Dependency analysis on package FDb.InfiniumMethylation.hg19

General information

Bioconductor link link
Package version2.2.0
Number of strong dependencies99
Number of all dependencies100
Number of parent packages5
Max heaviness from parent packages1
Total heaviness from parent packages2
Number of parent packages (including Suggests and Enhances)6
Max co-heaviness from parent packages ("TxDb.Hsapiens.UCSC.hg19.knownGene" and "GenomicFeatures")52

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of FDb.InfiniumMethylation.hg19 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 FDb.InfiniumMethylation.hg19.

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats tools graphics stats4 grDevices parallel grid BiocGenerics S4Vectors IRanges GenomeInfoDb RCurl XVector GenomeInfoDbData bitops zlibbioc crayon DBI RSQLite Biostrings Biobase KEGGREST bit64 blob memoise pkgconfig Rcpp plogr httr png bit rlang vctrs cachem R6 glue curl jsonlite mime openssl cli fastmap askpass sys AnnotationDbi GenomicRanges BiocIO rtracklayer biomaRt XML Rsamtools GenomicAlignments restfulr progress stringr digest BiocFileCache rappdirs xml2 BiocParallel Rhtslib SummarizedExperiment rjson yaml hms prettyunits magrittr stringi dbplyr dplyr filelock futile.logger snow codetools BH MatrixGenerics Matrix DelayedArray ellipsis lifecycle assertthat pillar purrr tibble tidyselect withr generics lambda.r futile.options matrixStats lattice fansi utf8 formatR GenomicFeatures 0 0.5 1 Imported methods 0 50 100 Required packages 0 0.5 1 Heaviness from parents org.Hs.eg.db GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene Biostrings AnnotationDbi FDb.UCSC.snp135common.hg19 In total 99 packages are required directly or indirectly (100) when installing 'FDb.InfiniumMethylation.hg19' (2.2.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'FDb.InfiniumMethylation.hg19' The whole namespace is imported


Dependency table

"Import" information is from the NAMESPACE file of FDb.InfiniumMethylation.hg19.

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 FDb.InfiniumMethylation.hg19: number of required packages that can be reduced if moving parent package to Suggests of FDb.InfiniumMethylation.hg19.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on FDb.InfiniumMethylation.hg19
org.Hs.eg.db Depends The whole set of functions/methods/classes from parent package is imported to the namespace of FDb.InfiniumMethylation.hg19. 45 1
TxDb.Hsapiens.UCSC.hg19.knownGene Depends The whole set of functions/methods/classes from parent package is imported to the namespace of FDb.InfiniumMethylation.hg19. 97 1
GenomicFeatures Depends The whole set of functions/methods/classes from parent package is imported to the namespace of FDb.InfiniumMethylation.hg19. 96 0
Biostrings Imports The whole set of functions/methods/classes from parent package is imported to the namespace of FDb.InfiniumMethylation.hg19. 17 0
AnnotationDbi Imports The whole set of functions/methods/classes from parent package is imported to the namespace of FDb.InfiniumMethylation.hg19. 44 0
FDb.UCSC.snp135common.hg19 Suggests No object is imported into the namespace of FDb.InfiniumMethylation.hg19. 97 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 FDb.InfiniumMethylation.hg19 Co-heaviness as Jaccard coeffcient
GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene 52 0.981

Analysis was done with pkgndep.