Dependency analysis on package limma

General information

Bioconductor link link
Package version3.52.1
Number of strong dependencies5
Number of all dependencies89
Number of parent packages5
Max heaviness from parent packages1
Total heaviness from parent packages5
Number of parent packages (including Suggests and Enhances)19

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests stats graphics utils methods grDevices stats4 tools grid splines BiocGenerics Biobase zlibbioc openssl askpass sys bitops pkgconfig rlang vctrs R6 crayon cli glue IRanges DBI RSQLite S4Vectors KEGGREST bit64 blob memoise Rcpp plogr httr png Biostrings bit cachem curl jsonlite mime XVector GenomeInfoDb fastmap RCurl GenomeInfoDbData lattice affyio BiocManager preprocessCore AnnotationDbi base64 gtools caTools KernSmooth affy limma ggplot2 digest gtable isoband MASS mgcv scales tibble withr nlme Matrix farver labeling lifecycle munsell RColorBrewer viridisLite ellipsis fansi magrittr pillar colorspace utf8 0 20 40 Imported methods 0 20 40 Required packages 0 20 40 Heaviness from parents grDevices graphics stats utils methods BiasedUrn splines ellipse statmod illuminaio Biobase MASS locfit gplots affy AnnotationDbi GO.db org.Hs.eg.db vsn In total 5 packages are required directly or indirectly (89) when installing 'limma' (3.52.1) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'limma' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on limma
grDevices Imports 5 0 0 0 1
graphics Imports 20 0 0 0 1
stats Imports 55 0 0 0 1
utils Imports 6 0 0 0 1
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of limma. 0 1
vsn Suggests No object is imported into the namespace of limma. 46 42
GO.db Suggests No object is imported into the namespace of limma. 45 41
org.Hs.eg.db Suggests No object is imported into the namespace of limma. 45 41
AnnotationDbi Suggests No object is imported into the namespace of limma. 44 40
affy Suggests No object is imported into the namespace of limma. 11 7
illuminaio Suggests No object is imported into the namespace of limma. 4 5
gplots Suggests No object is imported into the namespace of limma. 7 5
locfit Suggests No object is imported into the namespace of limma. 6 3
Biobase Suggests No object is imported into the namespace of limma. 5 2
BiasedUrn Suggests No object is imported into the namespace of limma. 0 1
splines Suggests No object is imported into the namespace of limma. 0 1
ellipse Suggests No object is imported into the namespace of limma. 2 1
statmod Suggests No object is imported into the namespace of limma. 2 1
MASS Suggests No object is imported into the namespace of limma. 5 1

Analysis was done with pkgndep.