Dependency analysis on package clusterProfiler

General information

Bioconductor link link
Package version4.4.2
Number of strong dependencies125
Number of all dependencies177
Number of parent packages16
Max heaviness from parent packages24
Total heaviness from parent packages25
Number of parent packages (including Suggests and Enhances)23
Max co-heaviness from parent packages ("enrichplot" and "DOSE")15

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests utils methods grDevices stats tools graphics stats4 grid splines parallel glue rlang R6 pkgconfig vctrs crayon cli magrittr jsonlite Rcpp fastmap digest tibble 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 stringr stringi AnnotationDbi withr generics tidyselect purrr dplyr ggplot2 reshape2 Matrix gtable isoband MASS mgcv scales plyr lattice nlme farver labeling munsell RColorBrewer viridisLite colorspace GO.db cpp11 BiocParallel DO.db fgsea GOSemSim qvalue futile.logger snow codetools BH data.table gridExtra fastmatch lambda.r futile.options formatR lazyeval aplot DOSE ggraph igraph scatterpie shadowtext ggtree yulab.utils ggfun ggplotify patchwork ggforce ggrepel viridis tidygraph graphlayouts tidyr ape tidytree treeio gridGraphics tweenr polyclip RcppEigen RcppArmadillo yaml evaluate rappdirs highr xfun htmltools bslib jquerylib base64enc sass fs knitr tinytex rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 BiocFileCache BiocManager BiocVersion interactiveDisplayBase dbplyr filelock shiny DT assertthat httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk enrichplot reactome.db graphite graph 0 5 10 Imported methods 0 50 100 Required packages 0 10 20 Heaviness from parents magrittr methods stats utils rlang yulab.utils downloader plyr dplyr tidyr AnnotationDbi qvalue GO.db GOSemSim DOSE enrichplot knitr rmarkdown prettydoc testthat org.Hs.eg.db AnnotationHub ReactomePA In total 125 packages are required directly or indirectly (177) when installing 'clusterProfiler' (4.4.2) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'clusterProfiler' Imported functions Imported S4 methods Imported S4 classes


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on clusterProfiler
enrichplot Imports 7 0 0 123 24
downloader Imports 1 0 0 2 1
magrittr Imports 2 0 0 0 0
methods Imports 1 0 1 0 0
stats Imports 2 0 0 0 0
utils Imports 11 0 0 0 0
rlang Imports 3 0 0 1 0
yulab.utils Imports 1 0 0 1 0
plyr Imports 3 0 0 3 0
dplyr Imports 9 0 0 20 0
tidyr Imports 1 0 0 22 0
AnnotationDbi Imports 6 2 0 44 0
qvalue Imports 1 0 0 44 0
GO.db Imports 8 0 0 45 0
GOSemSim Imports 3 0 0 46 0
DOSE Imports 4 2 3 92 0
AnnotationHub Suggests No object is imported into the namespace of clusterProfiler. 85 27
prettydoc Suggests No object is imported into the namespace of clusterProfiler. 28 15
rmarkdown Suggests No object is imported into the namespace of clusterProfiler. 27 14
testthat Suggests No object is imported into the namespace of clusterProfiler. 36 14
knitr Suggests No object is imported into the namespace of clusterProfiler. 12 5
ReactomePA Suggests No object is imported into the namespace of clusterProfiler. 128 5
org.Hs.eg.db Suggests No object is imported into the namespace of clusterProfiler. 45 1

The following table lists pairs of parent packages with co-heaviness larger than 10. The co-heaviness measures the number of additional dependencies that two parent packages simultaneously import and are only imported by the two parents.

Note the co-heaviness from parents can be always easily observed in the dependency heatmap.

Parent 1 Parent 2 Co-heaviness on clusterProfiler Co-heaviness as Jaccard coeffcient
DOSE enrichplot 15 0.385

Analysis was done with pkgndep.