1. scone
  2. NAMESPACE
Browse code

Remove unneeded function import

Davide Risso authored on 16/09/2021 09:00:34
Showing 1 changed files
NAMESPACE
History View file @ 21cbec3
... ... 
@@ -88,7 +88,6 @@ importFrom(rhdf5,h5createFile)
88 88 
 importFrom(rhdf5,h5ls)
89 89 
 importFrom(rhdf5,h5read)
90 90 
 importFrom(rhdf5,h5write)
91 
-importFrom(rhdf5,h5write.default)
92 91 
 importFrom(stats,approx)
93 92 
 importFrom(stats,as.formula)
94 93 
 importFrom(stats,binomial)
Browse code

Export PSINORM_FN wrapper

Davide Risso authored on 06/07/2021 15:04:26
Showing 1 changed files
NAMESPACE
History View file @ 8abd2f5
... ... 
@@ -4,6 +4,7 @@ export(CLR_FN)
4 4 
 export(DESEQ_FN)
5 5 
 export(FQT_FN)
6 6 
 export(FQ_FN)
7 
+export(PSINORM_FN)
7 8 
 export(SCRAN_FN)
8 9 
 export(SUM_FN)
9 10 
 export(SconeExperiment)
Browse code

Add PsiNorm normalization

Davide Risso authored on 06/05/2021 10:59:52
Showing 1 changed files
NAMESPACE
History View file @ a26bc47
... ... 
@@ -24,6 +24,7 @@ export(scone_easybake)
24 24 
 export(score_matrix)
25 25 
 export(simple_FNR_params)
26 26 
 exportClasses(SconeExperiment)
27 
+exportMethods(PsiNorm)
27 28 
 exportMethods(SconeExperiment)
28 29 
 exportMethods(get_batch)
29 30 
 exportMethods(get_bio)
... ... 
@@ -39,10 +40,13 @@ exportMethods(get_scores)
39 40 
 exportMethods(scone)
40 41 
 exportMethods(select_methods)
41 42 
 import(BiocParallel)
43 
+import(SingleCellExperiment)
42 44 
 import(SummarizedExperiment)
43 45 
 import(gplots)
44 46 
 import(methods)
45 47 
 importClassesFrom(SummarizedExperiment,SummarizedExperiment)
48 
+importFrom(MatrixGenerics,colMins)
49 
+importFrom(MatrixGenerics,colSums2)
46 50 
 importFrom(RColorBrewer,brewer.pal)
47 51 
 importFrom(RUVSeq,RUVg)
48 52 
 importFrom(aroma.light,normalizeQuantileRank.matrix)
... ... 
@@ -74,6 +78,8 @@ importFrom(limma,lmFit)
74 78 
 importFrom(matrixStats,colIQRs)
75 79 
 importFrom(matrixStats,colMedians)
76 80 
 importFrom(matrixStats,rowMedians)
81 
+importFrom(methods,setGeneric)
82 
+importFrom(methods,setMethod)
77 83 
 importFrom(mixtools,normalmixEM)
78 84 
 importFrom(rARPACK,svds)
79 85 
 importFrom(rhdf5,H5close)
Browse code

scone_1.1.3

mbcole authored on 19/10/2017 20:52:03
Showing 1 changed files
NAMESPACE
History View file @ af3da30
... ... 
@@ -60,6 +60,7 @@ importFrom(grDevices,pdf)
60 60 
 importFrom(graphics,abline)
61 61 
 importFrom(graphics,arrows)
62 62 
 importFrom(graphics,barplot)
63 
+importFrom(graphics,boxplot)
63 64 
 importFrom(graphics,hist)
64 65 
 importFrom(graphics,legend)
65 66 
 importFrom(graphics,lines)
... ... 
@@ -91,6 +92,7 @@ importFrom(stats,dist)
91 92 
 importFrom(stats,dnbinom)
92 93 
 importFrom(stats,fitted.values)
93 94 
 importFrom(stats,glm)
95 
+importFrom(stats,lm)
94 96 
 importFrom(stats,mad)
95 97 
 importFrom(stats,median)
96 98 
 importFrom(stats,model.matrix)
... ... 
@@ -101,7 +103,10 @@ importFrom(stats,prcomp)
101 103 
 importFrom(stats,quantile)
102 104 
 importFrom(stats,quasibinomial)
103 105 
 importFrom(stats,sd)
106 
+importFrom(stats,setNames)
107 
+importFrom(stats,var)
104 108 
 importFrom(utils,capture.output)
105 109 
 importFrom(utils,head)
106 110 
 importFrom(utils,sessionInfo)
111 
+importFrom(utils,write.csv)
107 112 
 importFrom(utils,write.table)
Browse code

remove EDASeq and scran dependencies

Davide Risso authored on 30/06/2017 22:14:15
Showing 1 changed files
NAMESPACE
History View file @ 0d72009
... ... 
@@ -81,7 +81,6 @@ importFrom(rhdf5,h5ls)
81 81 
 importFrom(rhdf5,h5read)
82 82 
 importFrom(rhdf5,h5write)
83 83 
 importFrom(rhdf5,h5write.default)
84 
-importFrom(scran,computeSumFactors)
85 84 
 importFrom(stats,approx)
86 85 
 importFrom(stats,as.formula)
87 86 
 importFrom(stats,binomial)
Browse code

Shiny app packages to Suggests:

Davide Risso authored on 30/06/2017 21:47:09
Showing 1 changed files
NAMESPACE
History View file @ d415a9d
... ... 
@@ -42,15 +42,7 @@ import(BiocParallel)
42 42 
 import(SummarizedExperiment)
43 43 
 import(gplots)
44 44 
 import(methods)
45 
-import(plotly)
46 
-import(visNetwork)
47 45 
 importClassesFrom(SummarizedExperiment,SummarizedExperiment)
48 
-importFrom(DT,dataTableOutput)
49 
-importFrom(DT,dataTableProxy)
50 
-importFrom(DT,formatSignif)
51 
-importFrom(DT,renderDataTable)
52 
-importFrom(DT,selectRows)
53 
-importFrom(NMF,aheatmap)
54 46 
 importFrom(RColorBrewer,brewer.pal)
55 47 
 importFrom(RUVSeq,RUVg)
56 48 
 importFrom(aroma.light,normalizeQuantileRank.matrix)
... ... 
@@ -62,18 +54,6 @@ importFrom(compositions,clr)
62 54 
 importFrom(diptest,dip.test)
63 55 
 importFrom(edgeR,calcNormFactors)
64 56 
 importFrom(fpc,pamk)
65 
-importFrom(ggplot2,aes)
66 
-importFrom(ggplot2,coord_cartesian)
67 
-importFrom(ggplot2,element_blank)
68 
-importFrom(ggplot2,geom_bar)
69 
-importFrom(ggplot2,geom_point)
70 
-importFrom(ggplot2,geom_violin)
71 
-importFrom(ggplot2,ggplot)
72 
-importFrom(ggplot2,guides)
73 
-importFrom(ggplot2,labs)
74 
-importFrom(ggplot2,scale_fill_manual)
75 
-importFrom(ggplot2,theme)
76 
-importFrom(ggplot2,ylim)
77 57 
 importFrom(grDevices,colorRampPalette)
78 58 
 importFrom(grDevices,dev.off)
79 59 
 importFrom(grDevices,pdf)
... ... 
@@ -95,7 +75,6 @@ importFrom(matrixStats,colMedians)
95 75 
 importFrom(matrixStats,rowMedians)
96 76 
 importFrom(mixtools,normalmixEM)
97 77 
 importFrom(rARPACK,svds)
98 
-importFrom(reshape2,melt)
99 78 
 importFrom(rhdf5,H5close)
100 79 
 importFrom(rhdf5,h5createFile)
101 80 
 importFrom(rhdf5,h5ls)
... ... 
@@ -103,32 +82,6 @@ importFrom(rhdf5,h5read)
103 82 
 importFrom(rhdf5,h5write)
104 83 
 importFrom(rhdf5,h5write.default)
105 84 
 importFrom(scran,computeSumFactors)
106 
-importFrom(shiny,br)
107 
-importFrom(shiny,column)
108 
-importFrom(shiny,downloadHandler)
109 
-importFrom(shiny,downloadLink)
110 
-importFrom(shiny,fluidPage)
111 
-importFrom(shiny,fluidRow)
112 
-importFrom(shiny,h5)
113 
-importFrom(shiny,h6)
114 
-importFrom(shiny,helpText)
115 
-importFrom(shiny,mainPanel)
116 
-importFrom(shiny,observeEvent)
117 
-importFrom(shiny,p)
118 
-importFrom(shiny,plotOutput)
119 
-importFrom(shiny,reactive)
120 
-importFrom(shiny,renderPlot)
121 
-importFrom(shiny,renderTable)
122 
-importFrom(shiny,selectInput)
123 
-importFrom(shiny,shinyApp)
124 
-importFrom(shiny,sidebarLayout)
125 
-importFrom(shiny,sidebarPanel)
126 
-importFrom(shiny,sliderInput)
127 
-importFrom(shiny,tabPanel)
128 
-importFrom(shiny,tableOutput)
129 
-importFrom(shiny,tabsetPanel)
130 
-importFrom(shiny,titlePanel)
131 
-importFrom(shiny,updateSelectInput)
132 85 
 importFrom(stats,approx)
133 86 
 importFrom(stats,as.formula)
134 87 
 importFrom(stats,binomial)
Browse code

shiny and miniUI in Suggests:

Davide Risso authored on 30/06/2017 21:29:49
Showing 1 changed files
NAMESPACE
History View file @ 3a7e0cb
... ... 
@@ -93,9 +93,6 @@ importFrom(limma,lmFit)
93 93 
 importFrom(matrixStats,colIQRs)
94 94 
 importFrom(matrixStats,colMedians)
95 95 
 importFrom(matrixStats,rowMedians)
96 
-importFrom(miniUI,gadgetTitleBar)
97 
-importFrom(miniUI,miniContentPanel)
98 
-importFrom(miniUI,miniPage)
99 96 
 importFrom(mixtools,normalmixEM)
100 97 
 importFrom(rARPACK,svds)
101 98 
 importFrom(reshape2,melt)
... ... 
@@ -107,7 +104,6 @@ importFrom(rhdf5,h5write)
107 104 
 importFrom(rhdf5,h5write.default)
108 105 
 importFrom(scran,computeSumFactors)
109 106 
 importFrom(shiny,br)
110 
-importFrom(shiny,brushedPoints)
111 107 
 importFrom(shiny,column)
112 108 
 importFrom(shiny,downloadHandler)
113 109 
 importFrom(shiny,downloadLink)
... ... 
@@ -123,20 +119,16 @@ importFrom(shiny,plotOutput)
123 119 
 importFrom(shiny,reactive)
124 120 
 importFrom(shiny,renderPlot)
125 121 
 importFrom(shiny,renderTable)
126 
-importFrom(shiny,renderText)
127 
-importFrom(shiny,runGadget)
128 122 
 importFrom(shiny,selectInput)
129 123 
 importFrom(shiny,shinyApp)
130 124 
 importFrom(shiny,sidebarLayout)
131 125 
 importFrom(shiny,sidebarPanel)
132 126 
 importFrom(shiny,sliderInput)
133 
-importFrom(shiny,stopApp)
134 127 
 importFrom(shiny,tabPanel)
135 128 
 importFrom(shiny,tableOutput)
136 129 
 importFrom(shiny,tabsetPanel)
137 130 
 importFrom(shiny,titlePanel)
138 131 
 importFrom(shiny,updateSelectInput)
139 
-importFrom(shiny,verbatimTextOutput)
140 132 
 importFrom(stats,approx)
141 133 
 importFrom(stats,as.formula)
142 134 
 importFrom(stats,binomial)
Browse code

Added documentation for fast fnr

mbcole authored on 12/05/2017 07:16:22
Showing 1 changed files
NAMESPACE
History View file @ b05fe70
... ... 
@@ -13,6 +13,7 @@ export(biplot_color)
13 13 
 export(biplot_interactive)
14 14 
 export(estimate_ziber)
15 15 
 export(factor_sample_filter)
16 
+export(fast_estimate_ziber)
16 17 
 export(impute_expectation)
17 18 
 export(impute_null)
18 19 
 export(lm_adjust)
Browse code

Added scran wrapper

mbcole authored on 05/04/2017 20:33:49
Showing 1 changed files
NAMESPACE
History View file @ 1302a82
... ... 
@@ -4,6 +4,7 @@ export(CLR_FN)
4 4 
 export(DESEQ_FN)
5 5 
 export(FQT_FN)
6 6 
 export(FQ_FN)
7 
+export(SCRAN_FN)
7 8 
 export(SUM_FN)
8 9 
 export(SconeExperiment)
9 10 
 export(TMM_FN)
... ... 
@@ -103,6 +104,7 @@ importFrom(rhdf5,h5ls)
103 104 
 importFrom(rhdf5,h5read)
104 105 
 importFrom(rhdf5,h5write)
105 106 
 importFrom(rhdf5,h5write.default)
107 
+importFrom(scran,computeSumFactors)
106 108 
 importFrom(shiny,br)
107 109 
 importFrom(shiny,brushedPoints)
108 110 
 importFrom(shiny,column)
Browse code

RLE = DESEQ and added CLR

mbcole authored on 05/04/2017 19:21:35
Showing 1 changed files
NAMESPACE
History View file @ cda2cbc
... ... 
@@ -1,9 +1,9 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(CLR_FN)
3 4 
 export(DESEQ_FN)
4 5 
 export(FQT_FN)
5 6 
 export(FQ_FN)
6 
-export(RLE_FN)
7 7 
 export(SUM_FN)
8 8 
 export(SconeExperiment)
9 9 
 export(TMM_FN)
... ... 
@@ -43,7 +43,6 @@ import(methods)
43 43 
 import(plotly)
44 44 
 import(visNetwork)
45 45 
 importClassesFrom(SummarizedExperiment,SummarizedExperiment)
46 
-importFrom(DESeq,estimateSizeFactorsForMatrix)
47 46 
 importFrom(DT,dataTableOutput)
48 47 
 importFrom(DT,dataTableProxy)
49 48 
 importFrom(DT,formatSignif)
... ... 
@@ -57,6 +56,7 @@ importFrom(boot,inv.logit)
57 56 
 importFrom(boot,logit)
58 57 
 importFrom(class,knn)
59 58 
 importFrom(cluster,silhouette)
59 
+importFrom(compositions,clr)
60 60 
 importFrom(diptest,dip.test)
61 61 
 importFrom(edgeR,calcNormFactors)
62 62 
 importFrom(fpc,pamk)
Browse code

Updated documentation

mbcole authored on 04/04/2017 21:37:54
Showing 1 changed files
NAMESPACE
History View file @ fa8db85
... ... 
@@ -1,13 +1,13 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export(DESEQ_FN)
4 
-export(DESEQ_FN_POS)
5 4 
 export(FQT_FN)
6 5 
 export(FQ_FN)
6 
+export(RLE_FN)
7 
+export(SUM_FN)
7 8 
 export(SconeExperiment)
8 9 
 export(TMM_FN)
9 10 
 export(UQ_FN)
10 
-export(UQ_FN_POS)
11 11 
 export(biplot_color)
12 12 
 export(biplot_interactive)
13 13 
 export(estimate_ziber)
... ... 
@@ -49,7 +49,6 @@ importFrom(DT,dataTableProxy)
49 49 
 importFrom(DT,formatSignif)
50 50 
 importFrom(DT,renderDataTable)
51 51 
 importFrom(DT,selectRows)
52 
-importFrom(EDASeq,betweenLaneNormalization)
53 52 
 importFrom(NMF,aheatmap)
54 53 
 importFrom(RColorBrewer,brewer.pal)
55 54 
 importFrom(RUVSeq,RUVg)
Browse code

Merge with bioc submission

mbcole authored on 10/01/2017 00:14:56
Showing 0 changed files
Browse code

Modified documentation, more examples and exported getters, added links between SconeExperiment and methods, and apply getters to setValidate

mbcole authored on 14/12/2016 00:54:28
Showing 1 changed files
NAMESPACE
History View file @ 53885e4
... ... 
@@ -4,6 +4,7 @@ export(DESEQ_FN)
4 4 
 export(DESEQ_FN_POS)
5 5 
 export(FQT_FN)
6 6 
 export(FQ_FN)
7 
+export(SconeExperiment)
7 8 
 export(TMM_FN)
8 9 
 export(UQ_FN)
9 10 
 export(UQ_FN_POS)
... ... 
@@ -16,19 +17,24 @@ export(impute_null)
16 17 
 export(lm_adjust)
17 18 
 export(make_design)
18 19 
 export(metric_sample_filter)
19 
-export(sconeExperiment)
20 20 
 export(sconeReport)
21 21 
 export(scone_easybake)
22 22 
 export(score_matrix)
23 23 
 export(simple_FNR_params)
24 24 
 exportClasses(SconeExperiment)
25 
+exportMethods(SconeExperiment)
26 
+exportMethods(get_batch)
27 
+exportMethods(get_bio)
25 28 
 exportMethods(get_design)
29 
+exportMethods(get_negconeval)
30 
+exportMethods(get_negconruv)
26 31 
 exportMethods(get_normalized)
27 32 
 exportMethods(get_params)
33 
+exportMethods(get_poscon)
34 
+exportMethods(get_qc)
28 35 
 exportMethods(get_score_ranks)
29 36 
 exportMethods(get_scores)
30 37 
 exportMethods(scone)
31 
-exportMethods(sconeExperiment)
32 38 
 exportMethods(select_methods)
33 39 
 import(BiocParallel)
34 40 
 import(SummarizedExperiment)
Browse code

Merge functional (R > 3.3) master into develop

mbcole authored on 29/11/2016 01:38:16
Showing 0 changed files
Browse code

Reformat lines and fixed bugs in easy wrapper

mbcole authored on 22/11/2016 22:48:59
Showing 1 changed files
NAMESPACE
History View file @ c9cd07e
... ... 
@@ -4,7 +4,6 @@ export(DESEQ_FN)
4 4 
 export(DESEQ_FN_POS)
5 5 
 export(FQT_FN)
6 6 
 export(FQ_FN)
7 
-export(SCRAN_FN)
8 7 
 export(TMM_FN)
9 8 
 export(UQ_FN)
10 9 
 export(UQ_FN_POS)
... ... 
@@ -98,8 +97,6 @@ importFrom(rhdf5,h5ls)
98 97 
 importFrom(rhdf5,h5read)
99 98 
 importFrom(rhdf5,h5write)
100 99 
 importFrom(rhdf5,h5write.default)
101 
-importFrom(scran,computeSumFactors)
102 
-importFrom(scran,quickCluster)
103 100 
 importFrom(shiny,br)
104 101 
 importFrom(shiny,brushedPoints)
105 102 
 importFrom(shiny,column)
Browse code

Faster svd with rARPACK

Davide Risso authored on 18/11/2016 00:38:50
Showing 1 changed files
NAMESPACE
History View file @ f4cbf2b
... ... 
@@ -91,6 +91,7 @@ importFrom(miniUI,gadgetTitleBar)
91 91 
 importFrom(miniUI,miniContentPanel)
92 92 
 importFrom(miniUI,miniPage)
93 93 
 importFrom(mixtools,normalmixEM)
94 
+importFrom(rARPACK,svds)
94 95 
 importFrom(reshape2,melt)
95 96 
 importFrom(rhdf5,H5close)
96 97 
 importFrom(rhdf5,h5createFile)
Browse code

Updated doumentations and S4 interface fixes

mbcole authored on 14/11/2016 22:31:36
Showing 1 changed files
NAMESPACE
History View file @ e9aed5e
... ... 
@@ -4,11 +4,11 @@ export(DESEQ_FN)
4 4 
 export(DESEQ_FN_POS)
5 5 
 export(FQT_FN)
6 6 
 export(FQ_FN)
7 
-export(LSF_FN)
7 
+export(SCRAN_FN)
8 8 
 export(TMM_FN)
9 9 
 export(UQ_FN)
10 10 
 export(UQ_FN_POS)
11 
-export(biplot_colored)
11 
+export(biplot_color)
12 12 
 export(biplot_interactive)
13 13 
 export(estimate_ziber)
14 14 
 export(factor_sample_filter)
Browse code

Remove zinb functions

Davide Risso authored on 04/11/2016 23:55:09
Showing 1 changed files
NAMESPACE
History View file @ 8cbe329
... ... 
@@ -11,11 +11,9 @@ export(UQ_FN_POS)
11 11 
 export(biplot_colored)
12 12 
 export(biplot_interactive)
13 13 
 export(estimate_ziber)
14 
-export(estimate_zinb)
15 14 
 export(factor_sample_filter)
16 15 
 export(impute_expectation)
17 16 
 export(impute_null)
18 
-export(impute_zinb)
19 17 
 export(lm_adjust)
20 18 
 export(make_design)
21 19 
 export(metric_sample_filter)
... ... 
@@ -47,7 +45,6 @@ importFrom(DT,formatSignif)
47 45 
 importFrom(DT,renderDataTable)
48 46 
 importFrom(DT,selectRows)
49 47 
 importFrom(EDASeq,betweenLaneNormalization)
50 
-importFrom(MASS,glm.nb)
51 48 
 importFrom(NMF,aheatmap)
52 49 
 importFrom(RColorBrewer,brewer.pal)
53 50 
 importFrom(RUVSeq,RUVg)
Browse code

Man page and NAMESPACE for LSF_FN

Davide Risso authored on 04/11/2016 23:46:46
Showing 1 changed files
NAMESPACE
History View file @ 38c19dc
... ... 
@@ -4,6 +4,7 @@ export(DESEQ_FN)
4 4 
 export(DESEQ_FN_POS)
5 5 
 export(FQT_FN)
6 6 
 export(FQ_FN)
7 
+export(LSF_FN)
7 8 
 export(TMM_FN)
8 9 
 export(UQ_FN)
9 10 
 export(UQ_FN_POS)
... ... 
@@ -100,6 +101,8 @@ importFrom(rhdf5,h5ls)
100 101 
 importFrom(rhdf5,h5read)
101 102 
 importFrom(rhdf5,h5write)
102 103 
 importFrom(rhdf5,h5write.default)
104 
+importFrom(scran,computeSumFactors)
105 
+importFrom(scran,quickCluster)
103 106 
 importFrom(shiny,br)
104 107 
 importFrom(shiny,brushedPoints)
105 108 
 importFrom(shiny,column)
Browse code

Updated Default Scaling Documentation and Removed FQP

mbcole authored on 03/11/2016 22:53:13
Showing 1 changed files
NAMESPACE
History View file @ 4633ada
... ... 
@@ -4,7 +4,6 @@ export(DESEQ_FN)
4 4 
 export(DESEQ_FN_POS)
5 5 
 export(FQT_FN)
6 6 
 export(FQ_FN)
7 
-export(FQ_FN_POS)
8 7 
 export(TMM_FN)
9 8 
 export(UQ_FN)
10 9 
 export(UQ_FN_POS)
Browse code

Method for extracting params get_params()

Davide Risso authored on 07/10/2016 23:18:53
Showing 1 changed files
NAMESPACE
History View file @ 664a1a3
... ... 
@@ -27,6 +27,7 @@ export(simple_FNR_params)
27 27 
 exportClasses(SconeExperiment)
28 28 
 exportMethods(get_design)
29 29 
 exportMethods(get_normalized)
30 
+exportMethods(get_params)
30 31 
 exportMethods(get_score_ranks)
31 32 
 exportMethods(get_scores)
32 33 
 exportMethods(scone)
Browse code

get_scores() method

Davide Risso authored on 07/10/2016 23:11:54
Showing 1 changed files
NAMESPACE
History View file @ 4969446
... ... 
@@ -27,6 +27,8 @@ export(simple_FNR_params)
27 27 
 exportClasses(SconeExperiment)
28 28 
 exportMethods(get_design)
29 29 
 exportMethods(get_normalized)
30 
+exportMethods(get_score_ranks)
31 
+exportMethods(get_scores)
30 32 
 exportMethods(scone)
31 33 
 exportMethods(sconeExperiment)
32 34 
 exportMethods(select_methods)
Browse code

Implemented select_methods

Davide Risso authored on 07/10/2016 21:57:53
Showing 1 changed files
NAMESPACE
History View file @ 9685105
... ... 
@@ -29,6 +29,7 @@ exportMethods(get_design)
29 29 
 exportMethods(get_normalized)
30 30 
 exportMethods(scone)
31 31 
 exportMethods(sconeExperiment)
32 
+exportMethods(select_methods)
32 33 
 import(BiocParallel)
33 34 
 import(SummarizedExperiment)
34 35 
 import(gplots)
Browse code

Added get_design(); still need to add tests

Davide Risso authored on 07/10/2016 00:05:11
Showing 1 changed files
NAMESPACE
History View file @ 52bb0a2
... ... 
@@ -25,6 +25,7 @@ export(scone_easybake)
25 25 
 export(score_matrix)
26 26 
 export(simple_FNR_params)
27 27 
 exportClasses(SconeExperiment)
28 
+exportMethods(get_design)
28 29 
 exportMethods(get_normalized)
29 30 
 exportMethods(scone)
30 31 
 exportMethods(sconeExperiment)
Browse code

Added tests for the get_normalized() wrapper.

This exposed a few bugs and issues which are fixed with this
commit. I think it is now possible to close issues #36 and #49.

Davide Risso authored on 06/10/2016 19:54:58
Showing 1 changed files
NAMESPACE
History View file @ c440ebf
... ... 
@@ -90,6 +90,7 @@ importFrom(miniUI,miniContentPanel)
90 90 
 importFrom(miniUI,miniPage)
91 91 
 importFrom(mixtools,normalmixEM)
92 92 
 importFrom(reshape2,melt)
93 
+importFrom(rhdf5,H5close)
93 94 
 importFrom(rhdf5,h5createFile)
94 95 
 importFrom(rhdf5,h5ls)
95 96 
 importFrom(rhdf5,h5read)
Browse code

Wrapper get_normalized to retrieve a single normalization matrix

Davide Risso authored on 06/10/2016 18:36:19
Showing 1 changed files
NAMESPACE
History View file @ 019b4fe
... ... 
@@ -13,7 +13,6 @@ export(biplot_interactive)
13 13 
 export(estimate_ziber)
14 14 
 export(estimate_zinb)
15 15 
 export(factor_sample_filter)
16 
-export(get_normalized)
17 16 
 export(impute_expectation)
18 17 
 export(impute_null)
19 18 
 export(impute_zinb)
... ... 
@@ -26,6 +25,7 @@ export(scone_easybake)
26 25 
 export(score_matrix)
27 26 
 export(simple_FNR_params)
28 27 
 exportClasses(SconeExperiment)
28 
+exportMethods(get_normalized)
29 29 
 exportMethods(scone)
30 30 
 exportMethods(sconeExperiment)
31 31 
 import(BiocParallel)
Browse code

Porting the main scone() function into S4.

This is a partial commit, because I still need to write some helper
methods and to modify the tests. Hence, this will break the build.

Davide Risso authored on 28/09/2016 19:17:43
Showing 1 changed files
NAMESPACE
History View file @ 54e73b8
... ... 
@@ -20,13 +20,13 @@ export(impute_zinb)
20 20 
 export(lm_adjust)
21 21 
 export(make_design)
22 22 
 export(metric_sample_filter)
23 
-export(scone)
24 23 
 export(sconeExperiment)
25 24 
 export(sconeReport)
26 25 
 export(scone_easybake)
27 26 
 export(score_matrix)
28 27 
 export(simple_FNR_params)
29 28 
 exportClasses(SconeExperiment)
29 
+exportMethods(scone)
30 30 
 exportMethods(sconeExperiment)
31 31 
 import(BiocParallel)
32 32 
 import(SummarizedExperiment)
Browse code

Added constructors for the S4 object

Davide Risso authored on 28/09/2016 00:57:35
Showing 1 changed files
NAMESPACE
History View file @ 4206b15
... ... 
@@ -21,11 +21,13 @@ export(lm_adjust)
21 21 
 export(make_design)
22 22 
 export(metric_sample_filter)
23 23 
 export(scone)
24 
+export(sconeExperiment)
24 25 
 export(sconeReport)
25 26 
 export(scone_easybake)
26 27 
 export(score_matrix)
27 28 
 export(simple_FNR_params)
28 29 
 exportClasses(SconeExperiment)
30 
+exportMethods(sconeExperiment)
29 31 
 import(BiocParallel)
30 32 
 import(SummarizedExperiment)
31 33 
 import(gplots)
Browse code

First attempt at creating scone class

Davide Risso authored on 27/09/2016 18:47:30
Showing 1 changed files
NAMESPACE
History View file @ 4b6fc70
... ... 
@@ -25,10 +25,14 @@ export(sconeReport)
25 25 
 export(scone_easybake)
26 26 
 export(score_matrix)
27 27 
 export(simple_FNR_params)
28 
+exportClasses(SconeExperiment)
28 29 
 import(BiocParallel)
30 
+import(SummarizedExperiment)
29 31 
 import(gplots)
32 
+import(methods)
30 33 
 import(plotly)
31 34 
 import(visNetwork)
35 
+importClassesFrom(SummarizedExperiment,SummarizedExperiment)
32 36 
 importFrom(DESeq,estimateSizeFactorsForMatrix)
33 37 
 importFrom(DT,dataTableOutput)
34 38 
 importFrom(DT,dataTableProxy)
Browse code

Added SCONE Report Function, Fixed RLE_IQR metric, and Changed Mean Score to Mean Score Rank to avoidmetric-dependent variances.

mbcole authored on 26/09/2016 07:17:49
Showing 1 changed files
NAMESPACE
History View file @ d9a7803
... ... 
@@ -12,7 +12,6 @@ export(biplot_colored)
12 12 
 export(biplot_interactive)
13 13 
 export(estimate_ziber)
14 14 
 export(estimate_zinb)
15 
-export(simple_FNR_params)
16 15 
 export(factor_sample_filter)
17 16 
 export(get_normalized)
18 17 
 export(impute_expectation)
... ... 
@@ -22,13 +21,23 @@ export(lm_adjust)
22 21 
 export(make_design)
23 22 
 export(metric_sample_filter)
24 23 
 export(scone)
24 
+export(sconeReport)
25 25 
 export(scone_easybake)
26 26 
 export(score_matrix)
27 
+export(simple_FNR_params)
27 28 
 import(BiocParallel)
28 29 
 import(gplots)
30 
+import(plotly)
31 
+import(visNetwork)
29 32 
 importFrom(DESeq,estimateSizeFactorsForMatrix)
33 
+importFrom(DT,dataTableOutput)
34 
+importFrom(DT,dataTableProxy)
35 
+importFrom(DT,formatSignif)
36 
+importFrom(DT,renderDataTable)
37 
+importFrom(DT,selectRows)
30 38 
 importFrom(EDASeq,betweenLaneNormalization)
31 39 
 importFrom(MASS,glm.nb)
40 
+importFrom(NMF,aheatmap)
32 41 
 importFrom(RColorBrewer,brewer.pal)
33 42 
 importFrom(RUVSeq,RUVg)
34 43 
 importFrom(aroma.light,normalizeQuantileRank.matrix)
... ... 
@@ -39,6 +48,18 @@ importFrom(cluster,silhouette)
39 48 
 importFrom(diptest,dip.test)
40 49 
 importFrom(edgeR,calcNormFactors)
41 50 
 importFrom(fpc,pamk)
51 
+importFrom(ggplot2,aes)
52 
+importFrom(ggplot2,coord_cartesian)
53 
+importFrom(ggplot2,element_blank)
54 
+importFrom(ggplot2,geom_bar)
55 
+importFrom(ggplot2,geom_point)
56 
+importFrom(ggplot2,geom_violin)
57 
+importFrom(ggplot2,ggplot)
58 
+importFrom(ggplot2,guides)
59 
+importFrom(ggplot2,labs)
60 
+importFrom(ggplot2,scale_fill_manual)
61 
+importFrom(ggplot2,theme)
62 
+importFrom(ggplot2,ylim)
42 63 
 importFrom(grDevices,colorRampPalette)
43 64 
 importFrom(grDevices,dev.off)
44 65 
 importFrom(grDevices,pdf)
... ... 
@@ -62,18 +83,42 @@ importFrom(miniUI,gadgetTitleBar)
62 83 
 importFrom(miniUI,miniContentPanel)
63 84 
 importFrom(miniUI,miniPage)
64 85 
 importFrom(mixtools,normalmixEM)
86 
+importFrom(reshape2,melt)
65 87 
 importFrom(rhdf5,h5createFile)
66 88 
 importFrom(rhdf5,h5ls)
67 89 
 importFrom(rhdf5,h5read)
68 90 
 importFrom(rhdf5,h5write)
69 91 
 importFrom(rhdf5,h5write.default)
92 
+importFrom(shiny,br)
70 93 
 importFrom(shiny,brushedPoints)
94 
+importFrom(shiny,column)
95 
+importFrom(shiny,downloadHandler)
96 
+importFrom(shiny,downloadLink)
97 
+importFrom(shiny,fluidPage)
98 
+importFrom(shiny,fluidRow)
99 
+importFrom(shiny,h5)
100 
+importFrom(shiny,h6)
101 
+importFrom(shiny,helpText)
102 
+importFrom(shiny,mainPanel)
71 103 
 importFrom(shiny,observeEvent)
104 
+importFrom(shiny,p)
72 105 
 importFrom(shiny,plotOutput)
106 
+importFrom(shiny,reactive)
73 107 
 importFrom(shiny,renderPlot)
108 
+importFrom(shiny,renderTable)
74 109 
 importFrom(shiny,renderText)
75 110 
 importFrom(shiny,runGadget)
111 
+importFrom(shiny,selectInput)
112 
+importFrom(shiny,shinyApp)
113 
+importFrom(shiny,sidebarLayout)
114 
+importFrom(shiny,sidebarPanel)
115 
+importFrom(shiny,sliderInput)
76 116 
 importFrom(shiny,stopApp)
117 
+importFrom(shiny,tabPanel)
118 
+importFrom(shiny,tableOutput)
119 
+importFrom(shiny,tabsetPanel)
120 
+importFrom(shiny,titlePanel)
121 
+importFrom(shiny,updateSelectInput)
77 122 
 importFrom(shiny,verbatimTextOutput)
78 123 
 importFrom(stats,approx)
79 124 
 importFrom(stats,as.formula)
Browse code

added simple_FNR_params to NAMESPACE export

allonwag authored on 04/08/2016 00:41:40
Showing 1 changed files
NAMESPACE
History View file @ e5abfe6
... ... 
@@ -12,6 +12,7 @@ export(biplot_colored)
12 12 
 export(biplot_interactive)
13 13 
 export(estimate_ziber)
14 14 
 export(estimate_zinb)
15 
+export(simple_FNR_params)
15 16 
 export(factor_sample_filter)
16 17 
 export(get_normalized)
17 18 
 export(impute_expectation)
Browse code

easybake with checks

mbcole authored on 28/07/2016 01:40:23
Showing 1 changed files
NAMESPACE
History View file @ 4b0215e
... ... 
@@ -25,7 +25,6 @@ export(scone_easybake)
25 25 
 export(score_matrix)
26 26 
 import(BiocParallel)
27 27 
 import(gplots)
28 
-import(shiny)
29 28 
 importFrom(DESeq,estimateSizeFactorsForMatrix)
30 29 
 importFrom(EDASeq,betweenLaneNormalization)
31 30 
 importFrom(MASS,glm.nb)
... ... 
@@ -40,12 +39,17 @@ importFrom(diptest,dip.test)
40 39 
 importFrom(edgeR,calcNormFactors)
41 40 
 importFrom(fpc,pamk)
42 41 
 importFrom(grDevices,colorRampPalette)
42 
+importFrom(grDevices,dev.off)
43 
+importFrom(grDevices,pdf)
43 44 
 importFrom(graphics,abline)
44 45 
 importFrom(graphics,arrows)
45 46 
 importFrom(graphics,barplot)
46 47 
 importFrom(graphics,hist)
48 
+importFrom(graphics,legend)
49 
+importFrom(graphics,lines)
47 50 
 importFrom(graphics,par)
48 51 
 importFrom(graphics,plot)
52 
+importFrom(graphics,points)
49 53 
 importFrom(graphics,text)
50 54 
 importFrom(hexbin,hexbin)
51 55 
 importFrom(hexbin,plot)
... ... 
@@ -91,3 +95,6 @@ importFrom(stats,quantile)
91 95 
 importFrom(stats,quasibinomial)
92 96 
 importFrom(stats,sd)
93 97 
 importFrom(utils,capture.output)
98 
+importFrom(utils,head)
99 
+importFrom(utils,sessionInfo)
100 
+importFrom(utils,write.table)
Browse code

easybake

mbcole authored on 28/07/2016 00:54:22
Showing 1 changed files
NAMESPACE
History View file @ d1e9956
... ... 
@@ -21,10 +21,11 @@ export(lm_adjust)
21 21 
 export(make_design)
22 22 
 export(metric_sample_filter)
23 23 
 export(scone)
24 
-export(scone_wrapper)
24 
+export(scone_easybake)
25 25 
 export(score_matrix)
26 26 
 import(BiocParallel)
27 27 
 import(gplots)
28 
+import(shiny)
28 29 
 importFrom(DESeq,estimateSizeFactorsForMatrix)
29 30 
 importFrom(EDASeq,betweenLaneNormalization)
30 31 
 importFrom(MASS,glm.nb)
Browse code

Scone Wrapper Phase I

mbcole authored on 27/07/2016 16:40:13
Showing 1 changed files
NAMESPACE
History View file @ e1597fc
... ... 
@@ -21,12 +21,14 @@ export(lm_adjust)
21 21 
 export(make_design)
22 22 
 export(metric_sample_filter)
23 23 
 export(scone)
24 
+export(scone_wrapper)
24 25 
 export(score_matrix)
25 26 
 import(BiocParallel)
26 27 
 import(gplots)
27 28 
 importFrom(DESeq,estimateSizeFactorsForMatrix)
28 29 
 importFrom(EDASeq,betweenLaneNormalization)
29 30 
 importFrom(MASS,glm.nb)
31 
+importFrom(RColorBrewer,brewer.pal)
30 32 
 importFrom(RUVSeq,RUVg)
31 33 
 importFrom(aroma.light,normalizeQuantileRank.matrix)
32 34 
 importFrom(boot,inv.logit)
... ... 
@@ -44,6 +46,8 @@ importFrom(graphics,hist)
44 46 
 importFrom(graphics,par)
45 47 
 importFrom(graphics,plot)
46 48 
 importFrom(graphics,text)
49 
+importFrom(hexbin,hexbin)
50 
+importFrom(hexbin,plot)
47 51 
 importFrom(limma,lmFit)
48 52 
 importFrom(matrixStats,colIQRs)
49 53 
 importFrom(matrixStats,colMedians)
Browse code

Fixed test cases and documentation

mbcole authored on 19/07/2016 18:14:49
Showing 1 changed files
NAMESPACE
History View file @ 412cd2d
... ... 
@@ -13,9 +13,9 @@ export(biplot_interactive)
13 13 
 export(estimate_ziber)
14 14 
 export(estimate_zinb)
15 15 
 export(factor_sample_filter)
16 
+export(get_normalized)
16 17 
 export(impute_expectation)
17 18 
 export(impute_null)
18 
-export(get_normalized)
19 19 
 export(impute_zinb)
20 20 
 export(lm_adjust)
21 21 
 export(make_design)
Browse code

Merge branch 'develop' of https://github.com/YosefLab/scone into develop

mbcole authored on 19/07/2016 02:13:00
Showing 0 changed files
Browse code

Major imputation modifications

mbcole authored on 19/07/2016 01:57:36
Showing 1 changed files
NAMESPACE
History View file @ 6e63d95
... ... 
@@ -12,7 +12,8 @@ export(biplot_colored)
12 12 
 export(estimate_ziber)
13 13 
 export(estimate_zinb)
14 14 
 export(factor_sample_filter)
15 
-export(impute_ziber_simp)
15 
+export(impute_expectation)
16 
+export(impute_null)
16 17 
 export(impute_zinb)
17 18 
 export(lm_adjust)
18 19 
 export(make_design)
Browse code

Merge branch 'feature/wrapper' into develop

Davide Risso authored on 15/07/2016 21:43:13
Showing 0 changed files
Browse code

Do not run interactive example (duh!)

Davide Risso authored on 15/07/2016 03:49:37
Showing 1 changed files
NAMESPACE
History View file @ 0b5c350
... ... 
@@ -54,7 +54,9 @@ importFrom(shiny,brushedPoints)
54 54 
 importFrom(shiny,observeEvent)
55 55 
 importFrom(shiny,plotOutput)
56 56 
 importFrom(shiny,renderPlot)
57 
+importFrom(shiny,renderText)
57 58 
 importFrom(shiny,runGadget)
59 
+importFrom(shiny,stopApp)
58 60 
 importFrom(shiny,verbatimTextOutput)
59 61 
 importFrom(stats,approx)
60 62 
 importFrom(stats,as.formula)
Browse code

Interactive biplot

Davide Risso authored on 15/07/2016 01:06:05
Showing 1 changed files
NAMESPACE
History View file @ 05319c0
... ... 
@@ -9,6 +9,7 @@ export(TMM_FN)
9 9 
 export(UQ_FN)
10 10 
 export(UQ_FN_POS)
11 11 
 export(biplot_colored)
12 
+export(biplot_interactive)
12 13 
 export(estimate_ziber)
13 14 
 export(estimate_zinb)
14 15 
 export(factor_sample_filter)
... ... 
@@ -45,7 +46,16 @@ importFrom(limma,lmFit)
45 46 
 importFrom(matrixStats,colIQRs)
46 47 
 importFrom(matrixStats,colMedians)
47 48 
 importFrom(matrixStats,rowMedians)
49 
+importFrom(miniUI,gadgetTitleBar)
50 
+importFrom(miniUI,miniContentPanel)
51 
+importFrom(miniUI,miniPage)
48 52 
 importFrom(mixtools,normalmixEM)
53 
+importFrom(shiny,brushedPoints)
54 
+importFrom(shiny,observeEvent)
55 
+importFrom(shiny,plotOutput)
56 
+importFrom(shiny,renderPlot)
57 
+importFrom(shiny,runGadget)
58 
+importFrom(shiny,verbatimTextOutput)
49 59 
 importFrom(stats,approx)
50 60 
 importFrom(stats,as.formula)
51 61 
 importFrom(stats,binomial)
Browse code

Import correct hdf5 functions

Davide Risso authored on 14/07/2016 23:55:41
Showing 1 changed files
NAMESPACE
History View file @ ac6774e
... ... 
@@ -49,6 +49,7 @@ importFrom(rhdf5,h5createFile)
49 49 
 importFrom(rhdf5,h5ls)
50 50 
 importFrom(rhdf5,h5read)
51 51 
 importFrom(rhdf5,h5write)
52 
+importFrom(rhdf5,h5write.default)
52 53 
 importFrom(stats,approx)
53 54 
 importFrom(stats,as.formula)
54 55 
 importFrom(stats,binomial)
Browse code

mem_used() is very costly; removed

Davide Risso authored on 08/07/2016 01:46:01
Showing 1 changed files
NAMESPACE
History View file @ ec8826f
... ... 
@@ -32,7 +32,6 @@ importFrom(cluster,silhouette)
32 32 
 importFrom(diptest,dip.test)
33 33 
 importFrom(edgeR,calcNormFactors)
34 34 
 importFrom(fpc,pamk)
35 
-importFrom(gdata,humanReadable)
36 35 
 importFrom(grDevices,colorRampPalette)
37 36 
 importFrom(graphics,abline)
38 37 
 importFrom(graphics,arrows)
... ... 
@@ -46,7 +45,6 @@ importFrom(matrixStats,colIQRs)
46 45 
 importFrom(matrixStats,colMedians)
47 46 
 importFrom(matrixStats,rowMedians)
48 47 
 importFrom(mixtools,normalmixEM)
49 
-importFrom(pryr,mem_used)
50 48 
 importFrom(rhdf5,h5createFile)
51 49 
 importFrom(rhdf5,h5ls)
52 50 
 importFrom(rhdf5,h5read)
Browse code

Bug fix to metric sample filter / redefinition of simple FNR estimation

mbcole authored on 08/07/2016 01:24:26
Showing 1 changed files
NAMESPACE
History View file @ 8e5d7a7
... ... 
@@ -26,6 +26,8 @@ importFrom(EDASeq,betweenLaneNormalization)
26 26 
 importFrom(MASS,glm.nb)
27 27 
 importFrom(RUVSeq,RUVg)
28 28 
 importFrom(aroma.light,normalizeQuantileRank.matrix)
29 
+importFrom(boot,inv.logit)
30 
+importFrom(boot,logit)
29 31 
 importFrom(class,knn)
30 32 
 importFrom(cluster,silhouette)
31 33 
 importFrom(diptest,dip.test)
Browse code

Updated documentation

Davide Risso authored on 08/07/2016 00:55:46
Showing 1 changed files
NAMESPACE
History View file @ fc8c8c3
... ... 
@@ -12,6 +12,7 @@ export(biplot_colored)
12 12 
 export(estimate_ziber)
13 13 
 export(estimate_zinb)
14 14 
 export(factor_sample_filter)
15 
+export(get_normalized)
15 16 
 export(impute_ziber_simp)
16 17 
 export(impute_zinb)
17 18 
 export(lm_adjust)
... ... 
@@ -31,6 +32,7 @@ importFrom(cluster,silhouette)
31 32 
 importFrom(diptest,dip.test)
32 33 
 importFrom(edgeR,calcNormFactors)
33 34 
 importFrom(fpc,pamk)
35 
+importFrom(gdata,humanReadable)
34 36 
 importFrom(grDevices,colorRampPalette)
35 37 
 importFrom(graphics,abline)
36 38 
 importFrom(graphics,arrows)
... ... 
@@ -44,6 +46,11 @@ importFrom(matrixStats,colIQRs)
44 46 
 importFrom(matrixStats,colMedians)
45 47 
 importFrom(matrixStats,rowMedians)
46 48 
 importFrom(mixtools,normalmixEM)
49 
+importFrom(pryr,mem_used)
50 
+importFrom(rhdf5,h5createFile)
51 
+importFrom(rhdf5,h5ls)
52 
+importFrom(rhdf5,h5read)
53 
+importFrom(rhdf5,h5write)
47 54 
 importFrom(stats,approx)
48 55 
 importFrom(stats,as.formula)
49 56 
 importFrom(stats,binomial)
Browse code

Fixed CMD check warnings and NAMESPACE issues.

mbcole authored on 14/06/2016 23:46:30
Showing 1 changed files
NAMESPACE
History View file @ 2424a11
... ... 
@@ -32,8 +32,36 @@ importFrom(diptest,dip.test)
32 32 
 importFrom(edgeR,calcNormFactors)
33 33 
 importFrom(fpc,pamk)
34 34 
 importFrom(grDevices,colorRampPalette)
35 
+importFrom(graphics,abline)
36 
+importFrom(graphics,arrows)
37 
+importFrom(graphics,barplot)
38 
+importFrom(graphics,hist)
39 
+importFrom(graphics,par)
40 
+importFrom(graphics,plot)
41 
+importFrom(graphics,text)
35 42 
 importFrom(limma,lmFit)
36 43 
 importFrom(matrixStats,colIQRs)
37 44 
 importFrom(matrixStats,colMedians)
38 45 
 importFrom(matrixStats,rowMedians)
39 46 
 importFrom(mixtools,normalmixEM)
47 
+importFrom(stats,approx)
48 
+importFrom(stats,as.formula)
49 
+importFrom(stats,binomial)
50 
+importFrom(stats,coefficients)
51 
+importFrom(stats,contr.sum)
52 
+importFrom(stats,cor)
53 
+importFrom(stats,dist)
54 
+importFrom(stats,dnbinom)
55 
+importFrom(stats,fitted.values)
56 
+importFrom(stats,glm)
57 
+importFrom(stats,mad)
58 
+importFrom(stats,median)
59 
+importFrom(stats,model.matrix)
60 
+importFrom(stats,na.omit)
61 
+importFrom(stats,p.adjust)
62 
+importFrom(stats,pnorm)
63 
+importFrom(stats,prcomp)
64 
+importFrom(stats,quantile)
65 
+importFrom(stats,quasibinomial)
66 
+importFrom(stats,sd)
67 
+importFrom(utils,capture.output)
Browse code

Multiple changes. See inst/NEWS

mbcole authored on 08/06/2016 21:32:39
Showing 1 changed files
NAMESPACE
History View file @ 2af67a4
... ... 
@@ -28,7 +28,6 @@ importFrom(RUVSeq,RUVg)
28 28 
 importFrom(aroma.light,normalizeQuantileRank.matrix)
29 29 
 importFrom(class,knn)
30 30 
 importFrom(cluster,silhouette)
31 
-importFrom(clusterExperiment,subsampleClustering)
32 31 
 importFrom(diptest,dip.test)
33 32 
 importFrom(edgeR,calcNormFactors)
34 33 
 importFrom(fpc,pamk)
Browse code

Handling of ties by FQ

Davide Risso authored on 06/06/2016 22:45:57
Showing 1 changed files
NAMESPACE
History View file @ 450e1a6
... ... 
@@ -2,6 +2,7 @@
2 2
3 3 
 export(DESEQ_FN)
4 4 
 export(DESEQ_FN_POS)
5 
+export(FQT_FN)
5 6 
 export(FQ_FN)
6 7 
 export(FQ_FN_POS)
7 8 
 export(TMM_FN)
Browse code

Added RLE measures to scone evaluation

Davide Risso authored on 06/06/2016 19:18:23
Showing 1 changed files
NAMESPACE
History View file @ 95a0cbf
... ... 
@@ -33,6 +33,7 @@ importFrom(edgeR,calcNormFactors)
33 33 
 importFrom(fpc,pamk)
34 34 
 importFrom(grDevices,colorRampPalette)
35 35 
 importFrom(limma,lmFit)
36 
+importFrom(matrixStats,colIQRs)
37 
+importFrom(matrixStats,colMedians)
36 38 
 importFrom(matrixStats,rowMedians)
37 39 
 importFrom(mixtools,normalmixEM)
38 
-importFrom(grDevices, dev.off, pdf)
Browse code

Fix R CMD check

Davide Risso authored on 02/06/2016 01:09:42
Showing 1 changed files
NAMESPACE
History View file @ 92d9925
... ... 
@@ -35,3 +35,4 @@ importFrom(grDevices,colorRampPalette)
35 35 
 importFrom(limma,lmFit)
36 36 
 importFrom(matrixStats,rowMedians)
37 37 
 importFrom(mixtools,normalmixEM)
38 
+importFrom(grDevices, dev.off, pdf)
Browse code

Updated clusterExperiment dependency

mbcole authored on 12/05/2016 15:54:48
Showing 1 changed files
NAMESPACE
History View file @ aad3b60
... ... 
@@ -27,7 +27,7 @@ importFrom(RUVSeq,RUVg)
27 27 
 importFrom(aroma.light,normalizeQuantileRank.matrix)
28 28 
 importFrom(class,knn)
29 29 
 importFrom(cluster,silhouette)
30 
-importFrom(clusterCells,subsampleClustering)
30 
+importFrom(clusterExperiment,subsampleClustering)
31 31 
 importFrom(diptest,dip.test)
32 32 
 importFrom(edgeR,calcNormFactors)
33 33 
 importFrom(fpc,pamk)
Browse code

Projection functions are now passed as arguments and evaluated per normalized matrix.

mbcole authored on 06/05/2016 23:55:23
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NAMESPACE
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@@ -35,4 +35,3 @@ importFrom(grDevices,colorRampPalette)
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 importFrom(limma,lmFit)
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 importFrom(matrixStats,rowMedians)
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 importFrom(mixtools,normalmixEM)
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-importFrom(scde,bwpca)
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Replaced BIO and BATCH KNN with SIL and replaced compactness with PAM SIL score.

mbcole authored on 06/05/2016 22:14:14
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NAMESPACE
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@@ -26,6 +26,7 @@ importFrom(MASS,glm.nb)
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 importFrom(RUVSeq,RUVg)
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 importFrom(aroma.light,normalizeQuantileRank.matrix)
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 importFrom(class,knn)
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+importFrom(cluster,silhouette)
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 importFrom(clusterCells,subsampleClustering)
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 importFrom(diptest,dip.test)
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 importFrom(edgeR,calcNormFactors)
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Biplot implementation

Davide Risso authored on 02/05/2016 22:19:31
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NAMESPACE