Dependency analysis on package scds

General information

Bioconductor link link
Package version1.12.0
Number of strong dependencies50
Number of all dependencies116
Number of parent packages9
Max heaviness from parent packages18
Total heaviness from parent packages25
Number of parent packages (including Suggests and Enhances)16
Max co-heaviness from parent packages ("SingleCellExperiment" and "SummarizedExperiment")14

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats grDevices graphics grid tools stats4 splines parallel lattice Matrix glue magrittr R6 rlang BiocGenerics Rcpp jsonlite lifecycle tibble vctrs pillar ellipsis fansi pkgconfig cli crayon utf8 S4Vectors GenomicRanges DelayedArray MatrixGenerics Biobase IRanges GenomeInfoDb XVector matrixStats RCurl GenomeInfoDbData zlibbioc bitops SummarizedExperiment plyr data.table generics tidyselect purrr digest yaml xfun evaluate highr stringr stringi knitr htmltools jquerylib tinytex bslib base64enc fastmap sass fs rappdirs ggplot2 RColorBrewer gtable isoband MASS mgcv scales withr viridisLite nlme farver labeling munsell colorspace bookdown rmarkdown BiocManager SingleCellExperiment scuttle gridExtra DelayedMatrixStats beachmat BiocNeighbors BiocSingular BiocParallel ggbeeswarm viridis Rtsne RcppML ggrepel sparseMatrixStats RcppHNSW ScaledMatrix irlba rsvd futile.logger snow codetools BH beeswarm vipor RcppEigen lambda.r futile.options formatR 0 2 4 6 8 Imported methods 0 20 40 60 80 Required packages 0 20 40 Heaviness from parents methods stats pROC S4Vectors Matrix xgboost dplyr SummarizedExperiment SingleCellExperiment Rtsne rsvd knitr rmarkdown BiocStyle cowplot scater In total 50 packages are required directly or indirectly (116) when installing 'scds' (1.12.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'scds' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on scds
dplyr Imports 1 0 0 20 18
pROC Imports 1 0 0 4 3
xgboost Imports 4 0 0 10 3
SingleCellExperiment Imports The whole set of functions/methods/classes from parent package is imported to the namespace of scds. 25 1
methods Imports 1 0 0 0 0
stats Imports 7 0 0 0 0
S4Vectors Imports 3 0 0 6 0
Matrix Imports 4 0 0 7 0
SummarizedExperiment Imports 9 0 0 24 0
scater Suggests No object is imported into the namespace of scds. 85 45
BiocStyle Suggests No object is imported into the namespace of scds. 30 21
rmarkdown Suggests No object is imported into the namespace of scds. 27 18
cowplot Suggests No object is imported into the namespace of scds. 38 17
knitr Suggests No object is imported into the namespace of scds. 12 7
Rtsne Suggests No object is imported into the namespace of scds. 4 1
rsvd Suggests No object is imported into the namespace of scds. 8 1

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 scds Co-heaviness as Jaccard coeffcient
SummarizedExperiment SingleCellExperiment 14 0.933

Analysis was done with pkgndep.