Dependency analysis on package AnnotationForge

General information

Bioconductor link link
Package version1.38.0
Number of strong dependencies46
Number of all dependencies125
Number of parent packages10
Max heaviness from parent packages20
Total heaviness from parent packages21
Number of parent packages (including Suggests and Enhances)25
Max co-heaviness from parent packages ("RSQLite" and "AnnotationDbi")14

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics tools grDevices stats4 parallel grid BiocGenerics glue rlang jsonlite mime R6 fastmap bitops IRanges DBI S4Vectors bit64 blob memoise pkgconfig Rcpp plogr bit vctrs cachem curl openssl crayon cli askpass zlibbioc RCurl GenomeInfoDbData sys Biobase RSQLite httr XVector GenomeInfoDb KEGGREST png Biostrings AnnotationDbi magrittr stringr stringi rappdirs xfun BiocManager yaml digest dbplyr dplyr filelock ellipsis lifecycle assertthat pillar purrr tibble tidyselect withr generics fansi utf8 evaluate highr org.Hs.eg.db XML progress BiocFileCache xml2 hms prettyunits affyio preprocessCore bookdown knitr rmarkdown htmltools jquerylib tinytex bslib base64enc sass fs OrganismDbi GenomicFeatures GO.db TxDb.Hsapiens.UCSC.hg19.knownGene GenomicRanges graph RBGL BiocIO rtracklayer biomaRt BH Rsamtools GenomicAlignments restfulr BiocParallel Rhtslib SummarizedExperiment rjson futile.logger snow codetools MatrixGenerics Matrix DelayedArray lambda.r futile.options matrixStats lattice formatR 0 0.5 1 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents methods utils BiocGenerics Biobase AnnotationDbi DBI XML RCurl S4Vectors RSQLite BiocManager markdown httr GenomeInfoDb affy knitr Biostrings BiocStyle human.db0 org.Hs.eg.db GO.db hgu95av2.db BiocFileCache biomaRt Homo.sapiens In total 46 packages are required directly or indirectly (125) when installing 'AnnotationForge' (1.38.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'AnnotationForge' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on AnnotationForge
AnnotationDbi Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationForge. 44 20
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationForge. 0 0
utils Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationForge. 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationForge. 4 0
Biobase Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationForge. 5 0
XML Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationForge. 2 1
DBI Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationForge. 1 0
RCurl Imports 1 0 0 2 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationForge. 6 0
RSQLite Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationForge. 17 0
Homo.sapiens Suggests No object is imported into the namespace of AnnotationForge. 104 59
biomaRt Suggests No object is imported into the namespace of AnnotationForge. 70 25
BiocStyle Suggests No object is imported into the namespace of AnnotationForge. 30 21
BiocFileCache Suggests No object is imported into the namespace of AnnotationForge. 46 17
knitr Suggests No object is imported into the namespace of AnnotationForge. 12 8
affy Suggests No object is imported into the namespace of AnnotationForge. 11 4
markdown Suggests No object is imported into the namespace of AnnotationForge. 5 2
hgu95av2.db Suggests No object is imported into the namespace of AnnotationForge. 46 2
BiocManager Suggests No object is imported into the namespace of AnnotationForge. 1 1
human.db0 Suggests No object is imported into the namespace of AnnotationForge. 45 1
org.Hs.eg.db Suggests No object is imported into the namespace of AnnotationForge. 45 1
GO.db Suggests No object is imported into the namespace of AnnotationForge. 45 1
httr Suggests No object is imported into the namespace of AnnotationForge. 9 0
GenomeInfoDb Suggests No object is imported into the namespace of AnnotationForge. 11 0
Biostrings Suggests No object is imported into the namespace of AnnotationForge. 17 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 AnnotationForge Co-heaviness as Jaccard coeffcient
AnnotationDbi RSQLite 14 0.412

Analysis was done with pkgndep.