Dependency analysis on package ensembldb

General information

Bioconductor link link
Package version2.20.1
Number of strong dependencies100
Number of all dependencies192
Number of parent packages17
Max heaviness from parent packages26
Total heaviness from parent packages29
Number of parent packages (including Suggests and Enhances)29
Max co-heaviness from parent packages ("rtracklayer" and "GenomicFeatures")14

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests Enhances methods utils stats graphics tools stats4 grDevices parallel grid splines BiocGenerics S4Vectors IRanges RCurl GenomeInfoDbData bitops glue GenomeInfoDb XVector zlibbioc crayon rlang yaml R6 magrittr jsonlite fastmap Biostrings pkgconfig Rcpp digest vctrs cli GenomicRanges DBI Biobase bit64 blob plogr rappdirs bit cachem ellipsis lifecycle memoise stringr BiocParallel Rhtslib stringi mime futile.logger snow codetools BH withr lambda.r futile.options formatR RSQLite BiocIO KEGGREST XML Rsamtools GenomicAlignments restfulr httr png SummarizedExperiment rjson curl openssl MatrixGenerics Matrix DelayedArray askpass pillar tibble generics matrixStats lattice sys fansi utf8 lazyeval AnnotationDbi rtracklayer BiocFileCache hms dbplyr dplyr filelock assertthat purrr tidyselect biomaRt progress xml2 prettyunits evaluate htmltools base64enc xfun highr knitr jquerylib bslib sass fs BiocManager rstudioapi BSgenome htmlwidgets ensembldb GenomicFeatures AnnotationFilter ProtGenerics tinytex httpuv xtable fontawesome sourcetools later promises commonmark ggplot2 gridExtra scales gtable Hmisc biovizBase VariantAnnotation isoband MASS mgcv farver labeling munsell RColorBrewer viridisLite survival Formula latticeExtra cluster rpart nnet foreign data.table htmlTable viridis dichromat nlme colorspace jpeg checkmate backports cpp11 bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot diffobj rematch2 BiocVersion interactiveDisplayBase shiny DT crosstalk reshape2 OrganismDbi GGally plyr graph RBGL forcats reshape tidyr lubridate 0 20 40 Imported methods 0 50 100 150 Required packages 0 20 40 Heaviness from parents BiocGenerics GenomicRanges AnnotationFilter GenomicFeatures methods curl DBI ProtGenerics Biobase S4Vectors IRanges GenomeInfoDb RSQLite Biostrings Rsamtools AnnotationDbi rtracklayer magrittr knitr rmarkdown BiocStyle testthat BSgenome.Hsapiens.NCBI.GRCh38 AnnotationHub EnsDb.Hsapiens.v86 Gviz ggbio RMariaDB shiny In total 100 packages are required directly or indirectly (192) when installing 'ensembldb' (2.20.1) Depends Imports Suggests Enhances Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'ensembldb' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on ensembldb
GenomicFeatures Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ensembldb. 96 26
AnnotationFilter Depends 24 5 25 17 2
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ensembldb. 4 0
GenomicRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ensembldb. 15 0
ProtGenerics Imports 0 1 0 1 1
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ensembldb. 0 0
curl Imports 1 0 0 0 0
DBI Imports 1 0 0 1 0
Biobase Imports 2 0 0 5 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ensembldb. 6 0
IRanges Imports 2 1 0 7 0
GenomeInfoDb Imports 10 0 0 11 0
RSQLite Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ensembldb. 17 0
Biostrings Imports 1 0 1 17 0
Rsamtools Imports 2 2 2 29 0
AnnotationDbi Imports 0 6 0 44 0
rtracklayer Imports 1 0 0 44 0
ggbio Suggests No object is imported into the namespace of ensembldb. 153 54
Gviz Suggests No object is imported into the namespace of ensembldb. 142 43
AnnotationHub Suggests No object is imported into the namespace of ensembldb. 85 21
BiocStyle Suggests No object is imported into the namespace of ensembldb. 30 15
testthat Suggests No object is imported into the namespace of ensembldb. 36 14
rmarkdown Suggests No object is imported into the namespace of ensembldb. 27 12
knitr Suggests No object is imported into the namespace of ensembldb. 12 4
BSgenome.Hsapiens.NCBI.GRCh38 Suggests No object is imported into the namespace of ensembldb. 46 2
EnsDb.Hsapiens.v86 Suggests No object is imported into the namespace of ensembldb. 101 2
magrittr Suggests No object is imported into the namespace of ensembldb. 0 0
shiny Enhances No object is imported into the namespace of ensembldb. 34 14
RMariaDB Enhances No object is imported into the namespace of ensembldb. 20 3

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 ensembldb Co-heaviness as Jaccard coeffcient
GenomicFeatures rtracklayer 14 0.35

Analysis was done with pkgndep.