Dependency analysis on package scRNAseq

General information

Bioconductor link link
Package version2.10.0
Number of strong dependencies124
Number of all dependencies145
Number of parent packages12
Max heaviness from parent packages3
Total heaviness from parent packages5
Number of parent packages (including Suggests and Enhances)19
Max co-heaviness from parent packages ("ensembldb" and "GenomicFeatures")25

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats tools graphics grDevices stats4 grid parallel glue BiocGenerics jsonlite R6 rlang magrittr S4Vectors IRanges GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops fastmap Biobase pkgconfig vctrs cli crayon rappdirs yaml digest curl RSQLite httr DBI bit64 blob memoise Rcpp plogr mime openssl bit cachem askpass sys lifecycle tibble pillar withr ellipsis fansi utf8 KEGGREST png Biostrings dplyr dbplyr filelock generics tidyselect assertthat purrr stringr stringi GenomicRanges DelayedArray MatrixGenerics Matrix matrixStats lattice BiocFileCache AnnotationDbi htmltools bslib jquerylib base64enc sass fs SummarizedExperiment BiocManager lazyeval BiocVersion interactiveDisplayBase shiny DT httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk rtracklayer Rsamtools BiocIO biomaRt XML GenomicAlignments restfulr BiocParallel Rhtslib progress xml2 rjson futile.logger snow codetools BH hms prettyunits lambda.r futile.options formatR AnnotationHub GenomicFeatures AnnotationFilter ProtGenerics evaluate xfun highr knitr tinytex bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 0 2 4 6 8 Imported methods 0 50 100 Required packages 0 5 10 Heaviness from parents SingleCellExperiment utils methods BiocGenerics S4Vectors GenomicRanges SummarizedExperiment AnnotationDbi AnnotationHub ExperimentHub GenomicFeatures ensembldb rappdirs tools knitr rmarkdown BiocStyle testthat BiocFileCache In total 124 packages are required directly or indirectly (145) when installing 'scRNAseq' (2.10.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'scRNAseq' Imported functions Imported S4 classes


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on scRNAseq
SingleCellExperiment Depends 9 0 0 25 1
ensembldb Imports 0 0 1 100 3
ExperimentHub Imports 1 0 0 86 1
utils Imports 3 0 0 0 0
methods Imports 1 0 0 0 0
BiocGenerics Imports 1 0 0 4 0
S4Vectors Imports 2 0 0 6 0
GenomicRanges Imports 0 0 1 15 0
SummarizedExperiment Imports 7 0 0 24 0
AnnotationDbi Imports 3 0 0 44 0
AnnotationHub Imports 1 0 0 85 0
GenomicFeatures Imports 1 0 0 96 0
testthat Suggests No object is imported into the namespace of scRNAseq. 36 14
BiocStyle Suggests No object is imported into the namespace of scRNAseq. 30 8
rmarkdown Suggests No object is imported into the namespace of scRNAseq. 27 6
knitr Suggests No object is imported into the namespace of scRNAseq. 12 4
rappdirs Suggests No object is imported into the namespace of scRNAseq. 0 0
tools Suggests No object is imported into the namespace of scRNAseq. 0 0
BiocFileCache Suggests No object is imported into the namespace of scRNAseq. 46 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 scRNAseq Co-heaviness as Jaccard coeffcient
GenomicFeatures ensembldb 25 0.893
AnnotationHub ExperimentHub 21 0.955

Analysis was done with pkgndep.