Dependency analysis on package SpatialExperiment

General information

Bioconductor link link
Package version1.6.0
Number of strong dependencies95
Number of all dependencies128
Number of parent packages11
Max heaviness from parent packages38
Total heaviness from parent packages66
Number of parent packages (including Suggests and Enhances)16
Max co-heaviness from parent packages ("BiocFileCache" and "magick")2

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats tools graphics grDevices stats4 grid parallel magrittr BiocGenerics glue S4Vectors Matrix IRanges lattice R6 rlang jsonlite GenomicRanges DelayedArray MatrixGenerics Biobase GenomeInfoDb XVector matrixStats RCurl GenomeInfoDbData zlibbioc bitops Rcpp rappdirs fastmap SummarizedExperiment curl cli lifecycle pillar tibble vctrs withr pkgconfig crayon ellipsis fansi utf8 dbplyr dplyr RSQLite DBI filelock httr assertthat blob purrr tidyselect generics bit64 memoise plogr mime openssl bit cachem askpass sys SingleCellExperiment BiocParallel DelayedMatrixStats HDF5Array rhdf5 edgeR R.utils dqrng beachmat scuttle Rhdf5lib BH futile.logger snow codetools sparseMatrixStats rhdf5filters limma locfit R.oo R.methodsS3 sitmo lambda.r futile.options formatR evaluate highr stringr yaml xfun stringi digest bslib htmltools jquerylib knitr tinytex sass base64enc fs bookdown rmarkdown BiocManager brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 0 2 4 6 Imported methods 0 20 40 Required packages 0 10 20 30 Heaviness from parents methods SingleCellExperiment rjson grDevices utils BiocGenerics magick S4Vectors SummarizedExperiment BiocFileCache DropletUtils knitr BumpyMatrix rmarkdown BiocStyle testthat In total 95 packages are required directly or indirectly (128) when installing 'SpatialExperiment' (1.6.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'SpatialExperiment' Imported functions Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on SpatialExperiment
methods Depends 4 0 0 0 0
SingleCellExperiment Depends 5 0 0 25 0
BiocFileCache Imports Parent package is listed in Imports of SpatialExperiment but no object from parent package is imported. 46 38
DropletUtils Imports 1 0 0 52 26
rjson Imports 1 0 0 0 1
magick Imports 3 0 0 5 1
grDevices Imports 2 0 0 0 0
utils Imports 4 0 0 0 0
BiocGenerics Imports 2 0 0 4 0
S4Vectors Imports 6 0 0 6 0
SummarizedExperiment Imports 6 0 0 24 0
BiocStyle Suggests No object is imported into the namespace of SpatialExperiment. 30 19
rmarkdown Suggests No object is imported into the namespace of SpatialExperiment. 27 16
testthat Suggests No object is imported into the namespace of SpatialExperiment. 36 15
knitr Suggests No object is imported into the namespace of SpatialExperiment. 12 7
BumpyMatrix Suggests No object is imported into the namespace of SpatialExperiment. 12 1

Analysis was done with pkgndep.