Dependency analysis on package scuttle

General information

Bioconductor link link
Package version1.6.2
Number of strong dependencies39
Number of all dependencies167
Number of parent packages14
Max heaviness from parent packages9
Total heaviness from parent packages13
Number of parent packages (including Suggests and Enhances)20
Max co-heaviness from parent packages ("SummarizedExperiment" and "SingleCellExperiment")2

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics grDevices tools stats4 grid parallel BiocGenerics S4Vectors IRanges lattice MatrixGenerics Matrix matrixStats DelayedArray GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops GenomicRanges Biobase Rcpp SummarizedExperiment futile.logger snow codetools BH lambda.r futile.options formatR sparseMatrixStats magrittr glue yaml evaluate stringr stringi jsonlite digest rlang R6 xfun highr htmltools jquerylib bslib base64enc fastmap sass fs rappdirs pkgconfig knitr tinytex BiocManager lifecycle tibble vctrs pillar crayon cli withr ellipsis fansi utf8 SingleCellExperiment BiocParallel bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 scuttle edgeR limma igraph statmod DelayedMatrixStats BiocSingular bluster metapod dqrng beachmat locfit ScaledMatrix irlba rsvd cluster BiocNeighbors sitmo RcppHNSW 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 Rhtslib progress xml2 assertthat purrr bit cachem httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk askpass rjson hms prettyunits sys 0 5 10 15 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents SingleCellExperiment methods utils stats Rcpp BiocGenerics S4Vectors Matrix BiocParallel DelayedArray GenomicRanges beachmat DelayedMatrixStats SummarizedExperiment knitr rmarkdown BiocStyle testthat scran scRNAseq In total 39 packages are required directly or indirectly (167) when installing 'scuttle' (1.6.2) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'scuttle' Imported functions Imported S4 classes


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on scuttle
SingleCellExperiment Depends 14 0 1 25 1
BiocParallel Imports 7 0 1 11 9
DelayedMatrixStats Imports 2 0 0 17 2
beachmat Imports 3 0 0 16 1
methods Imports 2 0 0 0 0
utils Imports 3 0 0 0 0
stats Imports 13 0 0 0 0
Rcpp Imports 1 0 0 2 0
BiocGenerics Imports 6 0 0 4 0
S4Vectors Imports 9 0 3 6 0
Matrix Imports 8 0 3 7 0
DelayedArray Imports 7 0 2 14 0
GenomicRanges Imports 2 0 0 15 0
SummarizedExperiment Imports 11 0 1 24 0
scRNAseq Suggests No object is imported into the namespace of scuttle. 124 89
testthat Suggests No object is imported into the namespace of scuttle. 36 31
BiocStyle Suggests No object is imported into the namespace of scuttle. 30 26
rmarkdown Suggests No object is imported into the namespace of scuttle. 27 23
scran Suggests No object is imported into the namespace of scuttle. 58 20
knitr Suggests No object is imported into the namespace of scuttle. 12 9

Analysis was done with pkgndep.