-
Notifications
You must be signed in to change notification settings - Fork 17
/
NAMESPACE
153 lines (152 loc) · 4.51 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
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
# Generated by roxygen2: do not edit by hand
export(TFIDF)
export(addDoublets)
export(aggregateFeatures)
export(amulet)
export(amuletFromCounts)
export(clamulet)
export(clusterStickiness)
export(computeDoubletDensity)
export(createDoublets)
export(cxds2)
export(directDblClassification)
export(doubletPairwiseEnrichment)
export(doubletThresholding)
export(fastcluster)
export(findDoubletClusters)
export(getArtificialDoublets)
export(getCellPairs)
export(getExpectedDoublets)
export(getFragmentOverlaps)
export(mockDoubletSCE)
export(plotDoubletMap)
export(plotThresholds)
export(propHomotypic)
export(recoverDoublets)
export(scDblFinder)
export(selFeatures)
exportMethods(computeDoubletDensity)
exportMethods(findDoubletClusters)
exportMethods(recoverDoublets)
import(BiocParallel)
import(SingleCellExperiment)
import(methods)
importClassesFrom(S4Vectors,SimpleList)
importFrom(BiocGenerics,"sizeFactors<-")
importFrom(BiocGenerics,score)
importFrom(BiocGenerics,sizeFactors)
importFrom(BiocNeighbors,AnnoyParam)
importFrom(BiocNeighbors,KmknnParam)
importFrom(BiocNeighbors,findDistance)
importFrom(BiocNeighbors,findKNN)
importFrom(BiocNeighbors,queryNeighbors)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bpmapply)
importFrom(BiocParallel,bpnworkers)
importFrom(BiocParallel,bpstart)
importFrom(BiocParallel,bpstop)
importFrom(BiocSingular,IrlbaParam)
importFrom(BiocSingular,bsparam)
importFrom(BiocSingular,runPCA)
importFrom(DelayedArray,as.matrix)
importFrom(DelayedArray,getAutoBPPARAM)
importFrom(DelayedArray,rowsum)
importFrom(DelayedArray,setAutoBPPARAM)
importFrom(DelayedArray,sweep)
importFrom(GenomeInfoDb,"seqlengths<-")
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsInUse)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,start)
importFrom(IRanges,IRanges)
importFrom(IRanges,Views)
importFrom(IRanges,coverage)
importFrom(IRanges,overlapsAny)
importFrom(IRanges,slice)
importFrom(IRanges,viewMaxs)
importFrom(IRanges,width)
importFrom(MASS,negative.binomial)
importFrom(MASS,theta.ml)
importFrom(Matrix,Diagonal)
importFrom(Matrix,colSums)
importFrom(Matrix,crossprod)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,t)
importFrom(Matrix,tcrossprod)
importFrom(Rsamtools,TabixFile)
importFrom(Rsamtools,seqnamesTabix)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,runValue)
importFrom(S4Vectors,splitAsList)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,colLabels)
importFrom(SingleCellExperiment,logcounts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,ranges)
importFrom(bluster,makeKNNGraph)
importFrom(igraph,cluster_louvain)
importFrom(igraph,membership)
importFrom(methods,as)
importFrom(methods,is)
importFrom(rtracklayer,import)
importFrom(scater,runPCA)
importFrom(scran,.logBH)
importFrom(scran,buildKNNGraph)
importFrom(scran,findMarkers)
importFrom(scuttle,.bpNotSharedOrUp)
importFrom(scuttle,.subset2index)
importFrom(scuttle,computeLibraryFactors)
importFrom(scuttle,librarySizeFactors)
importFrom(scuttle,logNormCounts)
importFrom(scuttle,normalizeCounts)
importFrom(scuttle,sumCountsAcrossCells)
importFrom(stats,aggregate)
importFrom(stats,as.formula)
importFrom(stats,chisq.test)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,dnbinom)
importFrom(stats,ecdf)
importFrom(stats,fitted)
importFrom(stats,glm)
importFrom(stats,kmeans)
importFrom(stats,lm)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,optimize)
importFrom(stats,p.adjust)
importFrom(stats,pbinom)
importFrom(stats,pcauchy)
importFrom(stats,pnbinom)
importFrom(stats,pnorm)
importFrom(stats,poisson)
importFrom(stats,ppois)
importFrom(stats,predict)
importFrom(stats,qnorm)
importFrom(stats,quantile)
importFrom(stats,relevel)
importFrom(stats,rnorm)
importFrom(stats,rpois)
importFrom(stats,setNames)
importFrom(stats,weighted.mean)
importFrom(utils,head)
importFrom(utils,read.delim)
importFrom(xgboost,xgb.cv)
importFrom(xgboost,xgboost)