Dependency analysis on package cola

General information

Bioconductor link link
Package version2.2.0
Number of strong dependencies64
Number of all dependencies252
Number of parent packages33
Max heaviness from parent packages8
Total heaviness from parent packages35
Number of parent packages (including Suggests and Enhances)59
Max co-heaviness from parent packages ("ComplexHeatmap" and "circlize")3

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests utils methods stats grDevices graphics tools grid stats4 parallel splines datasets R6 crayon glue Rcpp lattice jsonlite Matrix digest mime colorspace magrittr openssl askpass sys png BiocGenerics codetools curl stringi RColorBrewer IRanges S4Vectors cluster stringr iterators foreach xfun GlobalOptions RcppArmadillo evaluate matrixStats doParallel rjson clue shape polyclip highr yaml slam circlize GetoptLong GenSA polylabelr rlang pkgconfig vctrs cli withr fastmap bitops MASS ellipsis lifecycle fansi tibble pillar utf8 Biobase cachem DBI RSQLite KEGGREST httr bit64 blob memoise plogr Biostrings bit XVector GenomeInfoDb zlibbioc RCurl GenomeInfoDbData ggplot2 gtable isoband mgcv scales nlme farver labeling munsell viridisLite AnnotationDbi gridExtra GO.db rappdirs viridis reshape2 plyr GOSemSim BH data.table survival RcppEigen htmltools base64enc xtable qvalue BiocParallel DO.db fgsea futile.logger snow fastmatch lambda.r futile.options formatR class rprojroot bslib fs sass jquerylib knitr rstudioapi org.Hs.eg.db impute DOSE dplyr enrichplot tidyr yulab.utils generics tidyselect aplot ggraph igraph purrr scatterpie shadowtext ggtree cpp11 ggfun ggplotify patchwork ggforce ggrepel tidygraph graphlayouts ape tidytree treeio gridGraphics tweenr lazyeval gtools caTools KernSmooth scatterplot3d proxy modeltools reticulate RSpectra RcppTOML here tinytex brio callr desc pkgload praise processx ps waldo diffobj rematch2 shiny shinyFiles openxlsx GSA httpuv fontawesome sourcetools later promises commonmark zip annotate XML pkgmaker registry rngtools gridBase BiocManager assertthat ComplexHeatmap tm proxyC NLP xml2 RcppParallel dynamicTreeCut fastcluster Hmisc preprocessCore Formula latticeExtra rpart nnet foreign htmlTable jpeg checkmate htmlwidgets backports downloader reactome.db graphite graph 0 10 20 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents grDevices graphics grid stats utils matrixStats parallel RColorBrewer png methods impute brew xml2 digest GlobalOptions microbenchmark Rcpp crayon foreach cluster mclust BiocGenerics markdown doParallel GetoptLong clue skmeans irlba circlize httr eulerr knitr ComplexHeatmap BiocManager randomForest mvtnorm kohonen Rtsne data.tree gplots Polychrome e1071 pamr flexclust umap rmarkdown testthat cowplot dendextend AnnotationDbi hu6800.db samr genefilter NMF simplifyEnrichment DOSE WGCNA clusterProfiler ReactomePA In total 64 packages are required directly or indirectly (252) when installing 'cola' (2.2.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'cola' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on cola
knitr Imports 2 0 0 12 8
httr Imports 3 0 0 9 7
eulerr Imports 1 0 0 11 5
ComplexHeatmap Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 28 4
irlba Imports 1 0 0 8 3
skmeans Imports 1 0 0 8 2
impute Imports 1 0 0 0 1
brew Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 0 1
xml2 Imports 5 0 0 1 1
microbenchmark Imports 1 0 0 2 1
mclust Imports 3 0 0 4 1
markdown Imports 1 0 0 5 1
grDevices Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 0 0
graphics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 0 0
grid Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 0 0
stats Imports 25 0 0 0 0
utils Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 0 0
matrixStats Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 0 0
parallel Imports 1 0 0 0 0
RColorBrewer Imports 1 0 0 0 0
png Imports 1 0 0 0 0
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 0 0
digest Imports 1 0 0 1 0
GlobalOptions Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 2 0
Rcpp Imports 1 0 0 2 0
crayon Imports 2 0 0 3 0
foreach Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 3 0
cluster Imports 2 0 0 4 0
BiocGenerics Imports 4 0 0 4 0
doParallel Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 5 0
GetoptLong Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 6 0
clue Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 6 0
circlize Imports The whole set of functions/methods/classes from parent package is imported to the namespace of cola. 9 0
ReactomePA Suggests No object is imported into the namespace of cola. 128 94
clusterProfiler Suggests No object is imported into the namespace of cola. 125 91
WGCNA Suggests No object is imported into the namespace of cola. 108 65
DOSE Suggests No object is imported into the namespace of cola. 92 60
NMF Suggests No object is imported into the namespace of cola. 59 34
samr Suggests No object is imported into the namespace of cola. 49 33
simplifyEnrichment Suggests No object is imported into the namespace of cola. 76 32
genefilter Suggests No object is imported into the namespace of cola. 53 29
dendextend Suggests No object is imported into the namespace of cola. 41 27
hu6800.db Suggests No object is imported into the namespace of cola. 46 25
testthat Suggests No object is imported into the namespace of cola. 36 24
cowplot Suggests No object is imported into the namespace of cola. 38 24
AnnotationDbi Suggests No object is imported into the namespace of cola. 44 23
rmarkdown Suggests No object is imported into the namespace of cola. 27 11
umap Suggests No object is imported into the namespace of cola. 22 9
gplots Suggests No object is imported into the namespace of cola. 7 5
e1071 Suggests No object is imported into the namespace of cola. 8 4
flexclust Suggests No object is imported into the namespace of cola. 12 4
pamr Suggests No object is imported into the namespace of cola. 11 3
Polychrome Suggests No object is imported into the namespace of cola. 7 2
BiocManager Suggests No object is imported into the namespace of cola. 1 1
randomForest Suggests No object is imported into the namespace of cola. 1 1
mvtnorm Suggests No object is imported into the namespace of cola. 2 1
kohonen Suggests No object is imported into the namespace of cola. 3 1
Rtsne Suggests No object is imported into the namespace of cola. 4 1
data.tree Suggests No object is imported into the namespace of cola. 6 1

Analysis was done with pkgndep.