Dependency analysis on package edgeR

General information

Bioconductor link link
Package version3.38.1
Number of strong dependencies10
Number of all dependencies78
Number of parent packages7
Max heaviness from parent packages3
Total heaviness from parent packages5
Number of parent packages (including Suggests and Enhances)15
Max co-heaviness from parent packages ("locfit" and "limma")1

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils graphics stats grDevices grid stats4 tools lattice BiocGenerics Biobase IRanges S4Vectors XVector GenomeInfoDb zlibbioc RCurl GenomeInfoDbData bitops cli crayon R6 rlang glue pkgconfig vctrs bit64 bit DBI RSQLite KEGGREST blob memoise Rcpp plogr httr png Biostrings cachem curl jsonlite mime openssl fastmap askpass sys Rhdf5lib rhdf5filters MatrixGenerics GenomicRanges Matrix DelayedArray matrixStats clipr hms lifecycle tibble vroom cpp11 tzdb ellipsis fansi magrittr pillar tidyselect withr progress utf8 purrr prettyunits AnnotationDbi 0 10 20 30 Imported methods 0 20 40 Required packages 0 10 20 30 40 Heaviness from parents limma methods graphics stats utils Rcpp locfit splines jsonlite rhdf5 Biobase SummarizedExperiment readr AnnotationDbi org.Hs.eg.db In total 10 packages are required directly or indirectly (78) when installing 'edgeR' (3.38.1) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'edgeR' Imported functions Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on edgeR
limma Depends 27 0 4 5 1
locfit Imports 1 0 0 6 3
Rcpp Imports 1 0 0 2 1
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of edgeR. 0 0
graphics Imports 13 0 0 0 0
stats Imports 36 0 0 0 0
utils Imports 6 0 0 0 0
org.Hs.eg.db Suggests No object is imported into the namespace of edgeR. 45 40
AnnotationDbi Suggests No object is imported into the namespace of edgeR. 44 39
readr Suggests No object is imported into the namespace of edgeR. 31 27
SummarizedExperiment Suggests No object is imported into the namespace of edgeR. 24 18
rhdf5 Suggests No object is imported into the namespace of edgeR. 3 3
Biobase Suggests No object is imported into the namespace of edgeR. 5 2
splines Suggests No object is imported into the namespace of edgeR. 0 1
jsonlite Suggests No object is imported into the namespace of edgeR. 1 1

Analysis was done with pkgndep.