Dependency analysis on package TxDb.Hsapiens.UCSC.hg18.knownGene

General information

Bioconductor link link
Package version3.2.2
Number of strong dependencies97
Number of all dependencies97
Number of parent packages2
Max heaviness from parent packages52
Total heaviness from parent packages52
Number of parent packages (including Suggests and Enhances)2
Max co-heaviness from parent packages ("AnnotationDbi" and "GenomicFeatures")45

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of TxDb.Hsapiens.UCSC.hg18.knownGene 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 TxDb.Hsapiens.UCSC.hg18.knownGene.

Adjust heatmap size:
Base packages Other packages Depends Imports methods utils stats tools graphics stats4 grDevices parallel grid BiocGenerics S4Vectors IRanges GenomeInfoDb DBI RSQLite RCurl XVector Biostrings Biobase GenomeInfoDbData KEGGREST bit64 blob memoise pkgconfig Rcpp plogr bitops zlibbioc crayon httr png bit rlang vctrs cachem R6 glue curl jsonlite mime openssl cli fastmap askpass sys GenomicRanges AnnotationDbi 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 0 0.5 1 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents GenomicFeatures AnnotationDbi In total 97 packages are required directly or indirectly (97) when installing 'TxDb.Hsapiens.UCSC.hg18.knownGene' (3.2.2) Depends Imports Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'TxDb.Hsapiens.UCSC.hg18.knownGene' The whole namespace is imported


Dependency table

"Import" information is from the NAMESPACE file of TxDb.Hsapiens.UCSC.hg18.knownGene.

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 TxDb.Hsapiens.UCSC.hg18.knownGene: number of required packages that can be reduced if moving parent package to Suggests of TxDb.Hsapiens.UCSC.hg18.knownGene.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on TxDb.Hsapiens.UCSC.hg18.knownGene
GenomicFeatures Depends The whole set of functions/methods/classes from parent package is imported to the namespace of TxDb.Hsapiens.UCSC.hg18.knownGene. 96 52
AnnotationDbi Imports The whole set of functions/methods/classes from parent package is imported to the namespace of TxDb.Hsapiens.UCSC.hg18.knownGene. 44 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 TxDb.Hsapiens.UCSC.hg18.knownGene Co-heaviness as Jaccard coeffcient
GenomicFeatures AnnotationDbi 45 0.464

Analysis was done with pkgndep.