Dependency analysis on package BiocGenerics

General information

Bioconductor link link
Package version0.42.0
Number of strong dependencies4
Number of all dependencies127
Number of parent packages4
Max heaviness from parent packages1
Total heaviness from parent packages4
Number of parent packages (including Suggests and Enhances)19

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Suggests utils methods graphics stats stats4 grDevices tools parallel grid splines BiocGenerics S4Vectors zlibbioc IRanges Biobase GenomeInfoDb XVector RCurl GenomeInfoDbData bitops crayon Rcpp Biostrings BH pkgconfig rlang vctrs R6 cli glue affyio BiocManager preprocessCore Matrix lattice matrixStats BiocParallel futile.logger snow codetools lambda.r futile.options formatR DBI RSQLite KEGGREST bit64 blob memoise plogr httr png bit cachem curl jsonlite mime openssl fastmap askpass sys XML MatrixGenerics RcppArmadillo Rhdf5lib affy GenomicRanges AnnotationDbi xtable ggplot2 RColorBrewer digest gtable isoband MASS mgcv scales tibble withr nlme farver labeling lifecycle munsell viridisLite ellipsis fansi magrittr pillar colorspace utf8 graph flowCore cytolib RProtoBufLib RcppParallel gcrma Rhtslib mzR ProtGenerics MsCoreUtils plyr vsn impute pcaMethods MALDIquant mzID ncdf4 clue limma doParallel foreach iterators cluster SummarizedExperiment genefilter locfit geneplotter DelayedArray annotate survival 0 0.5 1 Imported methods 0 20 40 60 80 Required packages 0 20 40 60 80 Heaviness from parents methods utils graphics stats RUnit Biobase S4Vectors IRanges affy DelayedArray GenomicRanges Biostrings flowClust affyPLM Rsamtools AnnotationDbi annotate MSnbase DESeq2 In total 4 packages are required directly or indirectly (127) when installing 'BiocGenerics' (0.42.0) Depends Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'BiocGenerics' The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on BiocGenerics
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BiocGenerics. 0 1
utils Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BiocGenerics. 0 1
graphics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BiocGenerics. 0 1
stats Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BiocGenerics. 0 1
DESeq2 Suggests No object is imported into the namespace of BiocGenerics. 93 90
MSnbase Suggests No object is imported into the namespace of BiocGenerics. 76 73
annotate Suggests No object is imported into the namespace of BiocGenerics. 47 44
AnnotationDbi Suggests No object is imported into the namespace of BiocGenerics. 44 41
Rsamtools Suggests No object is imported into the namespace of BiocGenerics. 29 26
affyPLM Suggests No object is imported into the namespace of BiocGenerics. 25 22
flowClust Suggests No object is imported into the namespace of BiocGenerics. 20 17
Biostrings Suggests No object is imported into the namespace of BiocGenerics. 17 14
GenomicRanges Suggests No object is imported into the namespace of BiocGenerics. 15 12
DelayedArray Suggests No object is imported into the namespace of BiocGenerics. 14 11
affy Suggests No object is imported into the namespace of BiocGenerics. 11 8
IRanges Suggests No object is imported into the namespace of BiocGenerics. 7 4
S4Vectors Suggests No object is imported into the namespace of BiocGenerics. 6 3
Biobase Suggests No object is imported into the namespace of BiocGenerics. 5 2
RUnit Suggests No object is imported into the namespace of BiocGenerics. 3 1

Analysis was done with pkgndep.