Dependency analysis on package sctransform

General information

CRAN link link
Package version0.3.3
Number of strong dependencies58
Number of all dependencies101
Number of parent packages14
Max heaviness from parent packages13
Total heaviness from parent packages25
Number of parent packages (including Suggests and Enhances)18
Max co-heaviness from parent packages ("ggplot2" and "dplyr")11

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports LinkingTo Suggests Enhances utils methods stats grDevices graphics tools grid parallel splines stats4 glue magrittr lattice digest Rcpp lifecycle R6 rlang tibble vctrs pillar ellipsis fansi pkgconfig cli crayon utf8 Matrix gtable globals listenv parallelly codetools stringr stringi withr future plyr generics tidyselect purrr isoband MASS mgcv scales nlme farver labeling munsell RColorBrewer viridisLite colorspace evaluate highr yaml xfun brio callr desc jsonlite pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 DelayedMatrixStats matrixStats DelayedArray HDF5Array SummarizedExperiment BiocGenerics RcppArmadillo beachmat MatrixGenerics sparseMatrixStats S4Vectors IRanges rhdf5 rhdf5filters Rhdf5lib GenomicRanges Biobase GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops 0 2 4 6 Imported methods 0 10 20 30 Required packages 0 10 20 Heaviness from parents magrittr methods matrixStats rlang MASS gridExtra Matrix future future.apply reshape2 dplyr ggplot2 Rcpp RcppArmadillo irlba knitr testthat glmGamPoi In total 58 packages are required directly or indirectly (101) when installing 'sctransform' (0.3.3) Imports LinkingTo Suggests Enhances Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'sctransform' 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 sctransform.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on sctransform
ggplot2 Imports The whole set of functions/methods/classes from parent package is imported to the namespace of sctransform. 37 13
reshape2 Imports The whole set of functions/methods/classes from parent package is imported to the namespace of sctransform. 10 4
dplyr Imports 7 0 0 20 4
matrixStats Imports 3 0 0 0 1
gridExtra Imports 1 0 0 5 1
future.apply Imports 1 0 0 9 1
magrittr Imports 1 0 0 0 0
methods Imports 1 0 0 0 0
rlang Imports 1 0 0 1 0
MASS Imports 4 0 0 5 0
Matrix Imports The whole set of functions/methods/classes from parent package is imported to the namespace of sctransform. 7 0
future Imports Parent package is listed in Imports of sctransform but no object from parent package is imported. 8 0
RcppArmadillo LinkingTo Parent package is listed in LinkingTo of sctransform but no object from parent package is imported. 4 1
Rcpp LinkingTo Parent package is listed in LinkingTo of sctransform but no object from parent package is imported. 2 0
testthat Suggests No object is imported into the namespace of sctransform. 36 15
knitr Suggests No object is imported into the namespace of sctransform. 12 5
irlba Suggests No object is imported into the namespace of sctransform. 8 1
glmGamPoi Enhances No object is imported into the namespace of sctransform. 35 23

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 sctransform Co-heaviness as Jaccard coeffcient
dplyr ggplot2 11 0.393

Analysis was done with pkgndep.