Dependency analysis on package MethylAid

General information

Bioconductor link link
Package version1.30.0
Number of strong dependencies167
Number of all dependencies185
Number of parent packages17
Max heaviness from parent packages81
Total heaviness from parent packages106
Number of parent packages (including Suggests and Enhances)23
Max co-heaviness from parent packages ("minfi" and "SummarizedExperiment")13

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests utils methods stats graphics grDevices grid tools parallel stats4 splines glue magrittr lattice digest rlang R6 BiocGenerics Matrix withr lifecycle ellipsis crayon rappdirs jsonlite fastmap stringr yaml stringi futile.logger snow codetools BH lambda.r futile.options formatR GenomicRanges S4Vectors GenomeInfoDb Biobase IRanges DelayedArray XVector MatrixGenerics matrixStats RCurl GenomeInfoDbData zlibbioc bitops Rcpp xtable mime cachem MASS tibble nlme RColorBrewer fansi pillar pkgconfig vctrs cli utf8 SummarizedExperiment Biostrings bumphunter beanplot nor1mix siggenes limma preprocessCore illuminaio DelayedMatrixStats mclust genefilter reshape quadprog data.table GEOquery HDF5Array BiocParallel foreach iterators locfit doRNG GenomicFeatures AnnotationDbi multtest scrime base64 sparseMatrixStats annotate survival plyr readr xml2 dplyr tidyr curl R.utils rhdf5 rhdf5filters Rhdf5lib rngtools DBI RSQLite BiocIO rtracklayer biomaRt KEGGREST openssl XML httr clipr hms vroom cpp11 tzdb generics tidyselect purrr R.oo R.methodsS3 bit64 blob memoise plogr Rsamtools GenomicAlignments restfulr progress BiocFileCache png askpass bit Rhtslib rjson prettyunits dbplyr filelock sys assertthat htmltools bslib base64enc sass jquerylib fs httpuv fontawesome sourcetools later promises commonmark gtable isoband mgcv scales farver labeling munsell viridisLite colorspace minfi xfun evaluate highr bookdown knitr rmarkdown BiocManager tinytex IlluminaHumanMethylation450kmanifest IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICanno.ilm10b2.hg19 MethylAid ggplot2 gridBase hexbin shiny 0 2 4 6 8 Imported methods 0 50 100 150 Required packages 0 20 40 60 80 Heaviness from parents grid grDevices graphics matrixStats methods RColorBrewer stats utils gridBase BiocGenerics Biobase hexbin BiocParallel SummarizedExperiment shiny ggplot2 minfi RUnit knitr BiocStyle minfiData minfiDataEPIC MethylAidData In total 167 packages are required directly or indirectly (185) when installing 'MethylAid' (1.30.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'MethylAid' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on MethylAid
minfi Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MethylAid. 141 81
shiny Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MethylAid. 34 13
ggplot2 Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MethylAid. 37 10
gridBase Imports 1 0 0 2 1
hexbin Imports 2 0 0 7 1
grid Imports 2 0 0 0 0
grDevices Imports 4 0 0 0 0
graphics Imports 9 0 0 0 0
matrixStats Imports 2 0 0 0 0
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MethylAid. 0 0
RColorBrewer Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MethylAid. 0 0
stats Imports 3 0 0 0 0
utils Imports 2 0 0 0 0
BiocGenerics Imports 1 0 0 4 0
Biobase Imports 1 0 0 5 0
BiocParallel Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MethylAid. 11 0
SummarizedExperiment Imports 1 0 0 24 0
BiocStyle Suggests No object is imported into the namespace of MethylAid. 30 9
knitr Suggests No object is imported into the namespace of MethylAid. 12 4
minfiData Suggests No object is imported into the namespace of MethylAid. 144 3
minfiDataEPIC Suggests No object is imported into the namespace of MethylAid. 144 3
MethylAidData Suggests No object is imported into the namespace of MethylAid. 168 2
RUnit Suggests No object is imported into the namespace of MethylAid. 3 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 MethylAid Co-heaviness as Jaccard coeffcient
SummarizedExperiment minfi 13 0.138

Analysis was done with pkgndep.