Dependency analysis on package TENxBrainData

General information

Bioconductor link link
Package version1.16.0
Number of strong dependencies100
Number of all dependencies120
Number of parent packages4
Max heaviness from parent packages4
Total heaviness from parent packages8
Number of parent packages (including Suggests and Enhances)11
Max co-heaviness from parent packages ("ExperimentHub" and "AnnotationHub")69

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats tools grDevices graphics stats4 grid parallel glue magrittr rappdirs yaml jsonlite R6 rlang fastmap S4Vectors BiocGenerics IRanges htmltools bslib jquerylib digest base64enc sass fs Biobase GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops RSQLite BiocManager curl httr dplyr dbplyr DBI filelock bit64 blob memoise pkgconfig Rcpp plogr mime openssl generics lifecycle tibble tidyselect vctrs pillar assertthat cli purrr withr bit cachem crayon ellipsis askpass fansi utf8 sys DelayedArray MatrixGenerics Matrix matrixStats lattice BiocFileCache BiocVersion AnnotationDbi interactiveDisplayBase KEGGREST shiny DT png Biostrings httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk lazyeval rhdf5 rhdf5filters Rhdf5lib SummarizedExperiment GenomicRanges AnnotationHub evaluate highr stringr xfun stringi knitr tinytex futile.logger snow codetools BH lambda.r futile.options formatR bookdown rmarkdown 0 0.5 1 Imported methods 0 20 40 60 80 Required packages 0 5 10 Heaviness from parents HDF5Array SingleCellExperiment AnnotationHub ExperimentHub snow data.table BiocParallel knitr rmarkdown BiocStyle BiocFileCache In total 100 packages are required directly or indirectly (120) when installing 'TENxBrainData' (1.16.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'TENxBrainData' Imported functions


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on TENxBrainData
HDF5Array Depends 1 0 0 19 4
SingleCellExperiment Depends 1 0 0 25 3
ExperimentHub Imports 1 0 0 86 1
AnnotationHub Imports 1 0 0 85 0
BiocStyle Suggests No object is imported into the namespace of TENxBrainData. 30 10
BiocParallel Suggests No object is imported into the namespace of TENxBrainData. 11 9
rmarkdown Suggests No object is imported into the namespace of TENxBrainData. 27 8
knitr Suggests No object is imported into the namespace of TENxBrainData. 12 6
snow Suggests No object is imported into the namespace of TENxBrainData. 1 1
data.table Suggests No object is imported into the namespace of TENxBrainData. 1 1
BiocFileCache Suggests No object is imported into the namespace of TENxBrainData. 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 TENxBrainData Co-heaviness as Jaccard coeffcient
AnnotationHub ExperimentHub 69 0.986

Analysis was done with pkgndep.