Dependency analysis on package genefilter

General information

Bioconductor link link
Package version1.78.0
Number of strong dependencies53
Number of all dependencies85
Number of parent packages9
Max heaviness from parent packages5
Total heaviness from parent packages8
Number of parent packages (including Suggests and Enhances)17
Max co-heaviness from parent packages ("annotate" and "AnnotationDbi")38

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats graphics tools grDevices stats4 splines grid tcltk glue BiocGenerics Biobase rlang jsonlite R6 fastmap IRanges DBI RSQLite S4Vectors KEGGREST bit64 blob memoise pkgconfig Rcpp plogr httr png Biostrings bit vctrs cachem curl mime openssl XVector GenomeInfoDb crayon cli askpass zlibbioc RCurl GenomeInfoDbData sys bitops AnnotationDbi Matrix lattice XML xtable evaluate highr stringr yaml xfun magrittr stringi knitr MASS widgetTools DynDoc bookdown rmarkdown BiocManager htmltools jquerylib tinytex bslib digest base64enc sass fs rappdirs org.Hs.eg.db 0 5 10 Imported methods 0 20 40 Required packages 0 10 20 Heaviness from parents graphics methods stats grDevices BiocGenerics Biobase survival AnnotationDbi annotate RColorBrewer class tkWidgets ALL knitr ROC BiocStyle hgu95av2.db In total 53 packages are required directly or indirectly (85) when installing 'genefilter' (1.78.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'genefilter' Imported functions Imported S4 methods Imported S4 classes


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on genefilter
survival Imports 1 0 0 9 5
annotate Imports 1 0 0 47 3
graphics Imports 12 0 0 0 0
methods Imports 2 2 7 0 0
stats Imports 13 0 0 0 0
grDevices Imports 1 0 0 0 0
BiocGenerics Imports 4 0 0 4 0
Biobase Imports 2 6 1 5 0
AnnotationDbi Imports 0 8 0 44 0
BiocStyle Suggests No object is imported into the namespace of genefilter. 30 21
ROC Suggests No object is imported into the namespace of genefilter. 13 9
knitr Suggests No object is imported into the namespace of genefilter. 12 8
tkWidgets Suggests No object is imported into the namespace of genefilter. 6 4
class Suggests No object is imported into the namespace of genefilter. 6 2
hgu95av2.db Suggests No object is imported into the namespace of genefilter. 46 2
RColorBrewer Suggests No object is imported into the namespace of genefilter. 0 1
ALL Suggests No object is imported into the namespace of genefilter. 6 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 genefilter Co-heaviness as Jaccard coeffcient
AnnotationDbi annotate 38 0.927

Analysis was done with pkgndep.