Dependency analysis on package variancePartition

General information

Bioconductor link link
Package version1.26.0
Number of strong dependencies106
Number of all dependencies194
Number of parent packages25
Max heaviness from parent packages13
Total heaviness from parent packages39
Number of parent packages (including Suggests and Enhances)39
Max co-heaviness from parent packages ("pbkrtest" and "reshape2")2

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats grDevices graphics tools grid parallel splines stats4 datasets glue rlang R6 magrittr digest lifecycle pkgconfig vctrs lattice cli crayon ellipsis Rcpp tibble withr nlme Matrix RColorBrewer fansi pillar utf8 jsonlite MASS mgcv farver labeling munsell viridisLite colorspace evaluate gtable isoband scales stringr stringi yaml codetools ggplot2 highr xfun boot minqa nloptr RcppEigen testthat brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 knitr futile.logger snow BH lambda.r futile.options formatR BiocGenerics bitops lme4 numDeriv purrr tidyselect cpp11 iterators plyr hms prettyunits broom dplyr backports generics tidyr rbibutils foreach gtools caTools KernSmooth fastmap locfit bit64 bit survival limma htmltools jquerylib tinytex bslib base64enc sass fs rappdirs gridExtra GenomicRanges IRanges S4Vectors Biobase GenomeInfoDb XVector genefilter BiocParallel matrixStats XML Biostrings zlibbioc RCurl GenomeInfoDbData AnnotationDbi annotate SummarizedExperiment DBI RSQLite KEGGREST xtable httr MatrixGenerics DelayedArray blob memoise plogr png curl mime openssl cachem askpass sys bookdown rmarkdown BiocManager clipr vroom tzdb progress viridis sva rtracklayer edgeR Rsamtools GenomicAlignments BiocIO restfulr Rhtslib rjson geneplotter RcppArmadillo lmerTest pbkrtest afex data.table car reshape2 carData abind nnet quantreg maptools SparseM MatrixModels sp foreign 0 10 20 30 40 Imported methods 0 20 40 60 80 Required packages 0 20 40 Heaviness from parents limma BiocParallel ggplot2 RhpcBLASctl grDevices graphics methods utils stats iterators rlang aod foreach Rdpack MASS doParallel Biobase Matrix gplots reshape2 progress scales lme4 lmerTest pbkrtest tximportData tximport RUnit BiocGenerics pander edgeR knitr rmarkdown BiocStyle readr dendextend ballgown DESeq2 r2glmm In total 106 packages are required directly or indirectly (194) when installing 'variancePartition' (1.26.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'variancePartition' 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 variancePartition.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on variancePartition
BiocParallel Depends 5 0 0 11 7
limma Depends 3 0 0 5 1
ggplot2 Depends The whole set of functions/methods/classes from parent package is imported to the namespace of variancePartition. 37 0
pbkrtest Imports 1 0 0 76 13
gplots Imports 1 0 0 7 5
progress Imports 1 0 0 14 3
Rdpack Imports The whole set of functions/methods/classes from parent package is imported to the namespace of variancePartition. 4 2
Biobase Imports 2 0 0 5 2
reshape2 Imports 1 0 0 10 2
RhpcBLASctl Imports 1 0 0 0 1
aod Imports 1 0 0 2 1
doParallel Imports The whole set of functions/methods/classes from parent package is imported to the namespace of variancePartition. 5 1
lmerTest Imports Parent package is listed in Imports of variancePartition but no object from parent package is imported. 62 1
grDevices Imports 2 0 0 0 0
graphics Imports 13 0 0 0 0
methods Imports 3 0 0 0 0
utils Imports 2 0 0 0 0
stats Imports 39 0 0 0 0
iterators Imports 2 0 0 1 0
rlang Imports 5 0 0 1 0
foreach Imports 1 0 0 3 0
MASS Imports 1 0 0 5 0
Matrix Imports 8 0 0 7 0
scales Imports 1 0 0 15 0
lme4 Imports 10 0 0 49 0
ballgown Suggests No object is imported into the namespace of variancePartition. 83 48
DESeq2 Suggests No object is imported into the namespace of variancePartition. 93 41
r2glmm Suggests No object is imported into the namespace of variancePartition. 94 15
BiocStyle Suggests No object is imported into the namespace of variancePartition. 30 13
rmarkdown Suggests No object is imported into the namespace of variancePartition. 27 10
readr Suggests No object is imported into the namespace of variancePartition. 31 6
dendextend Suggests No object is imported into the namespace of variancePartition. 41 4
edgeR Suggests No object is imported into the namespace of variancePartition. 10 2
tximportData Suggests No object is imported into the namespace of variancePartition. 0 1
tximport Suggests No object is imported into the namespace of variancePartition. 3 1
RUnit Suggests No object is imported into the namespace of variancePartition. 3 1
pander Suggests No object is imported into the namespace of variancePartition. 8 1
BiocGenerics Suggests No object is imported into the namespace of variancePartition. 4 0
knitr Suggests No object is imported into the namespace of variancePartition. 12 0

Analysis was done with pkgndep.