Dependency analysis on package BSgenome.Hsapiens.UCSC.hg19.masked

General information

Bioconductor link link
Package version1.3.993
Number of strong dependencies47
Number of all dependencies47
Number of parent packages2
Max heaviness from parent packages1
Total heaviness from parent packages1
Number of parent packages (including Suggests and Enhances)2
Max co-heaviness from parent packages ("BSgenome.Hsapiens.UCSC.hg19" and "BSgenome")46

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of BSgenome.Hsapiens.UCSC.hg19.masked 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 BSgenome.Hsapiens.UCSC.hg19.masked.

Adjust heatmap size:
Base packages Other packages Depends methods utils stats graphics stats4 grDevices tools parallel grid BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges Biostrings rtracklayer matrixStats XVector Rsamtools RCurl GenomeInfoDbData crayon XML zlibbioc GenomicAlignments BiocIO restfulr bitops BiocParallel Rhtslib SummarizedExperiment rjson yaml futile.logger snow codetools BH MatrixGenerics Biobase Matrix DelayedArray lambda.r futile.options lattice formatR BSgenome 0 0.5 1 Imported methods 0 20 40 Required packages 0 0.5 1 Heaviness from parents BSgenome BSgenome.Hsapiens.UCSC.hg19 In total 47 packages are required directly or indirectly (47) when installing 'BSgenome.Hsapiens.UCSC.hg19.masked' (1.3.993) Depends Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'BSgenome.Hsapiens.UCSC.hg19.masked' The whole namespace is imported


Dependency table

"Import" information is from the NAMESPACE file of BSgenome.Hsapiens.UCSC.hg19.masked.

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 BSgenome.Hsapiens.UCSC.hg19.masked: number of required packages that can be reduced if moving parent package to Suggests of BSgenome.Hsapiens.UCSC.hg19.masked.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on BSgenome.Hsapiens.UCSC.hg19.masked
BSgenome.Hsapiens.UCSC.hg19 Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BSgenome.Hsapiens.UCSC.hg19.masked. 46 1
BSgenome Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BSgenome.Hsapiens.UCSC.hg19.masked. 45 0

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 BSgenome.Hsapiens.UCSC.hg19.masked Co-heaviness as Jaccard coeffcient
BSgenome BSgenome.Hsapiens.UCSC.hg19 46 0.979

Analysis was done with pkgndep.