Dependency analysis on package RaggedExperiment

General information

Bioconductor link link
Package version1.20.0
Number of strong dependencies25
Number of all dependencies82
Number of parent packages10
Max heaviness from parent packages3
Total heaviness from parent packages3
Number of parent packages (including Suggests and Enhances)15
Max co-heaviness from parent packages ("SummarizedExperiment" and "GenomicRanges")4

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics tools stats4 grDevices grid BiocGenerics S4Vectors IRanges RCurl GenomeInfoDbData bitops GenomeInfoDb XVector zlibbioc matrixStats lattice MatrixGenerics GenomicRanges Biobase Matrix DelayedArray glue magrittr evaluate rlang R6 yaml xfun highr stringr stringi jsonlite digest knitr htmltools jquerylib tinytex bslib base64enc fastmap sass fs rappdirs cli crayon ellipsis lifecycle fansi tibble pillar pkgconfig vctrs utf8 bookdown rmarkdown BiocManager brio callr desc pkgload praise processx ps waldo withr rprojroot rstudioapi diffobj rematch2 SummarizedExperiment tidyr dplyr purrr tidyselect cpp11 generics 0 1 2 3 Imported methods 0 20 40 Required packages 0 10 20 30 Heaviness from parents GenomicRanges methods stats MatrixGenerics BiocGenerics S4Vectors IRanges Matrix GenomeInfoDb SummarizedExperiment knitr rmarkdown BiocStyle testthat MultiAssayExperiment In total 25 packages are required directly or indirectly (82) when installing 'RaggedExperiment' (1.20.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'RaggedExperiment' Imported functions Imported S4 classes The whole namespace is imported Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on RaggedExperiment
GenomicRanges Depends 1 0 1 15 0
SummarizedExperiment Imports 3 0 0 24 3
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of RaggedExperiment. 0 0
stats Imports 1 0 0 0 0
MatrixGenerics Imports 1 0 0 2 0
BiocGenerics Imports 1 0 0 4 0
S4Vectors Imports 1 0 1 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of RaggedExperiment. 7 0
Matrix Imports Parent package is listed in Imports of RaggedExperiment but no object from parent package is imported. 7 0
GenomeInfoDb Imports 2 0 0 11 0
testthat Suggests No object is imported into the namespace of RaggedExperiment. 36 31
BiocStyle Suggests No object is imported into the namespace of RaggedExperiment. 30 26
rmarkdown Suggests No object is imported into the namespace of RaggedExperiment. 27 23
MultiAssayExperiment Suggests No object is imported into the namespace of RaggedExperiment. 45 21
knitr Suggests No object is imported into the namespace of RaggedExperiment. 12 9

Analysis was done with pkgndep.