Dependency analysis on package SC3

General information

Bioconductor link link
Package version1.24.0
Number of strong dependencies100
Number of all dependencies137
Number of parent packages23
Max heaviness from parent packages19
Total heaviness from parent packages50
Number of parent packages (including Suggests and Enhances)27
Max co-heaviness from parent packages ("SingleCellExperiment" and "SummarizedExperiment")12

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of SC3 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 SC3.

Adjust heatmap size:
Base packages Other packages Imports LinkingTo Suggests utils stats methods graphics grDevices grid tools stats4 parallel splines glue digest lattice R6 rlang magrittr codetools BiocGenerics bitops lifecycle Matrix iterators MASS gtable scales farver labeling munsell RColorBrewer viridisLite colorspace MatrixGenerics GenomicRanges Biobase S4Vectors IRanges GenomeInfoDb DelayedArray matrixStats XVector RCurl GenomeInfoDbData zlibbioc crayon withr ellipsis Rcpp foreach DEoptimR SummarizedExperiment jsonlite htmltools fastmap bslib base64enc sass jquerylib fs rappdirs isoband mgcv tibble nlme fansi pillar pkgconfig vctrs cli utf8 class proxy rngtools gplots gtools caTools KernSmooth robustbase mvtnorm pcaPP httpuv mime xtable fontawesome sourcetools later promises commonmark cachem evaluate highr stringr yaml xfun stringi knitr tinytex SingleCellExperiment scuttle ggplot2 gridExtra DelayedMatrixStats beachmat BiocNeighbors BiocSingular BiocParallel ggbeeswarm viridis Rtsne RcppML ggrepel sparseMatrixStats RcppHNSW ScaledMatrix irlba rsvd futile.logger snow BH beeswarm vipor RcppEigen lambda.r futile.options formatR 0 10 20 30 40 Imported methods 0 20 40 60 80 Required packages 0 10 20 Heaviness from parents graphics stats utils methods parallel WriteXLS Rcpp foreach cluster BiocGenerics doParallel robustbase S4Vectors e1071 doRNG ROCR rrcov pheatmap SummarizedExperiment SingleCellExperiment shiny ggplot2 RcppArmadillo mclust knitr rmarkdown scater In total 100 packages are required directly or indirectly (137) when installing 'SC3' (1.24.0) Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'SC3' Imported functions The whole namespace is imported Package is listed in 'Imports' but namespace is not imported


Dependency table

"Import" information is from the NAMESPACE file of SC3.

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 SC3: number of required packages that can be reduced if moving parent package to Suggests of SC3.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on SC3
shiny Imports 39 0 0 34 19
ggplot2 Imports 6 0 0 37 12
ROCR Imports 2 0 0 10 5
e1071 Imports 1 0 0 8 3
rrcov Imports 1 0 0 12 3
doRNG Imports 1 0 0 9 2
WriteXLS Imports 1 0 0 1 1
cluster Imports The whole set of functions/methods/classes from parent package is imported to the namespace of SC3. 4 1
doParallel Imports 1 0 0 5 1
pheatmap Imports 1 0 0 18 1
SingleCellExperiment Imports 1 0 0 25 1
graphics Imports 1 0 0 0 0
stats Imports 15 0 0 0 0
utils Imports 4 0 0 0 0
methods Imports 2 0 0 0 0
parallel Imports 3 0 0 0 0
Rcpp Imports 1 0 0 2 0
foreach Imports 2 0 0 3 0
BiocGenerics Imports 1 0 0 4 0
robustbase Imports 1 0 0 5 0
S4Vectors Imports 2 0 0 6 0
SummarizedExperiment Imports 5 0 0 24 0
RcppArmadillo LinkingTo Parent package is listed in LinkingTo of SC3 but no object from parent package is imported. 4 1
scater Suggests No object is imported into the namespace of SC3. 85 27
rmarkdown Suggests No object is imported into the namespace of SC3. 27 9
knitr Suggests No object is imported into the namespace of SC3. 12 7
mclust Suggests No object is imported into the namespace of SC3. 4 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 SC3 Co-heaviness as Jaccard coeffcient
SummarizedExperiment SingleCellExperiment 12 0.923

Analysis was done with pkgndep.