Dependency analysis on package BSgenome

General information

Bioconductor link link
Package version1.64.0
Number of strong dependencies45
Number of all dependencies112
Number of parent packages13
Max heaviness from parent packages14
Total heaviness from parent packages14
Number of parent packages (including Suggests and Enhances)28
Max co-heaviness from parent packages ("Rsamtools" and "rtracklayer")11

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods graphics stats stats4 tools grDevices parallel grid BiocGenerics S4Vectors IRanges RCurl GenomeInfoDbData bitops zlibbioc GenomeInfoDb XVector crayon Biostrings GenomicRanges BiocParallel Rhtslib futile.logger snow codetools BH Biobase lambda.r futile.options formatR XML Rsamtools GenomicAlignments BiocIO restfulr SummarizedExperiment rjson yaml MatrixGenerics Matrix DelayedArray matrixStats lattice rtracklayer BSgenome AnnotationDbi DBI RSQLite KEGGREST bit64 blob memoise pkgconfig Rcpp plogr httr png bit rlang vctrs cachem R6 glue curl jsonlite mime openssl cli fastmap askpass sys GenomicFeatures 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.Hsapiens.UCSC.hg38 0 2 4 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents methods BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges Biostrings rtracklayer utils stats matrixStats XVector Rsamtools BiocManager RUnit Biobase hgu95av2probe BSgenome.Celegans.UCSC.ce2 BSgenome.Hsapiens.UCSC.hg38 BSgenome.Mmusculus.UCSC.mm10 BSgenome.Rnorvegicus.UCSC.rn5 BSgenome.Scerevisiae.UCSC.sacCer1 BSgenome.Hsapiens.NCBI.GRCh38 SNPlocs.Hsapiens.dbSNP144.GRCh38 XtraSNPlocs.Hsapiens.dbSNP144.GRCh38 BSgenome.Hsapiens.UCSC.hg38.masked TxDb.Hsapiens.UCSC.hg38.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene In total 45 packages are required directly or indirectly (112) when installing 'BSgenome' (1.64.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'BSgenome' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on BSgenome
rtracklayer Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BSgenome. 44 14
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BSgenome. 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BSgenome. 4 0
S4Vectors Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BSgenome. 6 0
IRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BSgenome. 7 0
GenomeInfoDb Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BSgenome. 11 0
GenomicRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BSgenome. 15 0
Biostrings Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BSgenome. 17 0
utils Imports 5 0 0 0 0
stats Imports 1 0 0 0 0
matrixStats Imports 1 0 0 0 0
XVector Imports The whole set of functions/methods/classes from parent package is imported to the namespace of BSgenome. 10 0
Rsamtools Imports The whole set of functions/methods/classes from parent package is imported to the namespace of BSgenome. 29 0
TxDb.Hsapiens.UCSC.hg38.knownGene Suggests No object is imported into the namespace of BSgenome. 97 53
TxDb.Mmusculus.UCSC.mm10.knownGene Suggests No object is imported into the namespace of BSgenome. 97 53
hgu95av2probe Suggests No object is imported into the namespace of BSgenome. 45 27
BSgenome.Hsapiens.UCSC.hg38.masked Suggests No object is imported into the namespace of BSgenome. 47 3
BSgenome.Celegans.UCSC.ce2 Suggests No object is imported into the namespace of BSgenome. 46 2
BSgenome.Hsapiens.UCSC.hg38 Suggests No object is imported into the namespace of BSgenome. 46 2
BSgenome.Mmusculus.UCSC.mm10 Suggests No object is imported into the namespace of BSgenome. 46 2
BSgenome.Rnorvegicus.UCSC.rn5 Suggests No object is imported into the namespace of BSgenome. 46 2
BSgenome.Scerevisiae.UCSC.sacCer1 Suggests No object is imported into the namespace of BSgenome. 46 2
BSgenome.Hsapiens.NCBI.GRCh38 Suggests No object is imported into the namespace of BSgenome. 46 2
SNPlocs.Hsapiens.dbSNP144.GRCh38 Suggests No object is imported into the namespace of BSgenome. 46 2
XtraSNPlocs.Hsapiens.dbSNP144.GRCh38 Suggests No object is imported into the namespace of BSgenome. 46 2
BiocManager Suggests No object is imported into the namespace of BSgenome. 1 1
RUnit Suggests No object is imported into the namespace of BSgenome. 3 1
Biobase Suggests No object is imported into the namespace of BSgenome. 5 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 BSgenome Co-heaviness as Jaccard coeffcient
rtracklayer Rsamtools 11 0.44

Analysis was done with pkgndep.