Imports: BiocManager, xml2, Biobase, annotate, GEOquery, markdown,
R.utils

Depends: ggplot2, R (>= 4.0.0)
Imports: ape, Biostrings, ggpubr, genetics, GenomicRanges, lolliplot,
maps, methods, IRanges, pegas, reshape2, rlang, rtracklayer,
shiny, shinyjs, stats, stringdist, stringr, tibble, sf, tidyr,
utils, vcfR
Suggests: mapdata, knitr, rmarkdown, testthat (>= 3.0.0)

Depends: R (>= 3.6)
Imports: clusterProfiler, dplyr, europepmc, fst, geneset, ggplot2,
ggraph, ggvenn, igraph, magrittr, openxlsx, stringr, stringi,
tidyr, rlang
Suggests: AnnotationDbi, cowplot, ComplexUpset, forcats, fgsea,
futile.logger, ggplotify, ggsci, ggrepel, ggridges, ggnewscale,
GOplot, GOSemSim, labeling, pheatmap, tm, treemap,
RColorBrewer, RCurl, reshape2, rio, rrvgo, testthat (>= 3.0.0),
wordcloud, knitr, rmarkdown, XML, xml2, httr

Depends: R (>= 4.3.0)
Imports: RcppML, NMF, stats, Seurat (>= 4.3.0), cluster, pheatmap,
viridis
Suggests: knitr, rmarkdown, fgsea, dplyr, msigdbr

Imports: CVST, graphics, kernlab, mgcv, stats, xgboost

Suggests: VarianceGamma, actuar, SkewHyperbolic, RUnit

Depends: R (>= 3.0)
Imports: Rcpp (>= 1.0.8), RcppParallel (>= 5.1.4), ggplot2
LinkingTo: Rcpp, RcppArmadillo, RcppParallel
Suggests: DataVisualizations, rgl, grid, mgcv, png, reshape2, fields,
ABCanalysis, plotly, deldir, methods, knitr (>= 1.12),
rmarkdown (>= 0.9)

Depends: R (>= 3.1)
Imports: methods, stats, utils, Matrix, Rcpp, spam, spam64, parallel,
optimParallel, fields
LinkingTo: Rcpp, RcppEigen, BH, Matrix
Suggests: knitr, R.rsp, testthat (>= 3.0.0), mvtnorm, ggplot2,
gridExtra, dplyr, microbenchmark

Depends: ggplot2, mlr3, mlr3learners
Imports: sandwich, lmtest, splitstackshape, stats, parallel, abind
Suggests: glmnet, ranger, rpart, e1071, xgboost, kknn, DiceKriging,
testthat (>= 3.0.0)

Suggests: covr, pkgload, testthat (>= 3.0.0), tibble, withr

Depends: R (>= 3.1)
Suggests: testthat (>= 2.1.0), knitr, rmarkdown

Suggests: clusterProfiler (>= 4.6.2), GO.db (>= 3.17.0), knitr,
rmarkdown, BiocManager (>= 1.30.21), UpSetR (>= 1.4.0),
AnnotationHub (>= 3.8.0), ensembldb (>= 2.24.0), org.Hs.eg.db
(>= 3.17.0)