Dependency analysis on package GOSemSim

General information

Bioconductor link link
Package version2.22.0
Number of strong dependencies46
Number of all dependencies179
Number of parent packages5
Max heaviness from parent packages1
Total heaviness from parent packages1
Number of parent packages (including Suggests and Enhances)15
Max co-heaviness from parent packages ("GO.db" and "AnnotationDbi")42

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports LinkingTo Suggests utils methods stats grDevices tools graphics stats4 grid splines parallel glue rlang jsonlite R6 fastmap pkgconfig vctrs crayon cli bitops BiocGenerics Biobase IRanges DBI RSQLite S4Vectors KEGGREST bit64 blob memoise Rcpp plogr httr png Biostrings bit cachem curl mime openssl XVector GenomeInfoDb askpass zlibbioc RCurl GenomeInfoDbData sys AnnotationDbi magrittr digest stringr stringi yaml evaluate lifecycle tibble pillar withr ellipsis fansi utf8 highr xfun rappdirs htmltools bslib jquerylib base64enc sass fs knitr tinytex dplyr generics tidyselect purrr lazyeval GO.db GOSemSim plyr qvalue BiocParallel DO.db fgsea ggplot2 reshape2 RColorBrewer futile.logger snow codetools BH data.table gridExtra fastmatch Matrix gtable isoband MASS mgcv scales lambda.r futile.options lattice nlme farver labeling munsell viridisLite formatR colorspace gplots gtools caTools KernSmooth 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 downloader DOSE enrichplot tidyr yulab.utils aplot ggraph igraph scatterpie shadowtext ggtree cpp11 ggfun ggplotify patchwork ggforce ggrepel viridis tidygraph graphlayouts ape tidytree treeio gridGraphics tweenr polyclip RcppEigen RcppArmadillo 0 5 10 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents methods utils AnnotationDbi GO.db Rcpp BiocManager ROCR knitr rmarkdown prettydoc testthat org.Hs.eg.db AnnotationHub DOSE clusterProfiler In total 46 packages are required directly or indirectly (179) when installing 'GOSemSim' (2.22.0) Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'GOSemSim' Imported functions Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on GOSemSim
GO.db Imports 10 0 0 45 1
methods Imports 5 0 0 0 0
utils Imports 4 0 0 0 0
AnnotationDbi Imports 5 0 0 44 0
Rcpp LinkingTo Parent package is listed in LinkingTo of GOSemSim but no object from parent package is imported. 2 0
clusterProfiler Suggests No object is imported into the namespace of GOSemSim. 125 80
DOSE Suggests No object is imported into the namespace of GOSemSim. 92 47
AnnotationHub Suggests No object is imported into the namespace of GOSemSim. 85 41
testthat Suggests No object is imported into the namespace of GOSemSim. 36 23
prettydoc Suggests No object is imported into the namespace of GOSemSim. 28 19
rmarkdown Suggests No object is imported into the namespace of GOSemSim. 27 18
knitr Suggests No object is imported into the namespace of GOSemSim. 12 8
ROCR Suggests No object is imported into the namespace of GOSemSim. 10 5
BiocManager Suggests No object is imported into the namespace of GOSemSim. 1 1
org.Hs.eg.db Suggests No object is imported into the namespace of GOSemSim. 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 GOSemSim Co-heaviness as Jaccard coeffcient
AnnotationDbi GO.db 42 0.977

Analysis was done with pkgndep.