Dependency analysis on package OrganismDbi

General information

Bioconductor link link
Package version1.38.0
Number of strong dependencies100
Number of all dependencies137
Number of parent packages13
Max heaviness from parent packages50
Total heaviness from parent packages52
Number of parent packages (including Suggests and Enhances)23
Max co-heaviness from parent packages ("GenomicFeatures" and "AnnotationDbi")28

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils graphics stats stats4 tools grDevices parallel grid BiocGenerics S4Vectors IRanges XVector GenomeInfoDb zlibbioc RCurl GenomeInfoDbData bitops Biobase Biostrings crayon DBI bit64 blob pkgconfig Rcpp plogr bit rlang vctrs cli glue RSQLite KEGGREST memoise httr png cachem curl jsonlite mime openssl R6 fastmap askpass sys AnnotationDbi XML yaml BH ellipsis lifecycle generics GenomicRanges BiocIO Rsamtools GenomicAlignments restfulr digest BiocFileCache rappdirs BiocParallel Rhtslib SummarizedExperiment rjson hms magrittr dbplyr dplyr filelock futile.logger snow codetools MatrixGenerics Matrix DelayedArray assertthat pillar purrr tibble tidyselect withr lambda.r futile.options matrixStats lattice fansi utf8 formatR rtracklayer progress stringr xml2 prettyunits stringi biomaRt graph BiocManager GenomicFeatures OrganismDbi GO.db RBGL lubridate cpp11 BSgenome BiocVersion interactiveDisplayBase shiny DT httpuv xtable fontawesome htmltools sourcetools later promises commonmark bslib htmlwidgets crosstalk jquerylib base64enc sass lazyeval fs org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene org.Rn.eg.db TxDb.Rnorvegicus.UCSC.rn5.refGene 0 2 4 6 8 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents methods BiocGenerics AnnotationDbi GenomicFeatures stats BiocManager DBI Biobase graph S4Vectors IRanges RBGL GenomicRanges RUnit RMariaDB rtracklayer mirbase.db BSgenome.Hsapiens.UCSC.hg19 biomaRt AnnotationHub FDb.UCSC.tRNAs Homo.sapiens Rattus.norvegicus In total 100 packages are required directly or indirectly (137) when installing 'OrganismDbi' (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 'OrganismDbi' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on OrganismDbi
GenomicFeatures Depends The whole set of functions/methods/classes from parent package is imported to the namespace of OrganismDbi. 96 50
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of OrganismDbi. 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of OrganismDbi. 4 0
AnnotationDbi Depends The whole set of functions/methods/classes from parent package is imported to the namespace of OrganismDbi. 44 0
BiocManager Imports 1 0 0 1 1
RBGL Imports 0 1 0 8 1
stats Imports 1 0 0 0 0
DBI Imports 0 1 0 1 0
Biobase Imports 1 0 0 5 0
graph Imports 1 6 1 6 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of OrganismDbi. 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of OrganismDbi. 7 0
GenomicRanges Imports 0 0 1 15 0
AnnotationHub Suggests No object is imported into the namespace of OrganismDbi. 85 21
Homo.sapiens Suggests No object is imported into the namespace of OrganismDbi. 104 5
Rattus.norvegicus Suggests No object is imported into the namespace of OrganismDbi. 104 5
RMariaDB Suggests No object is imported into the namespace of OrganismDbi. 20 3
BSgenome.Hsapiens.UCSC.hg19 Suggests No object is imported into the namespace of OrganismDbi. 46 2
RUnit Suggests No object is imported into the namespace of OrganismDbi. 3 1
mirbase.db Suggests No object is imported into the namespace of OrganismDbi. 45 1
FDb.UCSC.tRNAs Suggests No object is imported into the namespace of OrganismDbi. 97 1
rtracklayer Suggests No object is imported into the namespace of OrganismDbi. 44 0
biomaRt Suggests No object is imported into the namespace of OrganismDbi. 70 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 OrganismDbi Co-heaviness as Jaccard coeffcient
AnnotationDbi GenomicFeatures 28 0.359

Analysis was done with pkgndep.