-
Notifications
You must be signed in to change notification settings - Fork 6
/
Copy pathNAMESPACE
59 lines (58 loc) · 1.91 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
# Generated by roxygen2: do not edit by hand
export(addReplicationTimingSignal)
export(addTriNucleotideDistribution)
export(calculatePvalueWithMutCategoryDistributionMatched7)
export(extractElementMutations)
export(get3utrPvalue)
export(get3utrPvalueWithPreFilter)
export(get5utrPvalue)
export(get5utrPvalueWithPreFilter)
export(getCDSPvalue)
export(getCDSPvalueWithPreFilter)
export(getCDSPvalueWithPreFilter2)
export(getEnhancerElementPvalue)
export(getEnhancerElementPvalueWithPreFilter2)
export(getEnhancerUnitPvalue)
export(getEnhancerUnitPvalueWithPreFilter)
export(getEnhancerUnitPvalueWithPreFilter2)
export(getLincRNAPvalue)
export(getLincRNAPvalueWithPreFilter)
export(getLincRNAPvalueWithPreFilter2)
export(getOpenChromatinElementPvalue)
export(getOpenChromatinElementPvalueWithPreFilter2)
export(getPromoterPvalue)
export(getPromoterPvalueWithPreFilter)
export(getPromoterPvalueWithPreFilter2)
export(makeElementReplicationTiming)
export(makeQQplot)
export(mergeVariantPosition)
export(mergeVariantPositionClusterEnhancerUnitV2)
export(mergeVariantPositionClusterV2)
export(mergeVariantPositionElementClusterV2)
export(mergeVariantPositionSimple)
export(parseMOTIFBR)
export(parseMOTIFG)
export(parseNCENC)
export(parsePosVariantByTriMutContextWithAnnotation5)
export(parsePosVariantByTriMutContextWithAnnotationCDS)
import(BSgenome.Hsapiens.UCSC.hg19)
import(GenomicRanges)
import(IRanges)
import(TxDb.Hsapiens.UCSC.hg19.knownGene)
import(doRNG)
import(ggplot2)
import(ggrepel)
importFrom(SomaticSignatures,mutationContext)
importFrom(SomaticSignatures,ucsc)
importFrom(VariantAnnotation,VRanges)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,foverlaps)
importFrom(data.table,fread)
importFrom(data.table,setkeyv)
importFrom(dbscan,dbscan)
importFrom(parallel,mclapply)
importFrom(plyr,rbind.fill)
importFrom(stats,p.adjust)
importFrom(stringr,str_extract_all)
importFrom(utils,write.table)