Dependency analysis on package rtracklayer

General information

Bioconductor link link
Package version1.56.0
Number of strong dependencies44
Number of all dependencies111
Number of parent packages16
Max heaviness from parent packages9
Total heaviness from parent packages13
Number of parent packages (including Suggests and Enhances)27
Max co-heaviness from parent packages ("GenomicAlignments" and "Rsamtools")11

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils graphics stats stats4 tools grDevices parallel grid splines BiocGenerics S4Vectors bitops IRanges RCurl GenomeInfoDbData zlibbioc GenomeInfoDb XVector crayon Biostrings Biobase XML GenomicRanges BiocParallel Rhtslib futile.logger snow codetools BH lambda.r futile.options formatR Matrix lattice rjson yaml SummarizedExperiment Rsamtools MatrixGenerics DelayedArray matrixStats AnnotationDbi DBI RSQLite KEGGREST bit64 blob memoise pkgconfig Rcpp plogr httr png bit rlang vctrs cachem curl jsonlite mime openssl R6 cli glue fastmap askpass sys rtracklayer GenomicAlignments BiocIO restfulr org.Hs.eg.db biomaRt progress stringr digest BiocFileCache rappdirs xml2 hms prettyunits magrittr stringi dbplyr dplyr filelock ellipsis lifecycle assertthat pillar purrr tibble tidyselect withr generics fansi utf8 BSgenome hgu133plus2.db annotate survival xtable GenomicFeatures 0 5 10 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents methods GenomicRanges zlibbioc tools XML RCurl BiocGenerics S4Vectors IRanges BiocIO XVector GenomeInfoDb restfulr Biostrings Rsamtools GenomicAlignments RUnit limma microRNA BSgenome org.Hs.eg.db hgu133plus2.db BSgenome.Hsapiens.UCSC.hg19 humanStemCell genefilter GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene In total 44 packages are required directly or indirectly (111) when installing 'rtracklayer' (1.56.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'rtracklayer' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on rtracklayer
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of rtracklayer. 0 0
GenomicRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of rtracklayer. 15 0
GenomicAlignments Imports 0 4 1 38 9
restfulr Imports The whole set of functions/methods/classes from parent package is imported to the namespace of rtracklayer. 12 3
BiocIO Imports The whole set of functions/methods/classes from parent package is imported to the namespace of rtracklayer. 8 1
zlibbioc Imports The whole set of functions/methods/classes from parent package is imported to the namespace of rtracklayer. 0 0
tools Imports 3 0 0 0 0
XML Imports 12 1 0 2 0
RCurl Imports 8 0 0 2 0
BiocGenerics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of rtracklayer. 4 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of rtracklayer. 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of rtracklayer. 7 0
XVector Imports The whole set of functions/methods/classes from parent package is imported to the namespace of rtracklayer. 10 0
GenomeInfoDb Imports The whole set of functions/methods/classes from parent package is imported to the namespace of rtracklayer. 11 0
Biostrings Imports 8 3 2 17 0
Rsamtools Imports 4 5 3 29 0
TxDb.Hsapiens.UCSC.hg19.knownGene Suggests No object is imported into the namespace of rtracklayer. 97 54
GenomicFeatures Suggests No object is imported into the namespace of rtracklayer. 96 53
genefilter Suggests No object is imported into the namespace of rtracklayer. 53 31
humanStemCell Suggests No object is imported into the namespace of rtracklayer. 47 29
hgu133plus2.db Suggests No object is imported into the namespace of rtracklayer. 46 28
org.Hs.eg.db Suggests No object is imported into the namespace of rtracklayer. 45 27
BSgenome.Hsapiens.UCSC.hg19 Suggests No object is imported into the namespace of rtracklayer. 46 3
BSgenome Suggests No object is imported into the namespace of rtracklayer. 45 2
RUnit Suggests No object is imported into the namespace of rtracklayer. 3 1
limma Suggests No object is imported into the namespace of rtracklayer. 5 1
microRNA Suggests No object is imported into the namespace of rtracklayer. 18 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 rtracklayer Co-heaviness as Jaccard coeffcient
Rsamtools GenomicAlignments 11 0.55

Analysis was done with pkgndep.