Dependency analysis on package DOSE

General information

Bioconductor link link
Package version3.22.0
Number of strong dependencies92
Number of all dependencies155
Number of parent packages11
Max heaviness from parent packages4
Total heaviness from parent packages8
Number of parent packages (including Suggests and Enhances)17
Max co-heaviness from parent packages ("fgsea" and "BiocParallel")9

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of DOSE 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 DOSE.

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats tools grDevices graphics stats4 grid splines parallel glue rlang R6 magrittr pkgconfig vctrs crayon cli Rcpp jsonlite digest fastmap stringr stringi tibble withr lifecycle ellipsis fansi pillar utf8 BiocGenerics Biobase IRanges DBI RSQLite S4Vectors KEGGREST bit64 blob memoise plogr httr png Biostrings bit cachem curl mime openssl XVector GenomeInfoDb askpass zlibbioc RCurl GenomeInfoDbData sys bitops Matrix gtable isoband MASS mgcv scales lattice nlme farver labeling munsell RColorBrewer viridisLite colorspace AnnotationDbi plyr futile.logger snow codetools BH lambda.r futile.options formatR ggplot2 reshape2 GO.db data.table BiocParallel gridExtra fastmatch evaluate xfun yaml highr bslib htmltools jquerylib knitr tinytex sass base64enc fs rappdirs rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 downloader DOSE dplyr enrichplot GOSemSim qvalue tidyr yulab.utils DO.db fgsea generics tidyselect aplot ggraph igraph purrr scatterpie shadowtext ggtree cpp11 ggfun ggplotify patchwork ggforce ggrepel viridis tidygraph graphlayouts ape tidytree treeio gridGraphics tweenr polyclip RcppEigen RcppArmadillo lazyeval 0 5 10 15 Imported methods 0 50 100 Required packages 0 10 20 30 Heaviness from parents methods stats utils reshape2 BiocParallel ggplot2 AnnotationDbi qvalue DO.db GOSemSim fgsea knitr rmarkdown prettydoc testthat org.Hs.eg.db clusterProfiler In total 92 packages are required directly or indirectly (155) when installing 'DOSE' (3.22.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'DOSE' Imported functions Imported S4 methods Imported S4 classes


Dependency table

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

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 DOSE: number of required packages that can be reduced if moving parent package to Suggests of DOSE.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on DOSE
fgsea Imports 1 0 0 51 4
GOSemSim Imports 3 0 1 46 2
qvalue Imports 1 0 0 44 1
DO.db Imports 4 0 0 45 1
methods Imports 2 0 1 0 0
stats Imports 3 0 0 0 0
utils Imports 7 0 0 0 0
reshape2 Imports 1 0 0 10 0
BiocParallel Imports 3 0 0 11 0
ggplot2 Imports 15 0 0 37 0
AnnotationDbi Imports 0 8 0 44 0
clusterProfiler Suggests No object is imported into the namespace of DOSE. 125 34
prettydoc Suggests No object is imported into the namespace of DOSE. 28 15
rmarkdown Suggests No object is imported into the namespace of DOSE. 27 14
testthat Suggests No object is imported into the namespace of DOSE. 36 14
knitr Suggests No object is imported into the namespace of DOSE. 12 5
org.Hs.eg.db Suggests No object is imported into the namespace of DOSE. 45 1

Analysis was done with pkgndep.