Dependency analysis on package apeglm

General information

Bioconductor link link
Package version1.18.0
Number of strong dependencies36
Number of all dependencies133
Number of parent packages9
Max heaviness from parent packages8
Total heaviness from parent packages14
Number of parent packages (including Suggests and Enhances)14
Max co-heaviness from parent packages ("SummarizedExperiment" and "GenomicRanges")11

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports LinkingTo Suggests utils methods stats graphics grDevices tools grid stats4 parallel splines lattice Matrix BiocGenerics S4Vectors IRanges GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops Rcpp MatrixGenerics GenomicRanges Biobase DelayedArray matrixStats MASS plyr coda bbmle numDeriv bdsmatrix mvtnorm RcppEigen glue magrittr evaluate digest rlang R6 jsonlite highr stringr yaml xfun stringi SummarizedExperiment fastmap tibble withr lifecycle ellipsis fansi pillar pkgconfig vctrs cli crayon utf8 bslib htmltools jquerylib knitr tinytex sass base64enc fs rappdirs brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 BiocParallel genefilter locfit geneplotter ggplot2 RcppArmadillo futile.logger snow codetools BH AnnotationDbi annotate survival RColorBrewer gtable isoband mgcv scales lambda.r futile.options DBI RSQLite KEGGREST XML xtable httr nlme farver labeling munsell viridisLite formatR bit64 blob memoise plogr png Biostrings curl mime openssl colorspace bit cachem askpass sys 0 5 10 Imported methods 0 20 40 60 80 Required packages 0 20 40 60 Heaviness from parents methods stats utils Rcpp GenomicRanges emdbook SummarizedExperiment RcppEigen RcppNumerical knitr airway rmarkdown testthat DESeq2 In total 36 packages are required directly or indirectly (133) when installing 'apeglm' (1.18.0) Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'apeglm' Imported functions Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on apeglm
emdbook Imports 1 0 0 17 8
SummarizedExperiment Imports 2 0 0 24 5
methods Imports 1 0 0 0 0
stats Imports 11 0 0 0 0
utils Imports 2 0 0 0 0
Rcpp Imports 1 0 0 2 0
GenomicRanges Imports 1 0 0 15 0
RcppNumerical LinkingTo Parent package is listed in LinkingTo of apeglm but no object from parent package is imported. 10 1
RcppEigen LinkingTo Parent package is listed in LinkingTo of apeglm but no object from parent package is imported. 9 0
DESeq2 Suggests No object is imported into the namespace of apeglm. 93 67
testthat Suggests No object is imported into the namespace of apeglm. 36 31
rmarkdown Suggests No object is imported into the namespace of apeglm. 27 23
knitr Suggests No object is imported into the namespace of apeglm. 12 9
airway Suggests No object is imported into the namespace of apeglm. 25 1

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 apeglm Co-heaviness as Jaccard coeffcient
GenomicRanges SummarizedExperiment 11 0.688

Analysis was done with pkgndep.