Dependency analysis on package MafDb.1Kgenomes.phase1.hs37d5

General information

Bioconductor link link
Package version3.10.0
Number of strong dependencies117
Number of all dependencies118
Number of parent packages7
Max heaviness from parent packages71
Total heaviness from parent packages89
Number of parent packages (including Suggests and Enhances)8
Max co-heaviness from parent packages ("BSgenome" and "GenomicScores")12

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of MafDb.1Kgenomes.phase1.hs37d5 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 MafDb.1Kgenomes.phase1.hs37d5.

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods stats utils stats4 graphics tools grDevices grid parallel BiocGenerics S4Vectors IRanges RCurl GenomeInfoDbData bitops GenomeInfoDb XVector zlibbioc GenomicRanges XML Biobase Biostrings DelayedArray crayon yaml Matrix MatrixGenerics lattice matrixStats rtracklayer Rsamtools GenomicAlignments BiocIO restfulr BiocParallel Rhtslib SummarizedExperiment rjson futile.logger snow codetools BH lambda.r futile.options formatR BiocManager BiocFileCache AnnotationHub rhdf5 HDF5Array dbplyr dplyr RSQLite DBI rappdirs filelock curl httr BiocVersion AnnotationDbi interactiveDisplayBase Rhdf5lib rhdf5filters assertthat blob cli glue lifecycle magrittr pillar purrr R6 rlang tibble tidyselect vctrs withr generics bit64 memoise pkgconfig Rcpp plogr jsonlite mime openssl KEGGREST shiny DT ellipsis fansi utf8 bit cachem askpass png httpuv xtable fontawesome htmltools sourcetools later promises fastmap commonmark bslib htmlwidgets crosstalk jquerylib sys digest base64enc sass lazyeval fs BSgenome 0 0.5 1 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents GenomicScores utils S4Vectors IRanges GenomeInfoDb GenomicRanges BSgenome SNPlocs.Hsapiens.dbSNP144.GRCh37 In total 117 packages are required directly or indirectly (118) when installing 'MafDb.1Kgenomes.phase1.hs37d5' (3.10.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'MafDb.1Kgenomes.phase1.hs37d5' The whole namespace is imported The whole namespace is imported except some functions


Dependency table

"Import" information is from the NAMESPACE file of MafDb.1Kgenomes.phase1.hs37d5.

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 MafDb.1Kgenomes.phase1.hs37d5: number of required packages that can be reduced if moving parent package to Suggests of MafDb.1Kgenomes.phase1.hs37d5.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on MafDb.1Kgenomes.phase1.hs37d5
GenomicScores Depends The whole set of functions/methods/classes from parent package is imported to the namespace of MafDb.1Kgenomes.phase1.hs37d5. 98 71
BSgenome Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MafDb.1Kgenomes.phase1.hs37d5. 45 18
utils Imports The whole set of functions/methods/classes from parent package excluding 1 objects is imported to the namespace of MafDb.1Kgenomes.phase1.hs37d5. 0 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MafDb.1Kgenomes.phase1.hs37d5. 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MafDb.1Kgenomes.phase1.hs37d5. 7 0
GenomeInfoDb Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MafDb.1Kgenomes.phase1.hs37d5. 11 0
GenomicRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MafDb.1Kgenomes.phase1.hs37d5. 15 0
SNPlocs.Hsapiens.dbSNP144.GRCh37 Suggests No object is imported into the namespace of MafDb.1Kgenomes.phase1.hs37d5. 46 1

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 MafDb.1Kgenomes.phase1.hs37d5 Co-heaviness as Jaccard coeffcient
GenomicScores BSgenome 12 0.119

Analysis was done with pkgndep.