Dependency analysis on package scater

General information

Bioconductor link link
Package version1.24.0
Number of strong dependencies85
Number of all dependencies197
Number of parent packages25
Max heaviness from parent packages4
Total heaviness from parent packages15
Number of parent packages (including Suggests and Enhances)37
Max co-heaviness from parent packages ("DelayedMatrixStats" and "scuttle")2

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats graphics grDevices grid stats4 tools parallel splines lattice Matrix BiocGenerics glue Rcpp rlang R6 magrittr S4Vectors digest IRanges withr lifecycle MatrixGenerics matrixStats tibble ellipsis fansi pillar pkgconfig vctrs cli crayon utf8 DelayedArray gtable scales farver labeling munsell RColorBrewer viridisLite colorspace BH Biobase GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops isoband MASS mgcv nlme futile.logger snow codetools lambda.r futile.options formatR GenomicRanges BiocParallel ggplot2 SummarizedExperiment irlba SingleCellExperiment beachmat sparseMatrixStats RcppEigen DelayedMatrixStats RcppHNSW ScaledMatrix rsvd gridExtra beeswarm vipor jsonlite stringr stringi rappdirs yaml evaluate fastmap xfun highr filelock png assertthat htmltools jquerylib bslib base64enc sass fs rprojroot knitr tinytex BiocManager XML AnnotationDbi progress httr BiocFileCache xml2 DBI RSQLite KEGGREST hms prettyunits curl mime openssl dbplyr dplyr bit64 blob memoise plogr Biostrings askpass purrr tidyselect generics bit cachem sys DEoptimR FNN RSpectra RcppAnnoy RcppProgress dqrng sitmo basilisk reticulate dir.expiry basilisk.utils RcppTOML here bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rstudioapi diffobj rematch2 ExperimentHub AnnotationHub ensembldb GenomicFeatures BiocVersion interactiveDisplayBase AnnotationFilter rtracklayer Rsamtools ProtGenerics BiocIO biomaRt shiny DT lazyeval GenomicAlignments restfulr Rhtslib httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk rjson 0 20 40 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents SingleCellExperiment ggplot2 scuttle stats utils methods grid RColorBrewer rlang BiocGenerics Rtsne gridExtra S4Vectors Matrix RcppML BiocParallel DelayedArray beachmat DelayedMatrixStats BiocNeighbors SummarizedExperiment BiocSingular viridis ggrepel ggbeeswarm robustbase Biobase knitr uwot pheatmap snifter rmarkdown BiocStyle testthat cowplot biomaRt scRNAseq In total 85 packages are required directly or indirectly (197) when installing 'scater' (1.24.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'scater' Imported functions Imported S4 methods Imported S4 classes Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on scater
scuttle Depends 4 0 0 39 1
SingleCellExperiment Depends 15 0 1 25 0
ggplot2 Depends 41 0 0 37 0
BiocSingular Imports 3 0 0 29 4
ggbeeswarm Imports 1 0 0 40 3
RcppML Imports Parent package is listed in Imports of scater but no object from parent package is imported. 10 2
BiocNeighbors Imports 2 0 0 22 2
Rtsne Imports Parent package is listed in Imports of scater but no object from parent package is imported. 4 1
viridis Imports 3 0 0 39 1
ggrepel Imports 1 0 0 39 1
stats Imports 5 0 0 0 0
utils Imports 1 0 0 0 0
methods Imports 1 0 0 0 0
grid Imports 1 0 0 0 0
RColorBrewer Imports Parent package is listed in Imports of scater but no object from parent package is imported. 0 0
rlang Imports 1 0 0 1 0
BiocGenerics Imports 6 0 0 4 0
gridExtra Imports 1 0 0 5 0
S4Vectors Imports 2 0 1 6 0
Matrix Imports 4 0 0 7 0
BiocParallel Imports 4 0 1 11 0
DelayedArray Imports 3 1 0 14 0
beachmat Imports 2 0 0 16 0
DelayedMatrixStats Imports 7 0 0 17 0
SummarizedExperiment Imports 7 0 1 24 0
scRNAseq Suggests No object is imported into the namespace of scater. 124 73
biomaRt Suggests No object is imported into the namespace of scater. 70 37
BiocStyle Suggests No object is imported into the namespace of scater. 30 21
rmarkdown Suggests No object is imported into the namespace of scater. 27 18
testthat Suggests No object is imported into the namespace of scater. 36 15
snifter Suggests No object is imported into the namespace of scater. 25 13
knitr Suggests No object is imported into the namespace of scater. 12 7
uwot Suggests No object is imported into the namespace of scater. 18 7
robustbase Suggests No object is imported into the namespace of scater. 5 2
pheatmap Suggests No object is imported into the namespace of scater. 18 1
cowplot Suggests No object is imported into the namespace of scater. 38 1
Biobase Suggests No object is imported into the namespace of scater. 5 0

Analysis was done with pkgndep.