Dependency analysis on package regioneR

General information

Bioconductor link link
Package version1.28.0
Number of strong dependencies50
Number of all dependencies98
Number of parent packages14
Max heaviness from parent packages4
Total heaviness from parent packages5
Number of parent packages (including Suggests and Enhances)19
Max co-heaviness from parent packages ("BSgenome" and "rtracklayer")25

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats graphics tools stats4 grDevices parallel grid BiocGenerics S4Vectors IRanges RCurl GenomeInfoDbData bitops yaml GenomeInfoDb XVector zlibbioc crayon rlang fastmap GenomicRanges Biostrings matrixStats Rsamtools XML GenomicAlignments BiocIO restfulr BiocParallel Rhtslib SummarizedExperiment rjson futile.logger snow codetools BH MatrixGenerics Biobase Matrix DelayedArray lambda.r futile.options lattice formatR rtracklayer cachem evaluate glue magrittr xfun highr stringr stringi jsonlite digest R6 knitr htmltools jquerylib tinytex bslib base64enc sass fs rappdirs bookdown rmarkdown BiocManager brio callr cli desc ellipsis lifecycle pkgload praise processx ps waldo withr rprojroot rstudioapi diffobj fansi rematch2 tibble pillar pkgconfig vctrs utf8 BSgenome BSgenome.Hsapiens.UCSC.hg19 0 5 10 Imported methods 0 20 40 Required packages 0 10 20 30 Heaviness from parents GenomicRanges parallel graphics stats utils methods tools memoise S4Vectors IRanges GenomeInfoDb Biostrings rtracklayer BSgenome knitr rmarkdown BiocStyle testthat BSgenome.Hsapiens.UCSC.hg19.masked In total 50 packages are required directly or indirectly (98) when installing 'regioneR' (1.28.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'regioneR' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on regioneR
GenomicRanges Depends 11 0 0 15 0
memoise Imports 2 0 0 4 4
BSgenome Imports The whole set of functions/methods/classes from parent package is imported to the namespace of regioneR. 45 1
parallel Imports The whole set of functions/methods/classes from parent package is imported to the namespace of regioneR. 0 0
graphics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of regioneR. 0 0
stats Imports 6 0 0 0 0
utils Imports 4 0 0 0 0
methods Imports 2 0 0 0 0
tools Imports 1 0 0 0 0
S4Vectors Imports 3 0 0 6 0
IRanges Imports 2 0 0 7 0
GenomeInfoDb Imports The whole set of functions/methods/classes from parent package is imported to the namespace of regioneR. 11 0
Biostrings Imports 2 0 0 17 0
rtracklayer Imports 1 0 0 44 0
testthat Suggests No object is imported into the namespace of regioneR. 36 29
BiocStyle Suggests No object is imported into the namespace of regioneR. 30 23
rmarkdown Suggests No object is imported into the namespace of regioneR. 27 20
knitr Suggests No object is imported into the namespace of regioneR. 12 8
BSgenome.Hsapiens.UCSC.hg19.masked Suggests No object is imported into the namespace of regioneR. 47 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 regioneR Co-heaviness as Jaccard coeffcient
rtracklayer BSgenome 25 0.962

Analysis was done with pkgndep.