Dependency analysis on package GSEABase

General information

Bioconductor link link
Package version1.58.0
Number of strong dependencies49
Number of all dependencies197
Number of parent packages7
Max heaviness from parent packages2
Total heaviness from parent packages3
Number of parent packages (including Suggests and Enhances)15
Max co-heaviness from parent packages ("AnnotationDbi" and "annotate")38

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics tools grDevices stats4 grid parallel splines BiocGenerics glue jsonlite R6 rlang pkgconfig vctrs crayon cli fastmap Biobase DBI httr IRanges RSQLite S4Vectors KEGGREST curl mime openssl bit64 blob memoise Rcpp plogr png Biostrings askpass bit cachem XVector GenomeInfoDb sys zlibbioc RCurl GenomeInfoDbData bitops AnnotationDbi XML xtable evaluate magrittr highr stringr yaml xfun stringi digest graph knitr htmltools base64enc BiocManager rappdirs tibble withr lifecycle ellipsis fansi pillar utf8 rstudioapi bookdown rmarkdown jquerylib tinytex bslib sass fs brio callr desc pkgload praise processx ps waldo rprojroot diffobj rematch2 org.Hs.eg.db hwriter Category GOstats limma lattice edgeR annotate PFAM.db GSEABase R.utils DESeq2 ggplot2 ggbio Matrix RBGL genefilter GO.db AnnotationForge Rgraphviz locfit R.oo R.methodsS3 GenomicRanges SummarizedExperiment BiocParallel geneplotter RcppArmadillo gtable isoband MASS mgcv scales gridExtra reshape2 Hmisc biovizBase Rsamtools GenomicAlignments BSgenome VariantAnnotation rtracklayer GenomicFeatures OrganismDbi GGally ensembldb AnnotationFilter BH survival MatrixGenerics DelayedArray futile.logger snow codetools RColorBrewer nlme farver labeling munsell viridisLite plyr Formula latticeExtra cluster rpart nnet foreign data.table htmlTable viridis dichromat Rhtslib matrixStats BiocIO restfulr biomaRt dplyr forcats progress reshape tidyr ProtGenerics lazyeval lambda.r futile.options colorspace jpeg checkmate htmlwidgets rjson BiocFileCache xml2 generics tidyselect hms prettyunits purrr cpp11 formatR backports dbplyr filelock assertthat 0 10 20 Imported methods 0 50 100 150 Required packages 0 50 100 Heaviness from parents methods BiocGenerics Biobase graph annotate XML AnnotationDbi Rgraphviz knitr BiocStyle testthat GO.db org.Hs.eg.db hgu95av2.db ReportingTools In total 49 packages are required directly or indirectly (197) when installing 'GSEABase' (1.58.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'GSEABase' Imported functions Imported S4 methods Imported S4 classes


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on GSEABase
annotate Depends 3 0 0 47 2
graph Depends 0 3 1 6 1
methods Depends 13 4 9 0 0
BiocGenerics Depends 5 0 0 4 0
Biobase Depends 8 1 3 5 0
XML Imports 4 2 0 2 0
AnnotationDbi Imports 1 17 3 44 0
ReportingTools Suggests No object is imported into the namespace of GSEABase. 174 126
testthat Suggests No object is imported into the namespace of GSEABase. 36 23
BiocStyle Suggests No object is imported into the namespace of GSEABase. 30 21
knitr Suggests No object is imported into the namespace of GSEABase. 12 8
Rgraphviz Suggests No object is imported into the namespace of GSEABase. 9 2
hgu95av2.db Suggests No object is imported into the namespace of GSEABase. 46 2
GO.db Suggests No object is imported into the namespace of GSEABase. 45 1
org.Hs.eg.db Suggests No object is imported into the namespace of GSEABase. 45 1

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 GSEABase Co-heaviness as Jaccard coeffcient
annotate AnnotationDbi 38 0.95

Analysis was done with pkgndep.