-
Notifications
You must be signed in to change notification settings - Fork 33
/
NAMESPACE
executable file
·83 lines (82 loc) · 2.36 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
# Generated by roxygen2: do not edit by hand
export(analyse)
export(chrLengths)
export(chrToX)
export(cohortAnalyseBatch)
export(cohortAnalyseBatchContrast)
export(downloadTemplate)
export(forceRedoEverything)
export(forceRedoNothing)
export(getCohortMutationMatrix)
export(getStories)
export(importSampleMetaData)
export(loadData)
export(makeHeatmap)
export(mcri)
export(mergeBatches)
export(plotCNAheatmapOverGoI)
export(plotCNAheatmapWithGoI)
export(plotCR)
export(plotCohortMutationHeatmap)
export(plotColourScatter)
export(plotMA)
export(plotRiver)
export(plotStories)
export(postAnalyseVEP)
export(printHTML)
export(qualityScatter)
export(runSummaryPostAnalysis)
export(superCohort)
export(superFreq)
export(superInputFiles)
export(superOutputDirectories)
export(superVersion)
export(vafScatter)
export(writeToVCF)
export(xToChr)
export(xToPos)
import(BSgenome)
import(BiocGenerics)
import(MutationalPatterns)
importFrom(BSgenome.Hsapiens.UCSC.hg19,BSgenome.Hsapiens.UCSC.hg19)
importFrom(BSgenome.Hsapiens.UCSC.hg38,BSgenome.Hsapiens.UCSC.hg38)
importFrom(BSgenome.Mmusculus.UCSC.mm10,BSgenome.Mmusculus.UCSC.mm10)
importFrom(BiocGenerics,"end<-")
importFrom(BiocGenerics,"start<-")
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicFeatures,makeTxDb)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,as.data.frame)
importFrom(GenomicRanges,as.factor)
importFrom(GenomicRanges,findOverlaps)
importFrom(IRanges,"%within%")
importFrom(IRanges,IRanges)
importFrom(R.oo,charToInt)
importFrom(Rsamtools,FaFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsubread,featureCounts)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(SummarizedExperiment,rowRanges)
importFrom(VariantAnnotation,AllVariants)
importFrom(VariantAnnotation,CodingVariants)
importFrom(VariantAnnotation,VCF)
importFrom(VariantAnnotation,locateVariants)
importFrom(VariantAnnotation,predictCoding)
importFrom(WriteXLS,WriteXLS)
importFrom(biomaRt,getBM)
importFrom(biomaRt,useMart)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,voom)
importFrom(parallel,mclapply)