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
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
|
# Generated by roxygen2: do not edit by hand
S3method("[",outlier.filter)
export(.assignIndicesToWorkers)
export(.bpNotSharedOrUp)
export(.guessMinMean)
export(.ranksafeQR)
export(.splitColsByWorkers)
export(.splitRowsByWorkers)
export(.splitVectorByWorkers)
export(.subset2index)
export(.unpackLists)
export(addPerCellQC)
export(addPerCellQCMetrics)
export(addPerFeatureQC)
export(addPerFeatureQCMetrics)
export(aggregateAcrossCells)
export(aggregateAcrossFeatures)
export(calculateAverage)
export(calculateCPM)
export(calculateFPKM)
export(calculateTPM)
export(cleanSizeFactors)
export(computeGeometricFactors)
export(computeLibraryFactors)
export(computeMedianFactors)
export(computePooledFactors)
export(computeSpikeFactors)
export(correctGroupSummary)
export(downsampleBatches)
export(downsampleMatrix)
export(fitLinearModel)
export(geometricSizeFactors)
export(isOutlier)
export(librarySizeFactors)
export(logNormCounts)
export(makePerCellDF)
export(makePerFeatureDF)
export(medianSizeFactors)
export(mockSCE)
export(normalizeCounts)
export(numDetectedAcrossCells)
export(numDetectedAcrossFeatures)
export(outlier.filter)
export(perCellQCFilters)
export(perCellQCMetrics)
export(perFeatureQCMetrics)
export(pooledSizeFactors)
export(quickPerCellQC)
export(readSparseCounts)
export(sumCountsAcrossCells)
export(sumCountsAcrossFeatures)
export(summarizeAssayByGroup)
export(uniquifyFeatureNames)
export(whichNonZero)
exportClasses(outlier.filter)
exportMethods(aggregateAcrossCells)
exportMethods(calculateAverage)
exportMethods(calculateCPM)
exportMethods(calculateTPM)
exportMethods(geometricSizeFactors)
exportMethods(librarySizeFactors)
exportMethods(logNormCounts)
exportMethods(medianSizeFactors)
exportMethods(normalizeCounts)
exportMethods(numDetectedAcrossCells)
exportMethods(numDetectedAcrossFeatures)
exportMethods(perCellQCMetrics)
exportMethods(perFeatureQCMetrics)
exportMethods(pooledSizeFactors)
exportMethods(quickPerCellQC)
exportMethods(sumCountsAcrossCells)
exportMethods(sumCountsAcrossFeatures)
exportMethods(summarizeAssayByGroup)
import(methods)
importClassesFrom(BiocParallel,MulticoreParam)
importClassesFrom(DelayedArray,DelayedArray)
importClassesFrom(DelayedArray,SparseArraySeed)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(Matrix,dgTMatrix)
importClassesFrom(Matrix,sparseMatrix)
importClassesFrom(S4Vectors,DFrame)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(S4Vectors,List)
importClassesFrom(SingleCellExperiment,SingleCellExperiment)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(BiocGenerics,"sizeFactors<-")
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,colnames)
importFrom(BiocGenerics,match)
importFrom(BiocGenerics,rownames)
importFrom(BiocGenerics,sizeFactors)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bpisup)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpmapply)
importFrom(BiocParallel,bpnworkers)
importFrom(BiocParallel,bpparam)
importFrom(BiocParallel,register)
importFrom(DelayedArray,DelayedArray)
importFrom(DelayedArray,currentViewport)
importFrom(DelayedArray,getAutoBPPARAM)
importFrom(DelayedArray,is_sparse)
importFrom(DelayedArray,makeNindexFromArrayViewport)
importFrom(DelayedArray,setAutoBPPARAM)
importFrom(DelayedArray,write_block)
importFrom(DelayedMatrixStats,colMedians)
importFrom(DelayedMatrixStats,rowMedians)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,qr)
importFrom(Matrix,qr.coef)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
importFrom(Rcpp,sourceCpp)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,I)
importFrom(S4Vectors,List)
importFrom(S4Vectors,bindROWS)
importFrom(S4Vectors,extractROWS)
importFrom(S4Vectors,make_zero_col_DFrame)
importFrom(S4Vectors,selfmatch)
importFrom(S4Vectors,split)
importFrom(S4Vectors,wmsg)
importFrom(SingleCellExperiment,"altExp<-")
importFrom(SingleCellExperiment,"altExps<-")
importFrom(SingleCellExperiment,"int_metadata<-")
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,"reducedDims<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,altExp)
importFrom(SingleCellExperiment,altExpNames)
importFrom(SingleCellExperiment,altExps)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,int_metadata)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assayNames<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(beachmat,colBlockApply)
importFrom(beachmat,rowBlockApply)
importFrom(beachmat,whichNonZero)
importFrom(methods,as)
importFrom(methods,is)
importFrom(stats,coef)
importFrom(stats,lm)
importFrom(stats,lm.fit)
importFrom(stats,lm.wfit)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,nls)
importFrom(stats,nls.control)
importFrom(stats,quantile)
importFrom(stats,residuals)
importFrom(stats,rnbinom)
importFrom(stats,runif)
importFrom(utils,head)
importFrom(utils,read.table)
importFrom(utils,tail)
useDynLib(scuttle, .registration=TRUE)
|
