-
Notifications
You must be signed in to change notification settings - Fork 24
/
NAMESPACE
126 lines (125 loc) · 3.75 KB
/
NAMESPACE
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
# Generated by roxygen2: do not edit by hand
export()
export(SangerAlignment)
export(SangerContig)
export(SangerRead)
export(chromatogram_overwrite)
export(generateReport)
export(launchApp)
export(writeFasta)
exportClasses(ChromatogramParam)
exportClasses(ObjectResults)
exportClasses(QualityReport)
exportClasses(SangerAlignment)
exportClasses(SangerContig)
exportClasses(SangerRead)
exportMethods(MakeBaseCalls)
exportMethods(generateReportSA)
exportMethods(generateReportSC)
exportMethods(generateReportSR)
exportMethods(launchAppSA)
exportMethods(launchAppSC)
exportMethods(qualityBasePlot)
exportMethods(readTable)
exportMethods(updateQualityParam)
exportMethods(writeFastaSA)
exportMethods(writeFastaSC)
exportMethods(writeFastaSR)
import(logger)
import(sangerseqR)
importFrom(Biostrings,AAStringSet)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,GENETIC_CODE)
importFrom(Biostrings,compareStrings)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,subseq)
importFrom(Biostrings,translate)
importFrom(Biostrings,trinucleotideFrequency)
importFrom(Biostrings,writeXStringSet)
importFrom(DECIPHER,AlignSeqs)
importFrom(DECIPHER,AlignTranslation)
importFrom(DECIPHER,BrowseSeqs)
importFrom(DECIPHER,ConsensusSequence)
importFrom(DECIPHER,CorrectFrameshifts)
importFrom(DECIPHER,DistanceMatrix)
importFrom(DECIPHER,RemoveGaps)
importFrom(DECIPHER,TreeLine)
importFrom(DT,dataTableOutput)
importFrom(DT,renderDataTable)
importFrom(ape,as.DNAbin)
importFrom(ape,bionjs)
importFrom(ape,dist.dna)
importFrom(ape,read.tree)
importFrom(data.table,tstrsplit)
importFrom(excelR,excelOutput)
importFrom(excelR,excelTable)
importFrom(excelR,renderExcel)
importFrom(ggdendro,ggdendrogram)
importFrom(gridExtra,grid.arrange)
importFrom(openxlsx,int2col)
importFrom(parallel,detectCores)
importFrom(parallel,mclapply)
importFrom(plotly,add_annotations)
importFrom(plotly,add_markers)
importFrom(plotly,add_trace)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(plotly,plotlyOutput)
importFrom(plotly,plotly_build)
importFrom(plotly,renderPlotly)
importFrom(rmarkdown,render)
importFrom(sangerseqR,chromatogram)
importFrom(sangerseqR,primarySeq)
importFrom(sangerseqR,read.abif)
importFrom(sangerseqR,sangerseq)
importFrom(seqinr,read.fasta)
importFrom(shiny,HTML)
importFrom(shiny,actionButton)
importFrom(shiny,checkboxInput)
importFrom(shiny,column)
importFrom(shiny,fluidRow)
importFrom(shiny,getShinyOption)
importFrom(shiny,h1)
importFrom(shiny,h3)
importFrom(shiny,h4)
importFrom(shiny,htmlOutput)
importFrom(shiny,icon)
importFrom(shiny,includeHTML)
importFrom(shiny,isolate)
importFrom(shiny,numericInput)
importFrom(shiny,observeEvent)
importFrom(shiny,p)
importFrom(shiny,plotOutput)
importFrom(shiny,reactiveValues)
importFrom(shiny,removeNotification)
importFrom(shiny,renderPlot)
importFrom(shiny,renderUI)
importFrom(shiny,showNotification)
importFrom(shiny,sliderInput)
importFrom(shiny,stopApp)
importFrom(shiny,tagList)
importFrom(shiny,tags)
importFrom(shiny,textInput)
importFrom(shiny,textOutput)
importFrom(shiny,uiOutput)
importFrom(shiny,verbatimTextOutput)
importFrom(shinyWidgets,actionBttn)
importFrom(shinycssloaders,withSpinner)
importFrom(shinydashboard,box)
importFrom(shinydashboard,dashboardBody)
importFrom(shinydashboard,dashboardHeader)
importFrom(shinydashboard,dashboardPage)
importFrom(shinydashboard,dashboardSidebar)
importFrom(shinydashboard,menuItem)
importFrom(shinydashboard,menuSubItem)
importFrom(shinydashboard,renderMenu)
importFrom(shinydashboard,sidebarMenu)
importFrom(shinydashboard,sidebarMenuOutput)
importFrom(shinydashboard,updateTabItems)
importFrom(shinydashboard,valueBox)
importFrom(shinyjs,html)
importFrom(shinyjs,useShinyjs)
importFrom(stringr,str_count)
importFrom(stringr,str_extract)
importFrom(tools,file_ext)