p values for frequency calculations (#136)

DESCRIPTION

@@ -20,11 +20,10 @@ License: MIT + file LICENSE
 URL: https://rnabioco.github.io/djvdj/, https://github.com/rnabioco/djvdj/
 BugReports: https://github.com/rnabioco/djvdj/issues
 Depends:
-    R (>= 4.2.0)
+    R (>= 4.3.0)
 Imports: 
     abdiv,
     boot,
-    broom,
     cli,
     ComplexHeatmap,
     dplyr,
@@ -41,18 +40,19 @@ Imports:
     rlang (>= 0.4.11),
     S4Vectors,
     scales,
-    Seurat (>= 4.0.0),
     SingleCellExperiment,
     stats,
     stringr,
     tibble,
     tidyr,
     utils
 Suggests: 
+    Seurat (>= 4.0.0),
     Biostrings,
     circlize,
     covr,
     dbscan,
+    edgeR,
     ggseqlogo,
     here,
     igraph (>= 1.3.0),
@@ -71,4 +71,4 @@ Config/Needs/website: pkgdown, rnabioco/rbitemplate
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%+replace%")
 export("%||%")
 export(":=")
 export(.data)
@@ -35,101 +36,14 @@ export(plot_similarity)
 export(plot_violin)
 export(summarize_vdj)
 import(dplyr)
-importFrom(ComplexHeatmap,Heatmap)
-importFrom(S4Vectors,DataFrame)
-importFrom(SingleCellExperiment,colData)
-importFrom(abdiv,jaccard)
-importFrom(abdiv,simpson)
-importFrom(boot,boot)
-importFrom(broom,tidy)
-importFrom(cli,cli_abort)
-importFrom(cli,cli_alert)
-importFrom(cli,cli_warn)
-importFrom(ggplot2,aes)
-importFrom(ggplot2,after_stat)
-importFrom(ggplot2,element_blank)
-importFrom(ggplot2,element_line)
-importFrom(ggplot2,element_text)
-importFrom(ggplot2,expansion)
-importFrom(ggplot2,facet_wrap)
-importFrom(ggplot2,geom_boxplot)
-importFrom(ggplot2,geom_col)
-importFrom(ggplot2,geom_density)
-importFrom(ggplot2,geom_histogram)
-importFrom(ggplot2,geom_line)
-importFrom(ggplot2,geom_point)
-importFrom(ggplot2,geom_tile)
-importFrom(ggplot2,geom_violin)
-importFrom(ggplot2,ggplot)
-importFrom(ggplot2,guide_legend)
-importFrom(ggplot2,guides)
-importFrom(ggplot2,labs)
-importFrom(ggplot2,position_dodge2)
-importFrom(ggplot2,scale_color_gradientn)
-importFrom(ggplot2,scale_color_manual)
-importFrom(ggplot2,scale_fill_gradientn)
-importFrom(ggplot2,scale_fill_manual)
-importFrom(ggplot2,scale_x_continuous)
-importFrom(ggplot2,scale_x_discrete)
-importFrom(ggplot2,scale_y_continuous)
-importFrom(ggplot2,stat_summary)
-importFrom(ggplot2,theme)
-importFrom(ggrepel,geom_text_repel)
-importFrom(ggtrace,geom_point_trace)
-importFrom(glue,glue)
-importFrom(graphics,par)
-importFrom(graphics,plot.new)
-importFrom(graphics,strwidth)
-importFrom(graphics,title)
-importFrom(grid,grid.rect)
-importFrom(grid,unit)
-importFrom(grid,viewport)
-importFrom(methods,as)
-importFrom(methods,formalArgs)
+importFrom(ggplot2,"%+replace%")
 importFrom(methods,slot)
-importFrom(purrr,as_mapper)
-importFrom(purrr,imap)
-importFrom(purrr,imap_dfr)
-importFrom(purrr,is_empty)
-importFrom(purrr,is_formula)
-importFrom(purrr,is_function)
-importFrom(purrr,iwalk)
-importFrom(purrr,keep)
-importFrom(purrr,map)
-importFrom(purrr,map2_int)
-importFrom(purrr,map_chr)
-importFrom(purrr,map_dbl)
-importFrom(purrr,map_dfr)
-importFrom(purrr,map_int)
-importFrom(purrr,map_lgl)
-importFrom(purrr,pwalk)
-importFrom(purrr,reduce)
-importFrom(readr,cols)
-importFrom(readr,guess_parser)
-importFrom(readr,read_csv)
 importFrom(rlang,"%||%")
 importFrom(rlang,":=")
 importFrom(rlang,.data)
 importFrom(rlang,as_label)
 importFrom(rlang,as_name)
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
-importFrom(rlang,is_installed)
-importFrom(scales,hue_pal)
-importFrom(stats,as.dist)
-importFrom(stats,as.formula)
-importFrom(stats,complete.cases)
-importFrom(stats,cutree)
-importFrom(stats,hclust)
-importFrom(stats,median)
 importFrom(stats,na.omit)
-importFrom(stringr,str_remove)
-importFrom(stringr,str_remove_all)
-importFrom(stringr,str_replace)
-importFrom(stringr,str_to_lower)
-importFrom(stringr,str_trunc)
-importFrom(tibble,as_tibble)
-importFrom(tibble,column_to_rownames)
-importFrom(tibble,rownames_to_column)
-importFrom(tibble,tibble)
 importFrom(utils,head)