Merge pull request #151 from BorchLab/dev

v2.5.0

Author: ncborcherding

.gitignore

@@ -3,4 +3,5 @@
 .RHistory
 escape.Rproj
 .Rproj*
-.RData
+.RData
+**/.tmp.driveupload

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: escape
 Title: Easy single cell analysis platform for enrichment
-Version: 2.3.1
+Version: 2.5.0
 Authors@R: c(
     person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"),
     person(given = "Jared", family = "Andrews", role = c("aut"), email = "jared.andrews07@gmail.com"),
@@ -13,42 +13,43 @@ LazyData: false
 RoxygenNote: 7.3.2
 biocViews: Software, SingleCell, Classification, Annotation, GeneSetEnrichment, Sequencing, GeneSignaling, Pathways
 Depends: R (>= 4.1)
-Imports: 
+Imports:
+    ggdist,
+    ggplot2 (>= 3.5.0),
+    grDevices,
+    Matrix,
+    MatrixGenerics,
+    methods,
+    stats,
+    SummarizedExperiment,
+    utils
+Suggests:
     AUCell,
     BiocParallel,
-    grDevices,
+    BiocStyle,
     dplyr,
-    ggdist,
-    ggplot2,
-    ggpointdensity,
+    fgsea,
     GSEABase,
-    GSVA,
-    SingleCellExperiment,
+    ggraph,
     ggridges,
-    msigdb,
-    stats,
-    reshape2,
-    patchwork,
-    MatrixGenerics,
-    utils,
-    SummarizedExperiment,
-    UCell,
-    stringr,
-    methods,
-    SeuratObject,
-    Matrix
-Suggests: 
-    Seurat,
+    ggpointdensity,
+    GSVA,
     hexbin,
-    scran,
+    igraph,
+    irlba,
     knitr,
+    msigdb,
+    patchwork,
     rmarkdown,
-    markdown,
-    BiocStyle,
-    RColorBrewer,
     rlang,
+    scran,
+    SeuratObject,
+    Seurat,
+    SingleCellExperiment,
     spelling,
+    stringr,
     testthat (>= 3.0.0),
-    vdiffr
+    UCell
 VignetteBuilder: knitr
 Language: en-US
+BugReports: https://github.com/BorchLab/escape/issues

NAMESPACE

@@ -1,9 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
 export(densityEnrichment)
+export(enrichIt)
+export(enrichItPlot)
 export(escape.matrix)
 export(getGeneSets)
 export(geyserEnrichment)
+export(gseaEnrichment)
 export(heatmapEnrichment)
 export(pcaEnrichment)
 export(performNormalization)
@@ -13,58 +16,17 @@ export(runEscape)
 export(scatterEnrichment)
 export(splitEnrichment)
 import(ggplot2)
-import(patchwork)
-importFrom(AUCell,AUCell_buildRankings)
-importFrom(AUCell,AUCell_calcAUC)
-importFrom(BiocParallel,BatchtoolsParam)
-importFrom(BiocParallel,MulticoreParam)
-importFrom(BiocParallel,SerialParam)
-importFrom(GSEABase,GeneSet)
-importFrom(GSEABase,GeneSetCollection)
-importFrom(GSEABase,geneIds)
-importFrom(GSVA,gsva)
-importFrom(GSVA,gsvaParam)
-importFrom(GSVA,ssgseaParam)
-importFrom(Matrix,colSums)
-importFrom(Matrix,t)
+importFrom(MatrixGenerics,rowMeans2)
 importFrom(MatrixGenerics,rowSds)
-importFrom(MatrixGenerics,rowSums2)
-importFrom(SeuratObject,Assays)
-importFrom(SeuratObject,CreateAssay5Object)
-importFrom(SeuratObject,CreateAssayObject)
-importFrom(SeuratObject,CreateDimReducObject)
-importFrom(SeuratObject,Idents)
-importFrom(SingleCellExperiment,"altExp<-")
-importFrom(SingleCellExperiment,"reducedDim<-")
-importFrom(SingleCellExperiment,altExp)
-importFrom(SingleCellExperiment,altExps)
-importFrom(SingleCellExperiment,colData)
-importFrom(SingleCellExperiment,reducedDim)
-importFrom(SummarizedExperiment,"assays<-")
-importFrom(SummarizedExperiment,SummarizedExperiment)
-importFrom(SummarizedExperiment,assay)
-importFrom(SummarizedExperiment,assays)
-importFrom(UCell,ScoreSignatures_UCell)
-importFrom(dplyr,"%>%")
-importFrom(dplyr,across)
-importFrom(dplyr,group_by)
-importFrom(dplyr,slice_max)
-importFrom(dplyr,summarise)
-importFrom(dplyr,summarise_at)
+importFrom(SummarizedExperiment,colData)
 importFrom(ggdist,stat_pointinterval)
-importFrom(ggpointdensity,geom_pointdensity)
-importFrom(ggridges,geom_density_ridges)
-importFrom(ggridges,geom_density_ridges2)
-importFrom(ggridges,geom_density_ridges_gradient)
-importFrom(ggridges,position_points_jitter)
-importFrom(grDevices,hcl.colors)
-importFrom(methods,slot)
-importFrom(msigdb,appendKEGG)
-importFrom(msigdb,getMsigdb)
-importFrom(reshape2,melt)
+importFrom(grDevices,hcl.pals)
+importFrom(stats,aggregate)
+importFrom(stats,as.formula)
 importFrom(stats,dist)
 importFrom(stats,hclust)
-importFrom(stats,prcomp)
-importFrom(stringr,str_replace_all)
-importFrom(stringr,str_sort)
-importFrom(utils,getFromNamespace)
+importFrom(stats,median)
+importFrom(stats,na.omit)
+importFrom(stats,p.adjust)
+importFrom(stats,setNames)
+importFrom(utils,head)