Depends: R (>= 4.1)
Imports: magrittr, dplyr, tibble, tidyr, jsonlite, stringr, readxl, cli
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), withr, readr, cards,
cardx, broom, parameters, broom.helpers, covr

Imports: Rcpp, combinat, glmnet, methods, MASS

Imports: graphics, stats, survival, ggplot2, ggpubr, scales, plyr, np

Depends: R (>= 3.6.0), methods, utils, stats
Suggests: rmarkdown (>= 2.20), knitr (>= 1.42)

Depends: R (>= 3.3.0)
Imports: pastecs (>= 1.3.21), stats, dplyr (>= 1.0.0), rlang (>=
0.4.3), tidyr (>= 1.0.0), tibble, purrr, glue, tidyselect
LinkingTo: cpp11
Suggests: knitr, ggplot2, testthat (>= 3.0.0), rmarkdown, mopac, hms,
stringr, readr

Imports: formula.tools, Matrix, msm, plyr, mvtnorm, stats, survey,
utils
Suggests: car, data.table, GGally, ggplot2, kableExtra, knitr, readxl,
reshape2, rmarkdown, tidyr, R.rsp

Imports: randomForest, stringr, pbivnorm, Formula, maxLik, xtable, MASS

Imports: htmlwidgets, dplyr (>= 0.7.0), magrittr, shiny, jsonlite,
igraph, htmltools, purrr, scales, crosstalk

Depends: R (>= 3.5)
Imports: cli (>= 2.0.0), cowplot, data.table, dplyr, furrr (>= 0.2.0),
future, ggplot2 (>= 3.3.0), ggpubr, maftools, magrittr,
methods, NMF, purrr, Rcpp, rlang (>= 0.1.2), stats, tidyr
LinkingTo: Rcpp
Suggests: Biobase, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19,
circlize, cluster, covr, digest, GenomicRanges, GenSA,
ggalluvial, ggcorrplot, ggfittext, ggplotify, ggrepel, IRanges,
knitr, lpSolve, markdown, matrixStats, nnls, parallel,
patchwork, pheatmap, quadprog, R.utils, RColorBrewer,
reticulate, rmarkdown, roxygen2, scales, synchronicity,
testthat (>= 3.0.0), tibble, UCSCXenaTools

Depends: R (>= 3.2.2)
Suggests: covr, knitr, rmarkdown, ggplot2, testthat

Depends: R(>= 3.4)
Imports: stats, utils, survcomp, survival, GSVA

Depends: R (>= 4.1.0), methods
Imports: GenomeInfoDb (>= 1.29.3), GenomicRanges, IRanges, Matrix,
Rsamtools, S4Vectors, SeuratObject (>= 5.0.2), data.table,
dplyr (>= 1.0.0), future, future.apply, ggplot2, rlang, irlba,
pbapply, tidyr, patchwork, stats, utils, BiocGenerics, stringi,
fastmatch, RcppRoll, scales, Rcpp, grid, tidyselect, vctrs,
lifecycle
LinkingTo: Rcpp
Suggests: Seurat (>= 5.0.2), ggforce, ggrepel, ggseqlogo, testthat (>=
2.1.0), chromVAR, SummarizedExperiment, TFBSTools, motifmatchr,
BSgenome, shiny, miniUI, rtracklayer, biovizBase, Biostrings,
lsa, MASS, wrswoR