Dependency analysis on package phyloseq

General information

Bioconductor link link
Package version1.40.0
Number of strong dependencies76
Number of all dependencies155
Number of parent packages17
Max heaviness from parent packages12
Total heaviness from parent packages43
Number of parent packages (including Suggests and Enhances)26
Max co-heaviness from parent packages ("ggplot2" and "scales")10

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests Enhances utils methods stats graphics grDevices grid tools splines parallel stats4 lattice glue Matrix magrittr Rcpp rlang R6 BiocGenerics jsonlite MASS pkgconfig crayon digest codetools stringr stringi nlme Biobase survival lifecycle RColorBrewer bitops vctrs cli iterators mgcv farver labeling munsell viridisLite colorspace S4Vectors IRanges XVector GenomeInfoDb zlibbioc RCurl GenomeInfoDbData tibble withr ellipsis fansi pillar utf8 plyr gtable isoband scales pixmap sp rhdf5 Rhdf5lib rhdf5filters permute cluster evaluate fastmap yaml xfun highr knitr htmltools jquerylib tinytex bslib base64enc sass fs rappdirs locfit matrixStats foreach AnnotationDbi annotate DBI RSQLite KEGGREST XML xtable httr bit64 blob memoise plogr png Biostrings curl mime openssl bit cachem askpass sys bookdown rmarkdown BiocManager limma glmnet gplots Wrench shape RcppEigen gtools caTools KernSmooth brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 GenomicRanges SummarizedExperiment BiocParallel genefilter geneplotter ggplot2 RcppArmadillo MatrixGenerics DelayedArray futile.logger snow BH lambda.r futile.options formatR 0 10 20 30 Imported methods 0 20 40 60 80 Required packages 0 10 20 30 Heaviness from parents methods data.table foreach plyr BiocGenerics cluster Biobase ade4 igraph reshape2 ape biomformat multtest vegan scales Biostrings ggplot2 magrittr knitr rmarkdown BiocStyle metagenomeSeq testthat genefilter DESeq2 doParallel In total 76 packages are required directly or indirectly (155) when installing 'phyloseq' (1.40.0) Imports Suggests Enhances Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'phyloseq' Imported functions Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on phyloseq
ggplot2 Imports 29 0 0 37 12
Biostrings Imports 1 0 14 17 9
biomformat Imports 4 0 0 14 5
foreach Imports The whole set of functions/methods/classes from parent package is imported to the namespace of phyloseq. 3 3
ade4 Imports 3 0 0 10 3
reshape2 Imports The whole set of functions/methods/classes from parent package is imported to the namespace of phyloseq. 10 3
ape Imports 15 0 0 11 2
multtest Imports 2 0 0 14 2
vegan Imports 15 0 0 14 2
data.table Imports 6 0 0 1 1
igraph Imports 20 0 0 10 1
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of phyloseq. 0 0
plyr Imports 4 0 0 3 0
BiocGenerics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of phyloseq. 4 0
cluster Imports 3 0 0 4 0
Biobase Imports 1 0 0 5 0
scales Imports 1 0 0 15 0
DESeq2 Suggests No object is imported into the namespace of phyloseq. 93 38
genefilter Suggests No object is imported into the namespace of phyloseq. 53 22
BiocStyle Suggests No object is imported into the namespace of phyloseq. 30 18
rmarkdown Suggests No object is imported into the namespace of phyloseq. 27 15
testthat Suggests No object is imported into the namespace of phyloseq. 36 14
metagenomeSeq Suggests No object is imported into the namespace of phyloseq. 30 12
knitr Suggests No object is imported into the namespace of phyloseq. 12 5
magrittr Suggests No object is imported into the namespace of phyloseq. 0 0
doParallel Enhances No object is imported into the namespace of phyloseq. 5 1

Analysis was done with pkgndep.