Dependency analysis on package MethylSeekR

General information

Bioconductor link link
Package version1.36.0
Number of strong dependencies78
Number of all dependencies79
Number of parent packages11
Max heaviness from parent packages30
Total heaviness from parent packages33
Number of parent packages (including Suggests and Enhances)12
Max co-heaviness from parent packages ("BSgenome" and "rtracklayer")21

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods stats stats4 utils graphics tools grDevices grid parallel BiocGenerics S4Vectors IRanges XVector GenomeInfoDb zlibbioc RCurl GenomeInfoDbData bitops XML Biostrings crayon Biobase lattice GenomicRanges Rsamtools GenomicAlignments BiocIO restfulr BiocParallel Rhtslib SummarizedExperiment rjson yaml futile.logger snow codetools BH MatrixGenerics Matrix DelayedArray lambda.r futile.options matrixStats formatR rtracklayer mvtnorm annotate AnnotationDbi RColorBrewer DBI xtable httr RSQLite KEGGREST curl jsonlite mime openssl R6 bit64 blob memoise pkgconfig Rcpp plogr png askpass bit rlang vctrs cachem sys cli glue fastmap BSgenome 0 5 10 Imported methods 0 20 40 Required packages 0 10 20 30 Heaviness from parents parallel mhsmm rtracklayer graphics grDevices stats utils IRanges GenomicRanges BSgenome geneplotter BSgenome.Hsapiens.UCSC.hg18 In total 78 packages are required directly or indirectly (79) when installing 'MethylSeekR' (1.36.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'MethylSeekR' 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 MethylSeekR.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on MethylSeekR
mhsmm Depends 4 0 0 3 2
parallel Depends 1 0 0 0 0
rtracklayer Depends Parent package is listed in Depends of MethylSeekR but no object from parent package is imported. 44 0
geneplotter Imports Parent package is listed in Imports of MethylSeekR but no object from parent package is imported. 51 30
BSgenome Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MethylSeekR. 45 1
graphics Imports 13 0 0 0 0
grDevices Imports 3 0 0 0 0
stats Imports 1 0 0 0 0
utils Imports 1 0 0 0 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MethylSeekR. 7 0
GenomicRanges Imports 1 0 0 15 0
BSgenome.Hsapiens.UCSC.hg18 Suggests No object is imported into the namespace of MethylSeekR. 46 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 MethylSeekR Co-heaviness as Jaccard coeffcient
rtracklayer BSgenome 21 0.955

Analysis was done with pkgndep.