Dependency analysis on package MultiAssayExperiment

General information

Bioconductor link link
Package version1.22.0
Number of strong dependencies45
Number of all dependencies158
Number of parent packages10
Max heaviness from parent packages20
Total heaviness from parent packages27
Number of parent packages (including Suggests and Enhances)21
Max co-heaviness from parent packages ("GenomicRanges" and "SummarizedExperiment")8

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics grDevices tools grid stats4 splines parallel Matrix BiocGenerics lattice glue magrittr rlang R6 S4Vectors IRanges RCurl zlibbioc bitops ellipsis lifecycle tibble vctrs pillar fansi pkgconfig cli crayon utf8 MatrixGenerics GenomeInfoDb DelayedArray matrixStats XVector GenomeInfoDbData GenomicRanges Biobase dplyr purrr tidyselect cpp11 generics digest evaluate yaml xfun highr stringr stringi jsonlite RColorBrewer knitr withr data.table survival htmltools jquerylib tinytex bslib base64enc fastmap sass fs rappdirs brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 ggplot2 gridExtra scales gtable isoband MASS mgcv Rcpp farver labeling munsell viridisLite nlme colorspace R.methodsS3 R.oo R.utils R.cache Rhtslib DNAcopy rhdf5 rhdf5filters Rhdf5lib SummarizedExperiment bookdown rmarkdown BiocManager plyr ggpubr maxstat broom tidyr survMisc ggtext ggrepel ggsci cowplot ggsignif polynom rstatix exactRankTests mvtnorm backports KMsurv zoo km.ci xtable gridtext corrplot car markdown png jpeg xml2 carData abind nnet pbkrtest quantreg maptools lme4 mime numDeriv SparseM MatrixModels sp foreign boot minqa nloptr RcppEigen testthat 0 0.5 1 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents SummarizedExperiment methods stats utils BiocGenerics Biobase S4Vectors IRanges GenomicRanges tidyr R.rsp survival knitr maftools HDF5Array RaggedExperiment rmarkdown BiocStyle testthat UpSetR survminer In total 45 packages are required directly or indirectly (158) when installing 'MultiAssayExperiment' (1.22.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'MultiAssayExperiment' 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 MultiAssayExperiment.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on MultiAssayExperiment
SummarizedExperiment Depends The whole set of functions/methods/classes from parent package is imported to the namespace of MultiAssayExperiment. 24 7
tidyr Imports Parent package is listed in Imports of MultiAssayExperiment but no object from parent package is imported. 22 20
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MultiAssayExperiment. 0 0
stats Imports Parent package is listed in Imports of MultiAssayExperiment but no object from parent package is imported. 0 0
utils Imports 1 0 0 0 0
BiocGenerics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MultiAssayExperiment. 4 0
Biobase Imports Parent package is listed in Imports of MultiAssayExperiment but no object from parent package is imported. 5 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MultiAssayExperiment. 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MultiAssayExperiment. 7 0
GenomicRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MultiAssayExperiment. 15 0
survminer Suggests No object is imported into the namespace of MultiAssayExperiment. 115 85
BiocStyle Suggests No object is imported into the namespace of MultiAssayExperiment. 30 22
UpSetR Suggests No object is imported into the namespace of MultiAssayExperiment. 41 20
rmarkdown Suggests No object is imported into the namespace of MultiAssayExperiment. 27 19
testthat Suggests No object is imported into the namespace of MultiAssayExperiment. 36 17
knitr Suggests No object is imported into the namespace of MultiAssayExperiment. 12 7
maftools Suggests No object is imported into the namespace of MultiAssayExperiment. 15 7
R.rsp Suggests No object is imported into the namespace of MultiAssayExperiment. 9 6
HDF5Array Suggests No object is imported into the namespace of MultiAssayExperiment. 19 4
survival Suggests No object is imported into the namespace of MultiAssayExperiment. 9 2
RaggedExperiment Suggests No object is imported into the namespace of MultiAssayExperiment. 25 1

Analysis was done with pkgndep.