerio.UCSC.danRer10.refGene,TxDb.Drerio.UCSC.danRer10.refGene)
66 
-importFrom(TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg19.knownGene)
67 
-importFrom(TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene)
68 
-importFrom(TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene)
69 
-importFrom(TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Rnorvegicus.UCSC.rn6.refGene)
70 63 
 importFrom(biomaRt,getBM)
71 64 
 importFrom(biomaRt,useEnsembl)
72 65 
 importFrom(biomaRt,useMart)
... ... 
@@ -96,18 +89,6 @@ importFrom(igraph,degree)
96 89 
 importFrom(igraph,graph_from_data_frame)
97 90 
 importFrom(igraph,layout_with_fr)
98 91 
 importFrom(igraph,norm_coords)
99 
-importFrom(org.Ce.eg.db,org.Ce.egPATH2EG)
100 
-importFrom(org.Ce.eg.db,org.Ce.egSYMBOL)
101 
-importFrom(org.Dr.eg.db,org.Dr.egPATH2EG)
102 
-importFrom(org.Dr.eg.db,org.Dr.egSYMBOL)
103 
-importFrom(org.Hs.eg.db,org.Hs.egPATH2EG)
104 
-importFrom(org.Hs.eg.db,org.Hs.egSYMBOL)
105 
-importFrom(org.Mm.eg.db,org.Mm.egPATH2EG)
106 
-importFrom(org.Mm.eg.db,org.Mm.egSYMBOL)
107 
-importFrom(org.Rn.eg.db,org.Rn.egPATH2EG)
108 
-importFrom(org.Rn.eg.db,org.Rn.egSYMBOL)
109 
-importFrom(org.Sc.sgd.db,org.Sc.sgdGENENAME)
110 
-importFrom(org.Sc.sgd.db,org.Sc.sgdPATH2ORF)
111 92 
 importFrom(png,readPNG)
112 93 
 importFrom(png,writePNG)
113 94 
 importFrom(psych,corr.test)
Browse code

update

guldenolgun authored on 29/05/2019 23:19:50
Showing 1 changed files
NAMESPACE
History View file @ 0ddbae9
... ... 
@@ -87,6 +87,8 @@ importFrom(ggplot2,theme_bw)
87 87 
 importFrom(grDevices,adjustcolor)
88 88 
 importFrom(grDevices,colorRampPalette)
89 89 
 importFrom(graphics,plot)
90 
+importFrom(igraph,"E<-")
91 
+importFrom(igraph,"V<-")
90 92 
 importFrom(igraph,E)
91 93 
 importFrom(igraph,V)
92 94 
 importFrom(igraph,cluster_optimal)
Browse code

Fixed examples run time

guldenolgun authored on 29/05/2019 10:42:07
Showing 1 changed files
NAMESPACE
History View file @ 955f280
... ... 
@@ -38,6 +38,7 @@ export(writeEnrichment)
38 38 
 exportClasses(NoRCE)
39 39 
 import(GenomicFeatures)
40 40 
 import(readr)
41 
+import(tidyr)
41 42 
 importFrom(DBI,dbConnect)
42 43 
 importFrom(GenomicFeatures,as.list)
43 44 
 importFrom(GenomicFeatures,intronsByTranscript)
... ... 
@@ -69,7 +70,9 @@ importFrom(TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Rnorvegicus.UCSC.rn6.refGene)
69 70 
 importFrom(biomaRt,getBM)
70 71 
 importFrom(biomaRt,useEnsembl)
71 72 
 importFrom(biomaRt,useMart)
73 
+importFrom(dplyr,arrange)
72 74 
 importFrom(dplyr,collect)
75 
+importFrom(dplyr,count)
73 76 
 importFrom(dplyr,filter)
74 77 
 importFrom(dplyr,mutate)
75 78 
 importFrom(dplyr,select)
... ... 
@@ -84,6 +87,8 @@ importFrom(ggplot2,theme_bw)
84 87 
 importFrom(grDevices,adjustcolor)
85 88 
 importFrom(grDevices,colorRampPalette)
86 89 
 importFrom(graphics,plot)
90 
+importFrom(igraph,E)
91 
+importFrom(igraph,V)
87 92 
 importFrom(igraph,cluster_optimal)
88 93 
 importFrom(igraph,degree)
89 94 
 importFrom(igraph,graph_from_data_frame)
Browse code

First Version

guldenolgun authored on 26/05/2019 12:07:28
Showing 1 changed files
NAMESPACE
History View file @ 5d9cac9
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,126 @@
1 
+# Generated by roxygen2: do not edit by hand
2 
+
3 
+export(KeggEnrichment)
4 
+export(WikiEnrichment)
5 
+export(calculateCorr)
6 
+export(convertGeneID)
7 
+export(corrbased)
8 
+export(corrbasedMrna)
9 
+export(createNetwork)
10 
+export(drawDotPlot)
11 
+export(extractBiotype)
12 
+export(filterBiotype)
13 
+export(geneGOEnricher)
14 
+export(genePathwayEnricher)
15 
+export(geneRegionGOEnricher)
16 
+export(geneRegionPathwayEnricher)
17 
+export(getGoDag)
18 
+export(getKeggDiagram)
19 
+export(getNearToExon)
20 
+export(getNearToIntron)
21 
+export(getReactomeDiagram)
22 
+export(getTADOverlap)
23 
+export(getUCSC)
24 
+export(getmiRNACount)
25 
+export(goEnrichment)
26 
+export(listTAD)
27 
+export(mirnaGOEnricher)
28 
+export(mirnaPathwayEnricher)
29 
+export(mirnaRegionGOEnricher)
30 
+export(mirnaRegionPathwayEnricher)
31 
+export(pathwayEnrichment)
32 
+export(predictmiTargets)
33 
+export(reactomeEnrichment)
34 
+export(readGMT)
35 
+export(readbed)
36 
+export(topEnrichment)
37 
+export(writeEnrichment)
38 
+exportClasses(NoRCE)
39 
+import(GenomicFeatures)
40 
+import(readr)
41 
+importFrom(DBI,dbConnect)
42 
+importFrom(GenomicFeatures,as.list)
43 
+importFrom(GenomicFeatures,intronsByTranscript)
44 
+importFrom(GenomicRanges,GRanges)
45 
+importFrom(GenomicRanges,as.data.frame)
46 
+importFrom(GenomicRanges,duplicated)
47 
+importFrom(GenomicRanges,end)
48 
+importFrom(GenomicRanges,findOverlaps)
49 
+importFrom(GenomicRanges,intersect)
50 
+importFrom(GenomicRanges,match)
51 
+importFrom(GenomicRanges,merge)
52 
+importFrom(GenomicRanges,order)
53 
+importFrom(GenomicRanges,pintersect)
54 
+importFrom(GenomicRanges,resize)
55 
+importFrom(GenomicRanges,split)
56 
+importFrom(GenomicRanges,start)
57 
+importFrom(GenomicRanges,strand)
58 
+importFrom(GenomicRanges,width)
59 
+importFrom(KEGGREST,keggGet)
60 
+importFrom(RCurl,postForm)
61 
+importFrom(RSQLite,SQLite)
62 
+importFrom(TxDb.Celegans.UCSC.ce11.refGene,TxDb.Celegans.UCSC.ce11.refGene)
63 
+importFrom(TxDb.Dmelanogaster.UCSC.dm6.ensGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene)
64 
+importFrom(TxDb.Drerio.UCSC.danRer10.refGene,TxDb.Drerio.UCSC.danRer10.refGene)
65 
+importFrom(TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg19.knownGene)
66 
+importFrom(TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene)
67 
+importFrom(TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene)
68 
+importFrom(TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Rnorvegicus.UCSC.rn6.refGene)
69 
+importFrom(biomaRt,getBM)
70 
+importFrom(biomaRt,useEnsembl)
71 
+importFrom(biomaRt,useMart)
72 
+importFrom(dplyr,collect)
73 
+importFrom(dplyr,filter)
74 
+importFrom(dplyr,mutate)
75 
+importFrom(dplyr,select)
76 
+importFrom(dplyr,tbl)
77 
+importFrom(ggplot2,aes)
78 
+importFrom(ggplot2,element_text)
79 
+importFrom(ggplot2,geom_point)
80 
+importFrom(ggplot2,ggplot)
81 
+importFrom(ggplot2,labs)
82 
+importFrom(ggplot2,theme)
83 
+importFrom(ggplot2,theme_bw)
84 
+importFrom(grDevices,adjustcolor)
85 
+importFrom(grDevices,colorRampPalette)
86 
+importFrom(graphics,plot)
87 
+importFrom(igraph,cluster_optimal)
88 
+importFrom(igraph,degree)
89 
+importFrom(igraph,graph_from_data_frame)
90 
+importFrom(igraph,layout_with_fr)
91 
+importFrom(igraph,norm_coords)
92 
+importFrom(org.Ce.eg.db,org.Ce.egPATH2EG)
93 
+importFrom(org.Ce.eg.db,org.Ce.egSYMBOL)
94 
+importFrom(org.Dr.eg.db,org.Dr.egPATH2EG)
95 
+importFrom(org.Dr.eg.db,org.Dr.egSYMBOL)
96 
+importFrom(org.Hs.eg.db,org.Hs.egPATH2EG)
97 
+importFrom(org.Hs.eg.db,org.Hs.egSYMBOL)
98 
+importFrom(org.Mm.eg.db,org.Mm.egPATH2EG)
99 
+importFrom(org.Mm.eg.db,org.Mm.egSYMBOL)
100 
+importFrom(org.Rn.eg.db,org.Rn.egPATH2EG)
101 
+importFrom(org.Rn.eg.db,org.Rn.egSYMBOL)
102 
+importFrom(org.Sc.sgd.db,org.Sc.sgdGENENAME)
103 
+importFrom(org.Sc.sgd.db,org.Sc.sgdPATH2ORF)
104 
+importFrom(png,readPNG)
105 
+importFrom(png,writePNG)
106 
+importFrom(psych,corr.test)
107 
+importFrom(rWikiPathways,downloadPathwayArchive)
108 
+importFrom(reactome.db,reactomePATHID2EXTID)
109 
+importFrom(reactome.db,reactomePATHID2NAME)
110 
+importFrom(readr,read_table)
111 
+importFrom(reshape2,melt)
112 
+importFrom(stats,chisq.test)
113 
+importFrom(stats,cor)
114 
+importFrom(stats,cor.test)
115 
+importFrom(stats,fisher.test)
116 
+importFrom(stats,na.omit)
117 
+importFrom(stats,p.adjust)
118 
+importFrom(stats,pbinom)
119 
+importFrom(stats,phyper)
120 
+importFrom(stats,reorder)
121 
+importFrom(stats,setNames)
122 
+importFrom(stats,var)
123 
+importFrom(tidyr,gather)
124 
+importFrom(utils,browseURL)
125 
+importFrom(utils,read.table)
126 
+importFrom(utils,write.table)