Dev

.Rbuildignore

@@ -8,3 +8,7 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.positai$
+^\.claude$
+^doc$
+^Meta$

.gitignore

@@ -53,3 +53,6 @@ rsconnect/
 .quarto
 inst/doc
 docs
+.positai
+/doc/
+/Meta/

DESCRIPTION

@@ -16,7 +16,6 @@ Authors@R: c(
 Description: This package contains functions that help in manipulating tables and generating plots for multi-omics analysis including genomics, transcriptomics, proteomics, methylomics and immunoinformatics.
 License: CC BY-NC-SA 4.0
 Encoding: UTF-8
-RoxygenNote: 7.3.3
 Imports:
     dplyr,
     ggplot2,
@@ -25,13 +24,18 @@ Imports:
     graphics,
     magrittr,
     rlang,
-    stats,
     umap,
     tibble,
     scales,
     grid,
     utils,
-    patchwork
+    patchwork,
+    Gviz,
+    rtracklayer,
+    GenomeInfoDb,
+    GenomicRanges,
+    stats,
+    S4Vectors
 Suggests: 
     biomaRt,
     circlize,
@@ -55,12 +59,16 @@ Suggests:
     tidygraph,
     tidyr,
     tidyselect,
-    tm
+    tm,
+    testthat (>= 3.0.0),
+    withr,
+    Rsamtools
 Roxygen: list(markdown = TRUE)
 Depends: 
-    R (>= 3.5)
+    R (>= 4.4.0)
 LazyData: true
 LazyDataCompression: xz
 VignetteBuilder: knitr
 URL: https://bigmindlab.github.io/OmicsKit
-
+Config/testthat/edition: 3
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -12,11 +12,14 @@ export(get_superterm)
 export(getgenesPA)
 export(heatmap_PA)
 export(heatmap_path_PA)
+export(list_ensembl_species)
+export(list_ensembl_versions)
 export(list_gmts)
 export(merge_PA)
 export(multiplot_PA)
 export(network_clust)
 export(network_clust_gg)
+export(nice_GenomeTrack)
 export(nice_KM)
 export(nice_PCA)
 export(nice_UMAP)
@@ -30,7 +33,10 @@ export(split_cases)
 export(splot_PA)
 export(tpm)
 import(ggplot2)
+importFrom(S4Vectors,"mcols<-")
+importFrom(S4Vectors,mcols)
 importFrom(magrittr,"%>%")
 importFrom(patchwork,plot_layout)
 importFrom(rlang,.data)
+importFrom(stats,na.omit)
 importFrom(utils,modifyList)