-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathNAMESPACE
78 lines (77 loc) · 2.38 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
# Generated by roxygen2: do not edit by hand
export(RleListToRleMatrix)
export(binnedCoverage)
export(constructBedRanges)
export(countFinalRegions)
export(createGranges)
export(cutGRangesPerChromosome)
export(divideEachSampleByChromosomes)
export(finalRegions)
export(findOverlapsOverSamples)
export(findPeaks)
export(fromSamplesToChrsGRangesList)
export(keepRelevantChrs)
export(readBamAsBed)
export(readBedFile)
export(readFilesAsGRangesList)
export(saveGRangesAsBed)
export(saveGRangesAsTsv)
export(setGRGenomeInfo)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpparam)
importFrom(ChIPpeakAnno,findOverlapsOfPeaks)
importFrom(DelayedArray,RleArray)
importFrom(GenomeInfoDb,Seqinfo)
importFrom(GenomeInfoDb,isCircular)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsInUse)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(GenomicAlignments,levels)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,summarizeOverlaps)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,coverage)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,sort)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,tileGenome)
importFrom(IRanges,IRanges)
importFrom(IRanges,RleList)
importFrom(IRanges,Views)
importFrom(IRanges,ranges)
importFrom(IRanges,viewMaxs)
importFrom(IRanges,viewMeans)
importFrom(IRanges,viewMins)
importFrom(IRanges,viewSums)
importFrom(Rcpp,evalCpp)
importFrom(S4Vectors,.Call2)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,nrun)
importFrom(S4Vectors,runLength)
importFrom(S4Vectors,runValue)
importFrom(S4Vectors,split)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(data.table,rbindlist)
importFrom(glue,glue_collapse)
importFrom(plyr,ldply)
importFrom(rtracklayer,export.bed)
importFrom(rtracklayer,import.bed)
importFrom(rtracklayer,ranges)
importFrom(rtracklayer,start)
importFrom(rtracklayer,strand)
importFrom(tools,file_ext)
importFrom(utils,unzip)
importFrom(utils,write.table)
useDynLib(DEScan2)