Merge branch 'release/v0.99.0'

.Rbuildignore

@@ -38,3 +38,4 @@ R/.Rhistory
 ^old_scripts/*
 ^.*\.Rproj$
 ^\.Rproj\.user$
+scripts

.travis.yml

@@ -21,8 +21,8 @@ r:
 ## Turn this to true before submission to CRAN/Bioconductor
 warnings_are_errors: false
 
-r_build_args: "--no-build-vignettes"
-r_check_args: "--no-vignettes"
+# r_build_args: "--no-build-vignettes"
+# r_check_args: "--no-vignettes"
 
 notifications:
   email:

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: scone
-Version: 0.0.8
+Version: 0.99.0
 Title: Single Cell Overview of Normalized Expression data
 Description: SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.
 Authors@R: c(person("Michael", "Cole", email = "[email protected]",
@@ -8,11 +8,15 @@ Authors@R: c(person("Michael", "Cole", email = "[email protected]",
 	          role = c("aut", "cph")))
 Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
 Maintainer: Michael Cole <[email protected]>
-Date: 2016-09-27
-License: file LICENSE
+License: Artistic-2.0
 Depends:
-  R (>= 3.3)
+  R (>= 3.3),
+  methods,
+  SummarizedExperiment
 Imports:
+  graphics,
+  stats,
+  utils,
   aroma.light,
   BiocParallel,
   class,
@@ -26,7 +30,6 @@ Imports:
   grDevices,
   hexbin,
   limma,
-  MASS,
   matrixStats,
   mixtools,
   RColorBrewer,
@@ -40,12 +43,23 @@ Imports:
   ggplot2,
   plotly,
   reshape2,
+  scran,
   visNetwork
 Suggests:
+  BiocStyle,
+  scRNAseq,
   knitr,
   rmarkdown,
   testthat
 VignetteBuilder: knitr
 LazyLoad: yes
+biocViews:
+  Normalization,
+  Preprocessing,
+  QualityControl,
+  GeneExpression,
+  RNASeq,
+  Software,
+  Transcriptomics
 BugReports: https://github.com/YosefLab/scone/issues
 RoxygenNote: 5.0.1

NAMESPACE

@@ -4,39 +4,47 @@ export(DESEQ_FN)
 export(DESEQ_FN_POS)
 export(FQT_FN)
 export(FQ_FN)
-export(FQ_FN_POS)
+export(SCRAN_FN)
 export(TMM_FN)
 export(UQ_FN)
 export(UQ_FN_POS)
-export(biplot_colored)
+export(biplot_color)
 export(biplot_interactive)
 export(estimate_ziber)
-export(estimate_zinb)
 export(factor_sample_filter)
-export(get_normalized)
 export(impute_expectation)
 export(impute_null)
-export(impute_zinb)
 export(lm_adjust)
 export(make_design)
 export(metric_sample_filter)
-export(scone)
+export(sconeExperiment)
 export(sconeReport)
 export(scone_easybake)
 export(score_matrix)
 export(simple_FNR_params)
+exportClasses(SconeExperiment)
+exportMethods(get_design)
+exportMethods(get_normalized)
+exportMethods(get_params)
+exportMethods(get_score_ranks)
+exportMethods(get_scores)
+exportMethods(scone)
+exportMethods(sconeExperiment)
+exportMethods(select_methods)
 import(BiocParallel)
+import(SummarizedExperiment)
 import(gplots)
+import(methods)
 import(plotly)
 import(visNetwork)
+importClassesFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(DESeq,estimateSizeFactorsForMatrix)
 importFrom(DT,dataTableOutput)
 importFrom(DT,dataTableProxy)
 importFrom(DT,formatSignif)
 importFrom(DT,renderDataTable)
 importFrom(DT,selectRows)
 importFrom(EDASeq,betweenLaneNormalization)
-importFrom(MASS,glm.nb)
 importFrom(NMF,aheatmap)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(RUVSeq,RUVg)
@@ -84,11 +92,14 @@ importFrom(miniUI,miniContentPanel)
 importFrom(miniUI,miniPage)
 importFrom(mixtools,normalmixEM)
 importFrom(reshape2,melt)
+importFrom(rhdf5,H5close)
 importFrom(rhdf5,h5createFile)
 importFrom(rhdf5,h5ls)
 importFrom(rhdf5,h5read)
 importFrom(rhdf5,h5write)
 importFrom(rhdf5,h5write.default)
+importFrom(scran,computeSumFactors)
+importFrom(scran,quickCluster)
 importFrom(shiny,br)
 importFrom(shiny,brushedPoints)
 importFrom(shiny,column)