Dependency analysis on package RTCGA

General information

Bioconductor link link
Package version1.26.0
Number of strong dependencies127
Number of all dependencies180
Number of parent packages15
Max heaviness from parent packages60
Total heaviness from parent packages71
Number of parent packages (including Suggests and Enhances)34
Max co-heaviness from parent packages ("survminer" and "knitr")5

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of RTCGA and columns are the dependency packages that each parent package brings in. On the right side of the heatmap, there are three barplot annotations: 1. number of imported functions/S4 methods/S4 classes from parent packages; 2. number of dependency packages from each parent package; 3. heaviness of each parent package on RTCGA.

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats grDevices graphics tools splines grid parallel stats4 magrittr rlang glue R6 lifecycle tibble ellipsis fansi pillar pkgconfig vctrs cli crayon utf8 digest stringr stringi withr Matrix lattice evaluate farver labeling munsell RColorBrewer viridisLite colorspace purrr jsonlite highr yaml xfun scales gtable isoband MASS mgcv nlme generics tidyselect xml2 mime ggplot2 cpp11 knitr brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 httr curl openssl askpass sys gridExtra dplyr Rcpp RCurl bitops testthat selectr ggpubr maxstat survival broom tidyr survMisc ggtext ggrepel ggsci cowplot ggsignif polynom rstatix exactRankTests mvtnorm backports KMsurv data.table zoo km.ci xtable gridtext corrplot car markdown png jpeg carData abind nnet pbkrtest quantreg maptools lme4 numDeriv SparseM MatrixModels sp foreign boot minqa nloptr RcppEigen RTCGA XML assertthat rvest survminer ggthemes viridis BiocGenerics S4Vectors fs rappdirs fastmap IRanges GenomeInfoDb XVector GenomeInfoDbData zlibbioc bslib htmltools jquerylib tinytex sass base64enc usethis memoise pkgbuild rcmdcheck remotes roxygen2 rversions sessioninfo clipr gert gh whisker cachem prettyunits xopen brew commonmark credentials zip gitcreds ini 0 1 2 3 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents assertthat data.table xml2 XML stringi purrr survival knitr scales dplyr rvest ggplot2 viridis ggthemes survminer magrittr Biobase S4Vectors IRanges pander GenomicRanges tidyr rmarkdown testthat devtools RTCGA.rnaseq RTCGA.clinical RTCGA.mutations RTCGA.RPPA RTCGA.mRNA RTCGA.miRNASeq RTCGA.methylation RTCGA.CNV RTCGA.PANCAN12 In total 127 packages are required directly or indirectly (180) when installing 'RTCGA' (1.26.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'RTCGA' Imported functions The whole namespace is imported


Dependency table

"Import" information is from the NAMESPACE file of RTCGA.

imports: number of imported functions/objects; importMethods: number of imported S4 methods; importClasses: number of imported S4 classes.

Required packages: number of strong dependency packages for each of the parent package (or in other words, number of dependency packages the parent package brings in).

Heaviness from parent on RTCGA: number of required packages that can be reduced if moving parent package to Suggests of RTCGA.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on RTCGA
survminer Imports The whole set of functions/methods/classes from parent package is imported to the namespace of RTCGA. 115 60
rvest Imports 3 0 0 30 7
assertthat Imports 1 0 0 1 1
XML Imports 1 0 0 2 1
viridis Imports 1 0 0 39 1
ggthemes Imports 3 0 0 42 1
data.table Imports 1 0 0 1 0
xml2 Imports 1 0 0 1 0
stringi Imports 1 0 0 3 0
purrr Imports 1 0 0 3 0
survival Imports The whole set of functions/methods/classes from parent package is imported to the namespace of RTCGA. 9 0
knitr Imports The whole set of functions/methods/classes from parent package is imported to the namespace of RTCGA. 12 0
scales Imports 1 0 0 15 0
dplyr Imports The whole set of functions/methods/classes from parent package is imported to the namespace of RTCGA. 20 0
ggplot2 Imports The whole set of functions/methods/classes from parent package is imported to the namespace of RTCGA. 37 0
devtools Suggests No object is imported into the namespace of RTCGA. 76 25
rmarkdown Suggests No object is imported into the namespace of RTCGA. 27 10
GenomicRanges Suggests No object is imported into the namespace of RTCGA. 15 9
IRanges Suggests No object is imported into the namespace of RTCGA. 7 4
S4Vectors Suggests No object is imported into the namespace of RTCGA. 6 3
Biobase Suggests No object is imported into the namespace of RTCGA. 5 2
RTCGA.rnaseq Suggests No object is imported into the namespace of RTCGA. 128 2
RTCGA.clinical Suggests No object is imported into the namespace of RTCGA. 128 2
RTCGA.mutations Suggests No object is imported into the namespace of RTCGA. 128 2
RTCGA.RPPA Suggests No object is imported into the namespace of RTCGA. 128 2
RTCGA.mRNA Suggests No object is imported into the namespace of RTCGA. 128 2
RTCGA.miRNASeq Suggests No object is imported into the namespace of RTCGA. 128 2
RTCGA.methylation Suggests No object is imported into the namespace of RTCGA. 128 2
RTCGA.CNV Suggests No object is imported into the namespace of RTCGA. 128 2
RTCGA.PANCAN12 Suggests No object is imported into the namespace of RTCGA. 128 2
pander Suggests No object is imported into the namespace of RTCGA. 8 1
magrittr Suggests No object is imported into the namespace of RTCGA. 0 0
tidyr Suggests No object is imported into the namespace of RTCGA. 22 0
testthat Suggests No object is imported into the namespace of RTCGA. 36 0

Analysis was done with pkgndep.