Dependency analysis on package DESeq2

General information

Bioconductor link link
Package version1.36.0
Number of strong dependencies93
Number of all dependencies207
Number of parent packages15
Max heaviness from parent packages21
Total heaviness from parent packages39
Number of parent packages (including Suggests and Enhances)32
Max co-heaviness from parent packages ("genefilter" and "geneplotter")23

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of DESeq2 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 DESeq2.

Adjust heatmap size:
Base packages Other packages Depends Imports LinkingTo Suggests utils methods stats graphics grDevices grid tools stats4 splines parallel BiocGenerics lattice glue S4Vectors zlibbioc Matrix R6 rlang IRanges GenomeInfoDb XVector RCurl GenomeInfoDbData bitops Biobase pkgconfig vctrs crayon cli magrittr Rcpp lifecycle MatrixGenerics GenomicRanges DelayedArray matrixStats digest tibble withr ellipsis fansi pillar utf8 jsonlite RColorBrewer bit64 bit fastmap gtable MASS scales farver labeling munsell viridisLite colorspace AnnotationDbi DBI RSQLite KEGGREST XML xtable httr blob memoise plogr png Biostrings curl mime openssl cachem askpass sys futile.logger snow codetools BH lambda.r futile.options formatR isoband mgcv nlme annotate survival SummarizedExperiment stringr stringi evaluate yaml RcppArmadillo rappdirs progress purrr tidyselect hms prettyunits highr xfun bslib htmltools jquerylib sass base64enc fs ggplot2 BiocManager BiocFileCache biomaRt Rsamtools dbplyr dplyr filelock xml2 BiocParallel Rhtslib assertthat generics truncnorm mixsqp SQUAREM etrunct invgamma irlba knitr tinytex clipr vroom cpp11 tzdb DelayedMatrixStats HDF5Array beachmat sparseMatrixStats rhdf5 rhdf5filters Rhdf5lib brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 emdbook RcppEigen RcppNumerical plyr coda bbmle numDeriv bdsmatrix mvtnorm affy limma affyio preprocessCore DEXSeq DESeq2 hwriter statmod geneplotter genefilter locfit tximport GenomicFeatures ensembldb AnnotationHub BiocIO rtracklayer AnnotationFilter ProtGenerics BiocVersion interactiveDisplayBase GenomicAlignments restfulr lazyeval shiny DT rjson httpuv fontawesome sourcetools later promises commonmark htmlwidgets crosstalk 0 2 4 6 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents S4Vectors IRanges GenomicRanges SummarizedExperiment methods stats4 Rcpp BiocGenerics Biobase locfit BiocParallel ggplot2 geneplotter genefilter RcppArmadillo RColorBrewer tximportData pbapply BiocManager tximport knitr ashr pheatmap airway rmarkdown readr glmGamPoi testthat apeglm vsn pasilla tximeta In total 93 packages are required directly or indirectly (207) when installing 'DESeq2' (1.36.0) Depends Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'DESeq2' 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 DESeq2.

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 DESeq2: number of required packages that can be reduced if moving parent package to Suggests of DESeq2.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on DESeq2
SummarizedExperiment Depends The whole set of functions/methods/classes from parent package is imported to the namespace of DESeq2. 24 4
S4Vectors Depends The whole set of functions/methods/classes from parent package is imported to the namespace of DESeq2. 6 0
IRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of DESeq2. 7 0
GenomicRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of DESeq2. 15 0
ggplot2 Imports 6 0 0 37 21
BiocParallel Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DESeq2. 11 9
genefilter Imports 2 0 0 53 2
locfit Imports 1 0 0 6 1
geneplotter Imports 1 0 0 51 1
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DESeq2. 0 0
stats4 Imports 1 0 0 0 0
Rcpp Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DESeq2. 2 0
BiocGenerics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DESeq2. 4 0
Biobase Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DESeq2. 5 0
RcppArmadillo LinkingTo Parent package is listed in LinkingTo of DESeq2 but no object from parent package is imported. 4 1
tximeta Suggests No object is imported into the namespace of DESeq2. 123 51
pasilla Suggests No object is imported into the namespace of DESeq2. 115 23
rmarkdown Suggests No object is imported into the namespace of DESeq2. 27 16
testthat Suggests No object is imported into the namespace of DESeq2. 36 14
readr Suggests No object is imported into the namespace of DESeq2. 31 10
apeglm Suggests No object is imported into the namespace of DESeq2. 36 10
glmGamPoi Suggests No object is imported into the namespace of DESeq2. 35 8
knitr Suggests No object is imported into the namespace of DESeq2. 12 7
ashr Suggests No object is imported into the namespace of DESeq2. 16 7
vsn Suggests No object is imported into the namespace of DESeq2. 46 6
tximportData Suggests No object is imported into the namespace of DESeq2. 0 1
pbapply Suggests No object is imported into the namespace of DESeq2. 1 1
BiocManager Suggests No object is imported into the namespace of DESeq2. 1 1
tximport Suggests No object is imported into the namespace of DESeq2. 3 1
pheatmap Suggests No object is imported into the namespace of DESeq2. 18 1
airway Suggests No object is imported into the namespace of DESeq2. 25 1
RColorBrewer Suggests No object is imported into the namespace of DESeq2. 0 0

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 DESeq2 Co-heaviness as Jaccard coeffcient
geneplotter genefilter 23 0.885

Analysis was done with pkgndep.