-
Notifications
You must be signed in to change notification settings - Fork 0
/
NAMESPACE
185 lines (184 loc) · 5.21 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
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
# Generated by roxygen2: do not edit by hand
S3method(compute_reference,hscreference)
S3method(compute_reference,screference)
S3method(deconverse_results,Seurat)
S3method(deconverse_results,scbench)
S3method(deconvolute,Seurat)
S3method(deconvolute,matrix)
S3method(deconvolute,scbench)
S3method(deconvolute_all,Seurat)
S3method(deconvolute_all,matrix)
S3method(deconvolute_all,scbench)
S3method(plt_comp_performance,hscreference)
S3method(plt_comp_performance,scbench)
S3method(plt_comp_performance,screference)
S3method(print,hscreference)
S3method(print,scbench)
S3method(print,screference)
S3method(results,scbench)
export("%>%")
export(adata_to_seurat)
export(autogenes_deconvolute)
export(autogenes_scref)
export(bayesprism_deconvolute)
export(bayesprism_scref)
export(bisque_deconvolute)
export(bulk_deconvolution_methods)
export(card_deconvolute)
export(card_scref)
export(cibersortx_deconvolute)
export(cibersortx_scref)
export(compute_reference)
export(deconverse_results)
export(deconvolute)
export(deconvolute_all)
export(deconvolution_methods)
export(dwls_deconvolute)
export(dwls_scref)
export(get_bounds)
export(get_deconv_populations)
export(install_cibersortx)
export(mixtures_lod)
export(mixtures_population)
export(mixtures_spillover)
export(music_deconvolute)
export(new_hscreference)
export(new_scbench)
export(new_screference)
export(ols_deconvolute)
export(plt_colocalization)
export(plt_comp_performance)
export(plt_cor_heatmap)
export(plt_cors_scatter)
export(plt_lod_heatmap)
export(plt_lod_scatter)
export(plt_method_concordance)
export(plt_method_correlation)
export(plt_population_mixtures)
export(plt_rmse_heatmap)
export(plt_spatial_correlation)
export(plt_spillover_heatmap)
export(plt_spillover_scatter)
export(pseudobulks)
export(rctd_deconvolute)
export(read_h5ad)
export(results)
export(scaden_deconvolute)
export(scaden_scref)
export(seurat_to_adata)
export(spatial_only_methods)
export(spotlight_deconvolute)
export(spotlight_scref)
export(svr_deconvolute)
export(test_markers)
import(Matrix)
import(Seurat)
import(SeuratObject)
import(SingleCellExperiment)
import(ggheatmapper)
import(hitandrun)
import(patchwork)
import(reticulate)
import(testit)
import(tidyverse)
importFrom(Biobase,AnnotatedDataFrame)
importFrom(Biobase,ExpressionSet)
importFrom(Biobase,exprs)
importFrom(Biobase,pData)
importFrom(Biobase,phenoData)
importFrom(CARD,CARDref)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(R.utils,filePath)
importFrom(R.utils,getAbsolutePath)
importFrom(Seurat,AddMetaData)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,FindAllMarkers)
importFrom(Seurat,FindVariableFeatures)
importFrom(Seurat,Idents)
importFrom(Seurat,NormalizeData)
importFrom(Seurat,PercentageFeatureSet)
importFrom(Seurat,SetIdent)
importFrom(Seurat,VariableFeatures)
importFrom(Seurat,as.SingleCellExperiment)
importFrom(SummarizedExperiment,colData)
importFrom(broom,tidy)
importFrom(corrr,autoplot)
importFrom(corrr,correlate)
importFrom(cowplot,plot_to_gtable)
importFrom(data.table,":=")
importFrom(data.table,.BY)
importFrom(data.table,.EACHI)
importFrom(data.table,.GRP)
importFrom(data.table,.I)
importFrom(data.table,.N)
importFrom(data.table,.NGRP)
importFrom(data.table,.SD)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,rbindlist)
importFrom(data.tree,as.Node)
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,relocate)
importFrom(dplyr,rename_with)
importFrom(dplyr,slice_max)
importFrom(e1071,svm)
importFrom(fastDummies,dummy_cols)
importFrom(formattable,color_bar)
importFrom(future,plan)
importFrom(ggdensity,geom_hdr_points)
importFrom(ggheatmapper,align_to_hm)
importFrom(ggheatmapper,get_hmPlot)
importFrom(ggheatmapper,ggheatmap)
importFrom(ggheatmapper,theme_scatter)
importFrom(ggheatmapper,theme_sparse2)
importFrom(ggheatmapper,update_hmPlot)
importFrom(ggnetwork,geom_edges)
importFrom(ggnetwork,geom_nodes)
importFrom(ggnetwork,geom_nodetext_repel)
importFrom(ggnetwork,ggnetwork)
importFrom(ggnetwork,theme_blank)
importFrom(ggpubr,as_ggplot)
importFrom(ggpubr,stat_cor)
importFrom(gtools,rdirichlet)
importFrom(hitandrun,hitandrun)
importFrom(kableExtra,add_header_above)
importFrom(kableExtra,cell_spec)
importFrom(kableExtra,kable_paper)
importFrom(kableExtra,kable_styling)
importFrom(kableExtra,kbl)
importFrom(kableExtra,scroll_box)
importFrom(kableExtra,spec_color)
importFrom(magrittr,"%>%")
importFrom(network,get.vertex.attribute)
importFrom(network,network)
importFrom(network,set.vertex.attribute)
importFrom(nnls,nnls)
importFrom(pbmcapply,pbmclapply)
importFrom(peakRAM,peakRAM)
importFrom(purrr,possibly)
importFrom(purrr,reduce)
importFrom(quadprog,solve.QP)
importFrom(rdist,rdist)
importFrom(remotes,install_bioc)
importFrom(remotes,install_github)
importFrom(reticulate,import)
importFrom(scales,label_log)
importFrom(stats,lm)
importFrom(stats,na.exclude)
importFrom(stats,resid)
importFrom(stats,sd)
importFrom(stringr,str_detect)
importFrom(stringr,str_remove)
importFrom(stringr,str_subset)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(yardstick,rmse_vec)