First packaged version

Author: vertesy

.Rbuildignore

@@ -0,0 +1,2 @@
+^gruffi\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -37,3 +37,4 @@ vignettes/*.pdf
 
 # R Environment Variables
 .Renviron
+.Rproj.user

DESCRIPTION

@@ -0,0 +1,52 @@
+Package: gruffi
+Title: gruffi is the fastest way to create, annotate and export plots in R
+Version: 0.6.0
+Authors@R: 
+    person("First", "Last", , "first.last@example.com", role = c("aut", "cre"),
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Author: Julia Naas <julia.naas@meduniwien.ac.at> [aut, cre]Abel Vertesy
+    <abel.vertesy@imba.oeaw.ac.at> [aut, cre]
+Description: The Gruffi R package helps you (1) to identify stressed cells
+    in single-cell RNA-seq datasets using *granular funcitonal filtering*,
+    and (2) you can use it to calculate any GO-term defined gene set's
+    pathway activity. Gruffi integrates into single-cell analysis with
+    Seurat and comes with a graphical user interface.
+License: GPL-3 + file LICENSE
+BugReports: https://github.com/jn-goe/gruffi/issues/
+Depends: 
+    magrittr,
+    Stringendo
+Imports: 
+    AnnotationDbi,
+    biomaRt,
+    clipr,
+    CodeAndRoll2,
+    cowplot,
+    ggExpress,
+    ggpubr,
+    graphics,
+    grDevices,
+    htmlwidgets,
+    IRanges,
+    MarkdownHelpers,
+    MarkdownReports,
+    Matrix,
+    methods,
+    org.Hs.eg.db,
+    raster,
+    RColorBrewer,
+    rgl,
+    rlang,
+    sessioninfo,
+    Seurat,
+    Seurat.utils,
+    shiny,
+    sm,
+    stats,
+    tictoc,
+    tidyverse,
+    viridis
+Encoding: UTF-8
+Packaged: 2022-03-15 09:51:05
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.2

NAMESPACE

@@ -0,0 +1,86 @@
+# Generated by roxygen2: do not edit by hand
+
+S3method(plot,clust.size.distr)
+export(AddCustomScore)
+export(AddGOGeneList.manual)
+export(AddGOScore)
+export(CalcTranscriptomePercentage)
+export(CalcTranscriptomePercentageGO)
+export(FeaturePlotSaveCustomScore)
+export(FeaturePlotSaveGO)
+export(FilterStressedCells)
+export(GO_score_evaluation)
+export(GetAllGOTerms)
+export(GetClusteringRuns)
+export(GetGOTerms)
+export(GetNamedClusteringRuns)
+export(IntersectWithExpressed)
+export(PasteUniqueGeneList)
+export(PlotGoTermScores)
+export(Shiny.GO.thresh)
+export(UMAP.3d.cubes)
+export(aut.res.clustering)
+export(calc.cluster.averages.new)
+export(clUMAP.thresholding)
+export(clean.duplicate.scorenames)
+export(fix.metad.Colname.rm.trailing.1)
+export(plot_norm_and_skew)
+export(reassign.small.clusters)
+export(saveData)
+export(saveRDS.compress.in.BG)
+export(sparse.cor)
+export(stand_dev_skewed)
+export(ww.convert.GO_term.2.score)
+export(ww.convert.score.2.GO_term)
+importFrom(AnnotationDbi,Term)
+importFrom(AnnotationDbi,select)
+importFrom(CodeAndRoll2,grepv)
+importFrom(CodeAndRoll2,sem)
+importFrom(CodeAndRoll2,sortbyitsnames)
+importFrom(IRanges,gsub)
+importFrom(MarkdownHelpers,filter_HP)
+importFrom(MarkdownHelpers,llprint)
+importFrom(MarkdownHelpers,stopif)
+importFrom(Matrix,colMeans)
+importFrom(Matrix,colSums)
+importFrom(Seurat,AddModuleScore)
+importFrom(Seurat,Cells)
+importFrom(Seurat,DefaultAssay)
+importFrom(Seurat,FeaturePlot)
+importFrom(Seurat,FindClusters)
+importFrom(Seurat,GetAssayData)
+importFrom(Seurat,Idents)
+importFrom(Seurat,RenameIdents)
+importFrom(Seurat,RunTSNE)
+importFrom(Seurat,RunUMAP)
+importFrom(Seurat.utils,calc.cluster.averages)
+importFrom(Stringendo,iprint)
+importFrom(Stringendo,percentage_formatter)
+importFrom(Stringendo,ww.FnP_parser)
+importFrom(biomaRt,getBM)
+importFrom(biomaRt,useEnsembl)
+importFrom(clipr,read_clip)
+importFrom(cowplot,save_plot)
+importFrom(dplyr,group_by_at)
+importFrom(dplyr,n)
+importFrom(dplyr,select_at)
+importFrom(dplyr,summarize)
+importFrom(dplyr,tibble)
+importFrom(ggExpress,qbarplot)
+importFrom(ggExpress,qhistogram)
+importFrom(ggplot2,labs)
+importFrom(htmlwidgets,saveWidget)
+importFrom(org.Hs.eg.db,org.Hs.eg.db)
+importFrom(raster,modal)
+importFrom(rgl,cube3d)
+importFrom(rgl,open3d)
+importFrom(rgl,rglwidget)
+importFrom(rgl,shade3d)
+importFrom(rgl,translate3d)
+importFrom(rlang,sym)
+importFrom(shiny,runApp)
+importFrom(shiny,shinyApp)
+importFrom(sm,binning)
+importFrom(tictoc,tic)
+importFrom(tictoc,toc)
+importFrom(viridis,cividis)

dev/Create.the.gruffi.Package.R

@@ -17,7 +17,7 @@ require('Stringendo')
 
 
 # Setup ------------------------
-PackageName = "gruffiDev"
+PackageName = "gruffi"
 package.version = "0.6.0"
 setwd("~/GitHub/Packages/")
 

gruffi.Rproj

@@ -1,16 +1,17 @@
 Version: 1.0
 
-RestoreWorkspace: Default
-SaveWorkspace: Default
+RestoreWorkspace: No
+SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
 Encoding: UTF-8
 
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace