Dependency analysis on package minfi

General information

Bioconductor link link
Package version1.42.0
Number of strong dependencies141
Number of all dependencies165
Number of parent packages34
Max heaviness from parent packages24
Total heaviness from parent packages57
Number of parent packages (including Suggests and Enhances)45
Max co-heaviness from parent packages ("GEOquery" and "bumphunter")16

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils stats methods graphics grDevices stats4 tools grid parallel splines BiocGenerics S4Vectors IRanges lattice Matrix RCurl GenomeInfoDbData bitops glue GenomeInfoDb XVector zlibbioc MatrixGenerics Biobase matrixStats rlang R6 magrittr crayon DelayedArray Rcpp stringr yaml stringi jsonlite fastmap digest bit64 pkgconfig rappdirs bit vctrs curl openssl cli askpass sys GenomicRanges limma AnnotationDbi codetools DBI RSQLite Biostrings KEGGREST blob memoise plogr XML progress httr xml2 png cachem hms prettyunits mime dplyr futile.logger snow BH ellipsis lifecycle pillar purrr tibble tidyselect withr generics lambda.r futile.options fansi utf8 formatR survival foreach iterators locfit doRNG GenomicFeatures rngtools BiocIO rtracklayer biomaRt Rsamtools GenomicAlignments restfulr BiocFileCache BiocParallel Rhtslib SummarizedExperiment rjson dbplyr filelock assertthat base64 plyr multtest scrime MASS sparseMatrixStats rhdf5 rhdf5filters Rhdf5lib readr data.table tidyr R.utils clipr vroom cpp11 tzdb R.oo R.methodsS3 annotate xtable minfi bumphunter beanplot RColorBrewer nor1mix siggenes preprocessCore illuminaio DelayedMatrixStats mclust genefilter nlme reshape quadprog GEOquery HDF5Array xfun evaluate highr knitr htmltools jquerylib tinytex bslib base64enc sass fs bookdown rmarkdown BiocManager IlluminaHumanMethylation450kmanifest IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICanno.ilm10b2.hg19 0 5 10 15 Imported methods 0 50 100 150 Required packages 0 10 20 Heaviness from parents methods BiocGenerics GenomicRanges Biostrings SummarizedExperiment bumphunter beanplot RColorBrewer quadprog stats grDevices graphics utils preprocessCore data.table nor1mix illuminaio mclust reshape Biobase lattice limma MASS S4Vectors nlme IRanges GenomeInfoDb BiocParallel DelayedArray siggenes DelayedMatrixStats HDF5Array GEOquery genefilter tools digest RUnit knitr rmarkdown BiocStyle IlluminaHumanMethylation450kmanifest IlluminaHumanMethylation450kanno.ilmn12.hg19 FlowSorted.Blood.450k minfiData minfiDataEPIC In total 141 packages are required directly or indirectly (165) when installing 'minfi' (1.42.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'minfi' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported The whole namespace is imported except some functions


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on minfi
bumphunter Depends 5 1 0 103 24
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of minfi. 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of minfi. 4 0
GenomicRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of minfi. 15 0
Biostrings Depends The whole set of functions/methods/classes from parent package excluding 1 objects is imported to the namespace of minfi. 17 0
SummarizedExperiment Depends The whole set of functions/methods/classes from parent package is imported to the namespace of minfi. 24 0
GEOquery Imports 1 0 0 45 10
HDF5Array Imports The whole set of functions/methods/classes from parent package is imported to the namespace of minfi. 19 4
siggenes Imports 2 0 0 16 3
genefilter Imports 2 0 0 53 3
illuminaio Imports 1 0 0 4 2
reshape Imports 6 0 0 4 2
DelayedMatrixStats Imports The whole set of functions/methods/classes from parent package is imported to the namespace of minfi. 17 2
beanplot Imports 1 0 0 0 1
RColorBrewer Imports 1 0 0 0 1
quadprog Imports 1 0 0 0 1
preprocessCore Imports 2 0 0 1 1
nor1mix Imports 3 0 0 2 1
mclust Imports 1 0 0 4 1
nlme Imports 2 0 0 6 1
stats Imports 17 0 0 0 0
grDevices Imports 1 0 0 0 0
graphics Imports 9 0 0 0 0
utils Imports 4 0 0 0 0
data.table Imports 1 0 0 1 0
Biobase Imports 6 8 0 5 0
lattice Imports 3 0 0 5 0
limma Imports 5 0 0 5 0
MASS Imports 1 0 0 5 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of minfi. 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of minfi. 7 0
GenomeInfoDb Imports 0 6 1 11 0
BiocParallel Imports The whole set of functions/methods/classes from parent package is imported to the namespace of minfi. 11 0
DelayedArray Imports The whole set of functions/methods/classes from parent package is imported to the namespace of minfi. 14 0
BiocStyle Suggests No object is imported into the namespace of minfi. 30 15
rmarkdown Suggests No object is imported into the namespace of minfi. 27 12
knitr Suggests No object is imported into the namespace of minfi. 12 4
minfiData Suggests No object is imported into the namespace of minfi. 144 4
minfiDataEPIC Suggests No object is imported into the namespace of minfi. 144 4
IlluminaHumanMethylation450kmanifest Suggests No object is imported into the namespace of minfi. 142 2
IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests No object is imported into the namespace of minfi. 142 2
FlowSorted.Blood.450k Suggests No object is imported into the namespace of minfi. 142 2
RUnit Suggests No object is imported into the namespace of minfi. 3 1
tools Suggests No object is imported into the namespace of minfi. 0 0
digest Suggests No object is imported into the namespace of minfi. 1 0

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 minfi Co-heaviness as Jaccard coeffcient
bumphunter GEOquery 16 0.320
bumphunter genefilter 14 0.341

Analysis was done with pkgndep.