Dependency analysis on package geneplast

General information

Bioconductor link link
Package version1.22.0
Number of strong dependencies18
Number of all dependencies158
Number of parent packages9
Max heaviness from parent packages5
Total heaviness from parent packages11
Number of parent packages (including Suggests and Enhances)20
Max co-heaviness from parent packages ("ape" and "igraph")2

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats graphics grDevices tools grid parallel splines stats4 magrittr lattice Matrix pkgconfig nlme Rcpp glue stringr evaluate highr yaml xfun stringi R6 rlang digest knitr jsonlite MASS mgcv RColorBrewer scales gtable farver labeling lifecycle munsell viridisLite ellipsis tibble vctrs pillar colorspace fansi isoband withr cli crayon utf8 car survival carData abind nnet pbkrtest quantreg maptools lme4 broom dplyr numDeriv SparseM MatrixModels sp foreign boot minqa nloptr RcppEigen backports generics purrr tidyr ggplot2 tidyselect testthat cpp11 brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 htmltools jquerylib tinytex bslib base64enc fastmap sass fs rappdirs RedeR minet viper mixtools snow limma data.table IRanges igraph S4Vectors SummarizedExperiment pwr pheatmap infotheo Biobase e1071 KernSmooth kernlab segmented BiocGenerics MatrixGenerics GenomicRanges GenomeInfoDb DelayedArray class proxy matrixStats XVector RCurl GenomeInfoDbData zlibbioc bitops bookdown rmarkdown BiocManager ggrepel ggsci cowplot ggsignif gridExtra polynom rstatix corrplot Fletcher2013a RTN VennDiagram gplots futile.logger gtools caTools lambda.r futile.options formatR 0 2 4 6 8 Imported methods 0 50 100 Required packages 0 50 100 Heaviness from parents methods grDevices graphics stats utils snow data.table igraph ape geneplast.data.string.v91 RUnit plyr BiocGenerics knitr rmarkdown BiocStyle ggplot2 ggpubr RTN Fletcher2013b In total 18 packages are required directly or indirectly (158) when installing 'geneplast' (1.22.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'geneplast' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on geneplast
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of geneplast. 0 0
ape Imports 9 0 0 11 5
igraph Imports 3 0 0 10 4
snow Imports 5 0 0 1 1
data.table Imports 1 0 0 1 1
grDevices Imports 4 0 0 0 0
graphics Imports 8 0 0 0 0
stats Imports 7 0 0 0 0
utils Imports 2 0 0 0 0
Fletcher2013b Suggests No object is imported into the namespace of geneplast. 131 115
RTN Suggests No object is imported into the namespace of geneplast. 121 105
ggpubr Suggests No object is imported into the namespace of geneplast. 96 83
ggplot2 Suggests No object is imported into the namespace of geneplast. 37 27
BiocStyle Suggests No object is imported into the namespace of geneplast. 30 25
rmarkdown Suggests No object is imported into the namespace of geneplast. 27 22
knitr Suggests No object is imported into the namespace of geneplast. 12 8
geneplast.data.string.v91 Suggests No object is imported into the namespace of geneplast. 0 1
RUnit Suggests No object is imported into the namespace of geneplast. 3 1
plyr Suggests No object is imported into the namespace of geneplast. 3 1
BiocGenerics Suggests No object is imported into the namespace of geneplast. 4 1

Analysis was done with pkgndep.