Dependency analysis on package AnnotationDbi

General information

Bioconductor link link
Package version1.58.0
Number of strong dependencies44
Number of all dependencies127
Number of parent packages11
Max heaviness from parent packages20
Total heaviness from parent packages35
Number of parent packages (including Suggests and Enhances)24
Max co-heaviness from parent packages ("KEGGREST" and "IRanges")1

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics stats4 tools grDevices parallel grid BiocGenerics glue S4Vectors rlang fastmap jsonlite R6 bit64 blob DBI memoise pkgconfig Rcpp plogr bit vctrs cachem cli httr png Biostrings curl mime openssl IRanges XVector GenomeInfoDb crayon askpass zlibbioc RCurl GenomeInfoDbData sys bitops AnnotationDbi Biobase RSQLite KEGGREST stringr yaml magrittr stringi digest rappdirs XML xfun evaluate highr GenomicFeatures GenomicRanges BiocIO rtracklayer biomaRt Rsamtools GenomicAlignments restfulr progress BiocFileCache xml2 BiocParallel Rhtslib SummarizedExperiment rjson hms prettyunits dbplyr dplyr filelock futile.logger snow codetools BH MatrixGenerics Matrix DelayedArray ellipsis lifecycle assertthat pillar purrr tibble tidyselect withr generics lambda.r futile.options matrixStats lattice fansi utf8 formatR bookdown knitr rmarkdown BiocManager htmltools jquerylib tinytex bslib base64enc sass fs org.Hs.eg.db ensembldb AnnotationFilter ProtGenerics lazyeval 0 0.5 1 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents methods utils stats4 BiocGenerics Biobase IRanges stats DBI S4Vectors RSQLite KEGGREST RUnit graph knitr BiocStyle GO.db org.Sc.sgd.db org.At.tair.db org.Hs.eg.db reactome.db hgu95av2.db AnnotationForge TxDb.Hsapiens.UCSC.hg19.knownGene EnsDb.Hsapiens.v75 In total 44 packages are required directly or indirectly (127) when installing 'AnnotationDbi' (1.58.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'AnnotationDbi' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on AnnotationDbi
Biobase Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationDbi. 5 1
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationDbi. 0 0
utils Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationDbi. 0 0
stats4 Depends 1 0 0 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationDbi. 4 0
IRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationDbi. 7 0
KEGGREST Imports 1 0 0 27 20
RSQLite Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationDbi. 17 14
stats Imports 1 0 0 0 0
DBI Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationDbi. 1 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationDbi. 6 0
EnsDb.Hsapiens.v75 Suggests No object is imported into the namespace of AnnotationDbi. 101 58
TxDb.Hsapiens.UCSC.hg19.knownGene Suggests No object is imported into the namespace of AnnotationDbi. 97 54
BiocStyle Suggests No object is imported into the namespace of AnnotationDbi. 30 21
knitr Suggests No object is imported into the namespace of AnnotationDbi. 12 8
hgu95av2.db Suggests No object is imported into the namespace of AnnotationDbi. 46 3
AnnotationForge Suggests No object is imported into the namespace of AnnotationDbi. 46 3
GO.db Suggests No object is imported into the namespace of AnnotationDbi. 45 2
org.Sc.sgd.db Suggests No object is imported into the namespace of AnnotationDbi. 45 2
org.At.tair.db Suggests No object is imported into the namespace of AnnotationDbi. 45 2
org.Hs.eg.db Suggests No object is imported into the namespace of AnnotationDbi. 45 2
reactome.db Suggests No object is imported into the namespace of AnnotationDbi. 45 2
RUnit Suggests No object is imported into the namespace of AnnotationDbi. 3 1
graph Suggests No object is imported into the namespace of AnnotationDbi. 6 1

Analysis was done with pkgndep.