Dependency analysis on package simplifyEnrichment

General information

Bioconductor link link
Package version1.6.0
Number of strong dependencies76
Number of all dependencies228
Number of parent packages23
Max heaviness from parent packages7
Total heaviness from parent packages16
Number of parent packages (including Suggests and Enhances)51
Max co-heaviness from parent packages ("ComplexHeatmap" and "GetoptLong")2

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils stats methods grDevices graphics grid tools stats4 parallel splines glue crayon Rcpp rlang R6 pkgconfig jsonlite vctrs mime cli png fastmap lattice BiocGenerics IRanges S4Vectors cachem httr curl openssl askpass sys digest RCurl bitops Matrix Biobase DBI RSQLite KEGGREST bit64 blob memoise plogr Biostrings bit XVector GenomeInfoDb zlibbioc GenomeInfoDbData AnnotationDbi colorspace RColorBrewer GlobalOptions cluster codetools rjson shape xml2 BH RcppArmadillo circlize GetoptLong clue matrixStats foreach doParallel iterators GO.db slam NLP RcppParallel magrittr lifecycle ellipsis withr stringr stringi tibble fansi pillar utf8 MASS gtable evaluate xfun scales farver labeling munsell viridisLite highr yaml htmltools bslib base64enc sass jquerylib fs rappdirs xtable isoband mgcv nlme knitr fontawesome httpuv sourcetools later promises commonmark ggplot2 modeltools class markdown mclust dplyr generics tidyselect purrr tinytex shiny callr processx ps rstudioapi polyclip ComplexHeatmap GOSemSim plyr qvalue BiocParallel DO.db fgsea reshape2 futile.logger snow data.table gridExtra fastmatch lambda.r futile.options formatR cpp11 expm jpeg flexmix prabclus diptest robustbase kernlab nnet DEoptimR babelgene brio desc pkgload praise waldo rprojroot diffobj rematch2 org.Hs.eg.db annotate survival XML skmeans microbenchmark impute brew eulerr irlba GenSA polylabelr kableExtra svglite clisymbols rvest rmarkdown webshot systemfonts selectr downloader DOSE enrichplot tidyr yulab.utils aplot ggraph igraph scatterpie shadowtext ggtree ggfun ggplotify patchwork ggforce ggrepel viridis tidygraph graphlayouts ape tidytree treeio gridGraphics tweenr RcppEigen lazyeval 0 5 10 15 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents grid BiocGenerics methods grDevices graphics stats utils digest slam GlobalOptions cluster colorspace GetoptLong clue Matrix circlize tm proxyC ComplexHeatmap AnnotationDbi GO.db org.Hs.eg.db GOSemSim dynamicTreeCut BiocManager gridGraphics mclust dbscan gridExtra apcluster MCL igraph knitr flexclust gridtext fpc msigdbr rmarkdown shiny shinydashboard testthat ggplot2 cowplot DO.db reactome.db hu6800.db genefilter cola DOSE InteractiveComplexHeatmap clusterProfiler In total 76 packages are required directly or indirectly (228) when installing 'simplifyEnrichment' (1.6.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'simplifyEnrichment' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on simplifyEnrichment
grid Depends The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 0 0
BiocGenerics Depends 2 0 0 4 0
ComplexHeatmap Imports The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 28 7
tm Imports The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 11 4
proxyC Imports 1 0 0 11 3
org.Hs.eg.db Imports The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 45 1
GOSemSim Imports The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 46 1
methods Imports 2 0 0 0 0
grDevices Imports 5 0 0 0 0
graphics Imports 5 0 0 0 0
stats Imports 19 0 0 0 0
utils Imports 4 0 0 0 0
digest Imports The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 1 0
slam Imports The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 1 0
GlobalOptions Imports The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 2 0
cluster Imports 1 0 0 4 0
colorspace Imports 2 0 0 4 0
GetoptLong Imports The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 6 0
clue Imports The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 6 0
Matrix Imports The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 7 0
circlize Imports 2 0 0 9 0
AnnotationDbi Imports The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 44 0
GO.db Imports The whole set of functions/methods/classes from parent package is imported to the namespace of simplifyEnrichment. 45 0
clusterProfiler Suggests No object is imported into the namespace of simplifyEnrichment. 125 69
InteractiveComplexHeatmap Suggests No object is imported into the namespace of simplifyEnrichment. 96 50
DOSE Suggests No object is imported into the namespace of simplifyEnrichment. 92 37
testthat Suggests No object is imported into the namespace of simplifyEnrichment. 36 22
cowplot Suggests No object is imported into the namespace of simplifyEnrichment. 38 21
shinydashboard Suggests No object is imported into the namespace of simplifyEnrichment. 35 20
ggplot2 Suggests No object is imported into the namespace of simplifyEnrichment. 37 20
cola Suggests No object is imported into the namespace of simplifyEnrichment. 64 20
shiny Suggests No object is imported into the namespace of simplifyEnrichment. 34 19
rmarkdown Suggests No object is imported into the namespace of simplifyEnrichment. 27 17
msigdbr Suggests No object is imported into the namespace of simplifyEnrichment. 22 13
fpc Suggests No object is imported into the namespace of simplifyEnrichment. 21 12
knitr Suggests No object is imported into the namespace of simplifyEnrichment. 12 8
gridtext Suggests No object is imported into the namespace of simplifyEnrichment. 20 7
genefilter Suggests No object is imported into the namespace of simplifyEnrichment. 53 6
flexclust Suggests No object is imported into the namespace of simplifyEnrichment. 12 4
gridExtra Suggests No object is imported into the namespace of simplifyEnrichment. 5 2
MCL Suggests No object is imported into the namespace of simplifyEnrichment. 9 2
igraph Suggests No object is imported into the namespace of simplifyEnrichment. 10 2
dynamicTreeCut Suggests No object is imported into the namespace of simplifyEnrichment. 1 1
BiocManager Suggests No object is imported into the namespace of simplifyEnrichment. 1 1
gridGraphics Suggests No object is imported into the namespace of simplifyEnrichment. 3 1
mclust Suggests No object is imported into the namespace of simplifyEnrichment. 4 1
dbscan Suggests No object is imported into the namespace of simplifyEnrichment. 5 1
apcluster Suggests No object is imported into the namespace of simplifyEnrichment. 9 1
DO.db Suggests No object is imported into the namespace of simplifyEnrichment. 45 1
reactome.db Suggests No object is imported into the namespace of simplifyEnrichment. 45 1
hu6800.db Suggests No object is imported into the namespace of simplifyEnrichment. 46 1

Analysis was done with pkgndep.