Dependency analysis on package sva

General information

Bioconductor link link
Package version3.44.0
Number of strong dependencies69
Number of all dependencies114
Number of parent packages9
Max heaviness from parent packages44
Total heaviness from parent packages58
Number of parent packages (including Suggests and Enhances)14
Max co-heaviness from parent packages ("genefilter" and "mgcv")2

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods stats utils graphics grDevices grid splines tools parallel stats4 lattice Matrix jsonlite R6 rlang glue BiocGenerics Biobase survival pkgconfig Rcpp vctrs crayon cli fastmap nlme futile.logger snow codetools BH lambda.r futile.options formatR AnnotationDbi annotate IRanges DBI RSQLite S4Vectors KEGGREST XML xtable httr bit64 blob memoise plogr png Biostrings curl mime openssl bit cachem XVector GenomeInfoDb askpass zlibbioc RCurl GenomeInfoDbData sys bitops limma locfit evaluate digest magrittr cluster bookdown knitr rmarkdown yaml BiocManager htmltools jquerylib xfun tinytex highr stringr bslib base64enc stringi sass fs rappdirs brio callr desc ellipsis lifecycle pkgload praise processx ps waldo withr rprojroot rstudioapi diffobj fansi rematch2 tibble pillar utf8 0 5 10 15 Imported methods 0 20 40 Required packages 0 20 40 Heaviness from parents mgcv BiocParallel genefilter matrixStats stats graphics utils limma edgeR zebrafishRNASeq bladderbatch pamr BiocStyle testthat In total 69 packages are required directly or indirectly (114) when installing 'sva' (3.44.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'sva' Imported functions The whole namespace is imported The whole namespace is imported except some functions


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on sva
genefilter Depends The whole set of functions/methods/classes from parent package is imported to the namespace of sva. 53 44
BiocParallel Depends The whole set of functions/methods/classes from parent package is imported to the namespace of sva. 11 9
mgcv Depends The whole set of functions/methods/classes from parent package is imported to the namespace of sva. 10 2
edgeR Imports 6 0 0 10 2
matrixStats Imports The whole set of functions/methods/classes from parent package excluding 2 objects is imported to the namespace of sva. 0 1
stats Imports 19 0 0 0 0
graphics Imports 2 0 0 0 0
utils Imports 2 0 0 0 0
limma Imports 1 0 0 5 0
testthat Suggests No object is imported into the namespace of sva. 36 23
BiocStyle Suggests No object is imported into the namespace of sva. 30 21
pamr Suggests No object is imported into the namespace of sva. 11 2
zebrafishRNASeq Suggests No object is imported into the namespace of sva. 0 1
bladderbatch Suggests No object is imported into the namespace of sva. 6 1

Analysis was done with pkgndep.