Dependency analysis on package beadarray

General information

Bioconductor link link
Package version2.46.0
Number of strong dependencies81
Number of all dependencies214
Number of parent packages13
Max heaviness from parent packages23
Total heaviness from parent packages50
Number of parent packages (including Suggests and Enhances)25
Max co-heaviness from parent packages ("AnnotationDbi" and "GenomicRanges")6

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils stats methods graphics grDevices tools grid stats4 splines parallel BiocGenerics glue magrittr zlibbioc rlang R6 S4Vectors pkgconfig vctrs crayon cli Biobase lattice openssl askpass sys Rcpp stringr stringi IRanges XVector GenomeInfoDb RCurl GenomeInfoDbData bitops digest jsonlite fastmap gtable tibble withr Matrix lifecycle ellipsis fansi pillar utf8 DBI RSQLite KEGGREST bit64 blob memoise plogr httr png Biostrings bit cachem curl mime isoband MASS mgcv scales nlme farver labeling munsell RColorBrewer viridisLite colorspace plyr base64 BiocManager yaml AnnotationDbi rappdirs ggplot2 GenomicRanges preprocessCore affyio xfun evaluate highr limma reshape2 GenomicFeatures matrixStats SummarizedExperiment BiocIO rtracklayer biomaRt XML DelayedArray BiocParallel MatrixGenerics Rsamtools GenomicAlignments restfulr progress BiocFileCache xml2 dplyr futile.logger snow codetools BH Rhtslib rjson hms prettyunits dbplyr filelock generics tidyselect purrr lambda.r futile.options assertthat formatR knitr htmltools base64enc affy org.Hs.eg.db illuminaio reshape data.table survival tidyr cpp11 bookdown rmarkdown jquerylib tinytex bslib sass fs beadarray hexbin BeadDataPackR gridExtra Hmisc biovizBase BSgenome VariantAnnotation OrganismDbi GGally ensembldb AnnotationFilter Formula latticeExtra cluster rpart nnet foreign htmlTable viridis dichromat graph RBGL forcats ProtGenerics lazyeval jpeg checkmate htmlwidgets rstudioapi backports methylumi annotate nleqslv KernSmooth FDb.InfiniumMethylation.hg19 minfi genefilter xtable TxDb.Hsapiens.UCSC.hg19.knownGene bumphunter beanplot nor1mix siggenes DelayedMatrixStats mclust quadprog GEOquery HDF5Array foreach iterators locfit doRNG multtest scrime sparseMatrixStats readr R.utils rhdf5 rhdf5filters Rhdf5lib rngtools clipr vroom tzdb R.oo R.methodsS3 0 10 20 Imported methods 0 50 100 150 Required packages 0 20 40 60 80 Heaviness from parents BiocGenerics Biobase hexbin stats4 methods BeadDataPackR illuminaio limma IRanges reshape2 GenomicRanges ggplot2 AnnotationDbi hwriter Nozzle.R1 gridExtra affy knitr BiocStyle vsn illuminaHumanv3.db beadarrayExampleData TxDb.Hsapiens.UCSC.hg19.knownGene ggbio lumi In total 81 packages are required directly or indirectly (214) when installing 'beadarray' (2.46.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'beadarray' Imported functions The whole namespace is imported Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on beadarray
hexbin Depends Parent package is listed in Depends of beadarray but no object from parent package is imported. 7 1
BiocGenerics Depends 5 0 0 4 0
Biobase Depends The whole set of functions/methods/classes from parent package is imported to the namespace of beadarray. 5 0
ggplot2 Imports 21 0 0 37 23
AnnotationDbi Imports The whole set of functions/methods/classes from parent package is imported to the namespace of beadarray. 44 17
reshape2 Imports 1 0 0 10 4
illuminaio Imports The whole set of functions/methods/classes from parent package is imported to the namespace of beadarray. 4 2
BeadDataPackR Imports The whole set of functions/methods/classes from parent package is imported to the namespace of beadarray. 2 1
limma Imports 7 0 0 5 1
GenomicRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of beadarray. 15 1
stats4 Imports 2 0 0 0 0
methods Imports 4 0 0 0 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of beadarray. 7 0
lumi Suggests No object is imported into the namespace of beadarray. 162 84
ggbio Suggests No object is imported into the namespace of beadarray. 153 78
TxDb.Hsapiens.UCSC.hg19.knownGene Suggests No object is imported into the namespace of beadarray. 97 38
BiocStyle Suggests No object is imported into the namespace of beadarray. 30 17
knitr Suggests No object is imported into the namespace of beadarray. 12 5
vsn Suggests No object is imported into the namespace of beadarray. 46 5
affy Suggests No object is imported into the namespace of beadarray. 11 4
illuminaHumanv3.db Suggests No object is imported into the namespace of beadarray. 46 2
beadarrayExampleData Suggests No object is imported into the namespace of beadarray. 82 2
hwriter Suggests No object is imported into the namespace of beadarray. 0 1
Nozzle.R1 Suggests No object is imported into the namespace of beadarray. 0 1
gridExtra Suggests No object is imported into the namespace of beadarray. 5 1

Analysis was done with pkgndep.