Dependency analysis on package ballgown

General information

Bioconductor link link
Package version2.28.0
Number of strong dependencies83
Number of all dependencies112
Number of parent packages11
Max heaviness from parent packages35
Total heaviness from parent packages47
Number of parent packages (including Suggests and Enhances)14
Max co-heaviness from parent packages ("sva" and "rtracklayer")16

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils stats methods graphics stats4 tools grDevices parallel grid splines BiocGenerics S4Vectors IRanges RCurl GenomeInfoDbData bitops GenomeInfoDb XVector zlibbioc crayon glue BiocParallel matrixStats Matrix Biobase futile.logger snow codetools BH lattice XML lambda.r futile.options Biostrings formatR yaml pkgconfig jsonlite mime R6 rlang vctrs cli GenomicRanges Rsamtools GenomicAlignments BiocIO restfulr Rhtslib SummarizedExperiment rjson MatrixGenerics DelayedArray mgcv genefilter limma edgeR nlme AnnotationDbi annotate survival locfit Rcpp DBI RSQLite KEGGREST xtable httr bit64 blob memoise plogr png curl openssl bit cachem askpass fastmap sys xfun evaluate magrittr highr stringr stringi brio callr desc digest ellipsis lifecycle pkgload praise processx ps waldo withr rprojroot rstudioapi diffobj fansi rematch2 tibble pillar utf8 0 1 2 3 Imported methods 0 20 40 60 Required packages 0 10 20 30 Heaviness from parents methods RColorBrewer splines limma Biobase S4Vectors IRanges GenomeInfoDb GenomicRanges rtracklayer sva markdown knitr testthat In total 83 packages are required directly or indirectly (112) when installing 'ballgown' (2.28.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'ballgown' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on ballgown
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ballgown. 0 0
sva Imports 1 0 0 69 35
rtracklayer Imports 1 0 0 44 11
RColorBrewer Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ballgown. 0 1
splines Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ballgown. 0 0
limma Imports 1 0 0 5 0
Biobase Imports 3 0 0 5 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ballgown. 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ballgown. 7 0
GenomeInfoDb Imports 1 0 0 11 0
GenomicRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ballgown. 15 0
testthat Suggests No object is imported into the namespace of ballgown. 36 23
knitr Suggests No object is imported into the namespace of ballgown. 12 7
markdown Suggests No object is imported into the namespace of ballgown. 5 2

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 ballgown Co-heaviness as Jaccard coeffcient
rtracklayer sva 16 0.258

Analysis was done with pkgndep.