dev/Dependencies.R

In jn-goe/gruffi: Gruffi identifies and removes stressed cells from brain organoid single-cell datasets.

Dependency file generated on Sat Mar  2 15:13:30 2024 

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gruffi.optional.R
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$`c("package:Seurat", "package:SeuratObject")`
[1] "Cells"

$`c("package:SeuratObject", "package:base")`
[1] "rowSums"

$`character(0)`
 [1] "binning"               "calc.cluster.averages" "cividis"              
 [4] "clUMAP"                "cube3d"                "GetClusteringRuns"    
 [7] "isave.RDS"             "modal"                 "open3d"               
[10] "qbarplot"              "qscatter"              "rglwidget"            
[13] "saveWidget"            "shade3d"               "tibble"               
[16] "translate3d"          

$`package:base`
 [1] "abs"          "all"          "as.character" "as.factor"    "as.logical"  
 [6] "c"            "cbind"        "colnames"     "data.frame"   "dim"         
[11] "factor"       "length"       "levels"       "logical"      "make.names"  
[16] "max"          "mean"         "names"        "paste0"       "print"       
[21] "rep"          "return"       "rownames"     "sample"       "sort"        
[26] "subset"       "table"        "unique"       "warning"      "which"       

$`package:CodeAndRoll2`
[1] "matrix.fromNames" "which_names"     

$`package:gruffi`
[1] ".convert.GO_term.2.score"

$`package:MarkdownHelpers`
[1] "filter_HP" "llprint"  

$`package:Seurat`
[1] "RunTSNE" "RunUMAP"

$`package:stats`
[1] "quantile"

$`package:Stringendo`
[1] "iprint"               "percentage_formatter"

c("Seurat", "SeuratObject")
c("SeuratObject", "base")
character(0)
base
CodeAndRoll2
gruffi
MarkdownHelpers
Seurat
stats
Stringendo
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gruffi.R
#################################################################################################### 
$.GlobalEnv
[1] "p0"

$`c("package:gruffi", "package:PackageTools", "devtools_shims", "package:base")`
[1] "system.file"

$`c("package:Seurat", "package:SeuratObject")`
[1] "DefaultAssay" "GetAssayData" "Idents"       "RenameIdents"

$`c("package:SeuratObject", "package:base")`
[1] "colSums"   "intersect"

$`character(0)`
 [1] "calc.cluster.averages"   "clUMAP"                  "geom_vline"             
 [4] "getBM"                   "GetClusteringRuns"       "group_by_at"            
 [7] "hue_pal"                 "imessage"                "kppws"                  
[10] "labs"                    "mixedsort"               "multiFeaturePlot.A4"    
[13] "n"                       "nbrOfWorkers"            "qbarplot"               
[16] "qhistogram"              "qqSave"                  "runApp"                 
[19] "save_plot"               "scBarplot.CellFractions" "select"                 
[22] "select_at"               "shinyApp"                "summarize"              
[25] "sym"                     "Term"                    "tic"                    
[28] "toc"                     "useEnsembl"             

$`package:base`
 [1] ".Deprecated"  "abs"          "all"          "anyNA"        "as.character"
 [6] "as.matrix"    "as.numeric"   "by"           "c"            "cat"         
[11] "ceiling"      "colnames"     "diag"         "dim"          "exists"      
[16] "file.path"    "floor"        "grep"         "grepl"        "gsub"        
[21] "inherits"     "is.character" "is.list"      "is.logical"   "is.na"       
[26] "is.null"      "is.numeric"   "length"       "levels"       "list"        
[31] "make.names"   "matrix"       "max"          "mean"         "message"     
[36] "min"          "names"        "nchar"        "ncol"         "new.env"     
[41] "paste"        "paste0"       "print"        "range"        "require"     
[46] "return"       "rev"          "round"        "rownames"     "scale"       
[51] "setdiff"      "signif"       "sort"         "source"       "sqrt"        
[56] "stop"         "stopifnot"    "strsplit"     "substitute"   "sum"         
[61] "system"       "table"        "try"          "unique"       "warning"     
[66] "which"        "which.min"   

$`package:CodeAndRoll2`
[1] "cv"             "grepv"          "pc_TRUE"        "sem"           
[5] "sortbyitsnames"

$`package:graphics`
[1] "hist"

$`package:gruffi`
 [1] ".convert.GO_term.2.score"         ".convert.score.2.GO_term"        
 [3] ".fix.metad.colname.rm.trailing.1" ".parse.GO"                       
 [5] ".round"                           "AddGOScore"                      
 [7] "CalcClusterAverages_Gruffi"       "CalcStandDevSkewedDistr"         
 [9] "CalculateAndPlotGoTermScores"     "CalculateMedianClusterSize"      
[11] "FeaturePlotSaveGO"                "GetGOTerms"                      
[13] "GetGruffiClusteringName"          "GrScoreHistogram"                
[15] "GrScoreUMAP"                      "IntersectWithExpressed"          
[17] "PlotNormAndSkew"                  "StressUMAP"                      

$`package:MarkdownHelpers`
[1] "stopif"        "ww.FnP_parser"

$`package:Seurat`
[1] "AddModuleScore" "FeaturePlot"    "FindClusters"   "NoAxes"        
[5] "RunUMAP"       

$`package:SeuratObject`
[1] "plan"

$`package:stats`
[1] "dist"     "median"   "qnorm"    "quantile"

$`package:Stringendo`
[1] "flag.nameiftrue"      "iprint"               "kpp"                 
[4] "kppd"                 "kpps"                 "kppu"                
[7] "percentage_formatter" "ppp"                 

$`package:utils`
[1] "head"

.GlobalEnv
c("gruffi", "PackageTools", "devtools_shims", "base")
c("Seurat", "SeuratObject")
c("SeuratObject", "base")
character(0)
base
CodeAndRoll2
graphics
gruffi
MarkdownHelpers
Seurat
SeuratObject
stats
Stringendo
utils