-
Notifications
You must be signed in to change notification settings - Fork 0
/
NAMESPACE
101 lines (100 loc) · 2.81 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
# Generated by roxygen2: do not edit by hand
export(AmpliconSupplementing)
export(CalculateAlleleFrequency)
export(CalculateAltReads)
export(CalculateConsensus)
export(CalculateCorrelationPValue)
export(CalculateCoverage)
export(CalculateFisherTestPValue)
export(CalculateQuality)
export(CalculateStrandCorrelation)
export(ClonalDefinition)
export(ClonalDiversity)
export(CombineSEobjects)
export(Enrichment_FisherTest)
export(Filtering)
export(GetCellInfoPerVariant)
export(GetVariantInfo)
export(HeatmapVoi)
export(LoadingMAEGATK_typewise)
export(LoadingVCF_typewise)
export(LoadingVarTrix_typewise)
export(Merging_SE_list)
export(RowWiseSplit)
export(SeparatingMatrixToList)
export(SetVariantInfo)
export(UMIQC)
export(UMI_seq)
export(VariantBurden)
export(VariantCloneSizeThresholding)
export(VariantCorrelationHeatmap)
export(VariantFisherTestHeatmap)
export(VariantQuantileThresholding)
export(VariantWiseCorrelation)
export(VariantWiseFisherTest)
export(char_to_numeric)
export(combine_NAMES)
export(combine_SparseMatrix)
export(computeAFMutMatrix)
export(getAltMatrix)
export(getMutMatrix)
export(getReadMatrix)
export(getRefMatrix)
export(get_consensus)
export(load_object)
export(save_object)
export(sdiv)
import(BiocGenerics)
import(archive)
importFrom(BiocGenerics,start)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,columnAnnotation)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(DropletUtils,read10xMolInfo)
importFrom(GenomeInfoDb,seqnames)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,readMM)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,summary)
importFrom(Matrix,t)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,merge)
importFrom(Seurat,AddMetaData)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(VariantAnnotation,ScanVcfParam)
importFrom(VariantAnnotation,alt)
importFrom(VariantAnnotation,geno)
importFrom(VariantAnnotation,info)
importFrom(VariantAnnotation,readVcf)
importFrom(VariantAnnotation,ref)
importFrom(circlize,colorRamp2)
importFrom(data.table,data.table)
importFrom(dplyr,"%>%")
importFrom(dplyr,left_join)
importFrom(dplyr,sym)
importFrom(grDevices,dev.off)
importFrom(grDevices,png)
importFrom(grid,gpar)
importFrom(grid,unit)
importFrom(methods,as)
importFrom(parallel,mclapply)
importFrom(scales,hue_pal)
importFrom(stats,cor.test)
importFrom(stats,fisher.test)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(vegan,diversity)