Dependency analysis on package GSVA

General information

Bioconductor link link
Package version1.44.1
Number of strong dependencies79
Number of all dependencies155
Number of parent packages18
Max heaviness from parent packages32
Total heaviness from parent packages43
Number of parent packages (including Suggests and Enhances)38
Max co-heaviness from parent packages ("BiocSingular" and "BiocParallel")8

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats graphics grDevices tools stats4 grid parallel splines Rcpp BiocGenerics R6 rlang glue lattice S4Vectors jsonlite fastmap Matrix IRanges crayon mime cachem MatrixGenerics matrixStats xtable Biobase GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops pkgconfig vctrs cli DelayedArray httr curl openssl askpass sys AnnotationDbi DBI RSQLite KEGGREST bit64 blob memoise plogr png Biostrings bit codetools annotate XML futile.logger snow BH lambda.r futile.options formatR GenomicRanges graph sparseMatrixStats rhdf5 rhdf5filters Rhdf5lib SummarizedExperiment BiocParallel ScaledMatrix irlba rsvd beachmat magrittr digest htmltools base64enc later jquerylib bslib sass fs rappdirs withr ellipsis lifecycle yaml promises httpuv fontawesome sourcetools commonmark xfun evaluate highr stringr stringi shiny knitr tinytex gtable isoband MASS mgcv scales tibble nlme farver labeling munsell RColorBrewer viridisLite fansi pillar colorspace utf8 htmlwidgets globals listenv parallelly limma locfit bookdown rmarkdown BiocManager GSEABase hgu95a.db org.Hs.eg.db survival ggplot2 tidyr dplyr lazyeval crosstalk purrr data.table tidyselect cpp11 generics 0 5 10 Imported methods 0 20 40 60 Required packages 0 10 20 30 40 Heaviness from parents methods stats utils graphics parallel Biobase S4Vectors IRanges Matrix BiocParallel sparseMatrixStats DelayedArray DelayedMatrixStats HDF5Array SummarizedExperiment SingleCellExperiment BiocSingular GSEABase RColorBrewer data.table RUnit BiocGenerics limma future promises edgeR knitr rmarkdown BiocStyle shiny shinydashboard shinyjs ggplot2 shinybusy org.Hs.eg.db GSVAdata genefilter plotly In total 79 packages are required directly or indirectly (155) when installing 'GSVA' (1.44.1) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'GSVA' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on GSVA
GSEABase Imports 3 2 1 49 32
BiocSingular Imports 1 0 0 29 5
HDF5Array Imports 2 0 1 19 4
DelayedMatrixStats Imports 1 0 0 17 1
SingleCellExperiment Imports 1 0 1 25 1
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of GSVA. 0 0
stats Imports 3 0 0 0 0
utils Imports 5 0 0 0 0
graphics Imports 1 0 0 0 0
parallel Imports 1 0 0 0 0
Biobase Imports 0 5 1 5 0
S4Vectors Imports 1 2 0 6 0
IRanges Imports 1 1 0 7 0
Matrix Imports 0 0 1 7 0
BiocParallel Imports 4 4 0 11 0
sparseMatrixStats Imports 1 0 0 11 0
DelayedArray Imports 9 0 1 14 0
SummarizedExperiment Imports 1 2 1 24 0
plotly Suggests No object is imported into the namespace of GSVA. 63 39
ggplot2 Suggests No object is imported into the namespace of GSVA. 37 23
shinybusy Suggests No object is imported into the namespace of GSVA. 37 22
BiocStyle Suggests No object is imported into the namespace of GSVA. 30 21
shinydashboard Suggests No object is imported into the namespace of GSVA. 35 20
shinyjs Suggests No object is imported into the namespace of GSVA. 35 20
shiny Suggests No object is imported into the namespace of GSVA. 34 19
rmarkdown Suggests No object is imported into the namespace of GSVA. 27 18
knitr Suggests No object is imported into the namespace of GSVA. 12 8
future Suggests No object is imported into the namespace of GSVA. 8 5
promises Suggests No object is imported into the namespace of GSVA. 8 3
edgeR Suggests No object is imported into the namespace of GSVA. 10 3
GSVAdata Suggests No object is imported into the namespace of GSVA. 52 3
genefilter Suggests No object is imported into the namespace of GSVA. 53 3
RColorBrewer Suggests No object is imported into the namespace of GSVA. 0 1
data.table Suggests No object is imported into the namespace of GSVA. 1 1
RUnit Suggests No object is imported into the namespace of GSVA. 3 1
limma Suggests No object is imported into the namespace of GSVA. 5 1
org.Hs.eg.db Suggests No object is imported into the namespace of GSVA. 45 1
BiocGenerics Suggests No object is imported into the namespace of GSVA. 4 0

Analysis was done with pkgndep.