Dependency analysis on package SingleCellExperiment

General information

Bioconductor link link
Package version1.18.0
Number of strong dependencies25
Number of all dependencies147
Number of parent packages8
Max heaviness from parent packages2
Total heaviness from parent packages2
Number of parent packages (including Suggests and Enhances)15
Max co-heaviness from parent packages ("GenomicRanges" and "SummarizedExperiment")8

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics tools grDevices stats4 grid parallel BiocGenerics S4Vectors IRanges lattice MatrixGenerics Matrix GenomeInfoDb matrixStats XVector RCurl GenomeInfoDbData zlibbioc bitops GenomicRanges Biobase DelayedArray magrittr glue evaluate yaml stringr stringi digest jsonlite R6 rlang xfun highr htmltools jquerylib bslib base64enc fastmap sass fs rappdirs Rcpp knitr tinytex BiocManager cli crayon ellipsis lifecycle withr fansi tibble pillar pkgconfig vctrs utf8 bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 SingleCellExperiment SummarizedExperiment ExperimentHub AnnotationHub AnnotationDbi ensembldb GenomicFeatures BiocFileCache curl RSQLite BiocVersion interactiveDisplayBase httr dplyr DBI KEGGREST AnnotationFilter rtracklayer Rsamtools ProtGenerics Biostrings BiocIO biomaRt dbplyr filelock bit64 blob memoise plogr shiny DT mime openssl generics tidyselect png lazyeval XML GenomicAlignments restfulr BiocParallel Rhtslib progress xml2 assertthat purrr bit cachem httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk askpass rjson futile.logger snow codetools BH hms prettyunits sys lambda.r futile.options formatR 0 10 20 Imported methods 0 50 100 Required packages 0 50 100 Heaviness from parents SummarizedExperiment methods utils stats BiocGenerics S4Vectors DelayedArray GenomicRanges Rtsne Matrix knitr rmarkdown BiocStyle testthat scRNAseq In total 25 packages are required directly or indirectly (147) when installing 'SingleCellExperiment' (1.18.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'SingleCellExperiment' Imported functions Imported S4 classes


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on SingleCellExperiment
SummarizedExperiment Depends 8 0 2 24 2
methods Imports 3 0 0 0 0
utils Imports 2 0 0 0 0
stats Imports 1 0 0 0 0
BiocGenerics Imports 11 0 0 4 0
S4Vectors Imports 22 0 5 6 0
DelayedArray Imports 2 0 0 14 0
GenomicRanges Imports 2 0 0 15 0
scRNAseq Suggests No object is imported into the namespace of SingleCellExperiment. 124 100
testthat Suggests No object is imported into the namespace of SingleCellExperiment. 36 31
BiocStyle Suggests No object is imported into the namespace of SingleCellExperiment. 30 26
rmarkdown Suggests No object is imported into the namespace of SingleCellExperiment. 27 23
knitr Suggests No object is imported into the namespace of SingleCellExperiment. 12 9
Rtsne Suggests No object is imported into the namespace of SingleCellExperiment. 4 2
Matrix Suggests No object is imported into the namespace of SingleCellExperiment. 7 0

Analysis was done with pkgndep.