Dependency analysis on package GOexpress

General information

Bioconductor link link
Package version1.30.0
Number of strong dependencies93
Number of all dependencies109
Number of parent packages11
Max heaviness from parent packages43
Total heaviness from parent packages63
Number of parent packages (including Suggests and Enhances)12
Max co-heaviness from parent packages ("biomaRt" and "ggplot2")15

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods stats utils graphics tools grDevices grid splines stats4 glue magrittr bitops stringi digest R6 rlang BiocGenerics crayon pkgconfig ellipsis lifecycle vctrs cli pillar tibble withr fansi utf8 stringr rappdirs jsonlite fastmap gtools caTools KernSmooth gtable isoband MASS mgcv scales nlme Matrix farver labeling munsell RColorBrewer viridisLite lattice colorspace XML AnnotationDbi progress httr BiocFileCache xml2 Biobase IRanges DBI RSQLite S4Vectors KEGGREST hms prettyunits curl mime openssl dbplyr dplyr filelock bit64 blob memoise Rcpp plogr png Biostrings askpass assertthat purrr tidyselect generics bit cachem XVector GenomeInfoDb sys zlibbioc RCurl GenomeInfoDbData bookdown knitr rmarkdown yaml BiocManager htmltools jquerylib xfun tinytex evaluate highr bslib base64enc sass fs 0 1 2 3 Imported methods 0 20 40 60 Required packages 0 20 40 Heaviness from parents grid stats graphics Biobase RColorBrewer randomForest RCurl stringr gplots ggplot2 biomaRt BiocStyle In total 93 packages are required directly or indirectly (109) when installing 'GOexpress' (1.30.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'GOexpress' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on GOexpress
grid Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GOexpress. 0 0
stats Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GOexpress. 0 0
graphics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GOexpress. 0 0
Biobase Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GOexpress. 5 0
biomaRt Imports The whole set of functions/methods/classes from parent package is imported to the namespace of GOexpress. 70 43
ggplot2 Imports The whole set of functions/methods/classes from parent package is imported to the namespace of GOexpress. 37 15
gplots Imports 3 0 0 7 4
randomForest Imports 2 0 0 1 1
RColorBrewer Imports The whole set of functions/methods/classes from parent package is imported to the namespace of GOexpress. 0 0
RCurl Imports 1 0 0 2 0
stringr Imports 1 0 0 7 0
BiocStyle Suggests No object is imported into the namespace of GOexpress. 30 16

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 GOexpress Co-heaviness as Jaccard coeffcient
ggplot2 biomaRt 15 0.205

Analysis was done with pkgndep.