Dependency analysis on package GenomeInfoDb

General information

Bioconductor link link
Package version1.32.2
Number of strong dependencies11
Number of all dependencies118
Number of parent packages9
Max heaviness from parent packages2
Total heaviness from parent packages4
Number of parent packages (including Suggests and Enhances)21
Max co-heaviness from parent packages ("IRanges" and "S4Vectors")1

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics stats4 tools grDevices parallel grid BiocGenerics S4Vectors bitops IRanges GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc yaml GenomicRanges Biostrings BiocParallel Rhtslib crayon futile.logger snow codetools BH lambda.r futile.options formatR SummarizedExperiment Rsamtools MatrixGenerics Biobase Matrix DelayedArray matrixStats lattice BiocIO rtracklayer XML GenomicAlignments restfulr rjson stringr glue magrittr stringi digest rappdirs rlang R6 jsonlite fastmap BSgenome xfun evaluate highr AnnotationDbi DBI RSQLite biomaRt KEGGREST bit64 blob memoise pkgconfig Rcpp plogr progress httr BiocFileCache xml2 png bit vctrs cachem hms prettyunits curl mime openssl dbplyr dplyr filelock cli ellipsis lifecycle askpass assertthat pillar purrr tibble tidyselect withr generics sys fansi utf8 bookdown knitr rmarkdown BiocManager htmltools jquerylib tinytex bslib base64enc sass fs GenomicFeatures 0 2 4 6 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents methods BiocGenerics S4Vectors IRanges stats stats4 utils GenomeInfoDbData RCurl RUnit knitr GenomicRanges Rsamtools BiocStyle GenomicAlignments BSgenome BSgenome.Scerevisiae.UCSC.sacCer2 BSgenome.Celegans.UCSC.ce2 BSgenome.Hsapiens.NCBI.GRCh38 GenomicFeatures TxDb.Dmelanogaster.UCSC.dm3.ensGene In total 11 packages are required directly or indirectly (118) when installing 'GenomeInfoDb' (1.32.2) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'GenomeInfoDb' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on GenomeInfoDb
IRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomeInfoDb. 7 1
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomeInfoDb. 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomeInfoDb. 4 0
S4Vectors Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomeInfoDb. 6 0
RCurl Imports 1 0 0 2 2
GenomeInfoDbData Imports The whole set of functions/methods/classes from parent package is imported to the namespace of GenomeInfoDb. 0 1
stats Imports 1 0 0 0 0
stats4 Imports 1 0 0 0 0
utils Imports 6 0 0 0 0
TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests No object is imported into the namespace of GenomeInfoDb. 97 87
GenomicFeatures Suggests No object is imported into the namespace of GenomeInfoDb. 96 86
BSgenome.Scerevisiae.UCSC.sacCer2 Suggests No object is imported into the namespace of GenomeInfoDb. 46 36
BSgenome.Celegans.UCSC.ce2 Suggests No object is imported into the namespace of GenomeInfoDb. 46 36
BSgenome.Hsapiens.NCBI.GRCh38 Suggests No object is imported into the namespace of GenomeInfoDb. 46 36
BSgenome Suggests No object is imported into the namespace of GenomeInfoDb. 45 35
BiocStyle Suggests No object is imported into the namespace of GenomeInfoDb. 30 28
GenomicAlignments Suggests No object is imported into the namespace of GenomeInfoDb. 38 28
Rsamtools Suggests No object is imported into the namespace of GenomeInfoDb. 29 19
knitr Suggests No object is imported into the namespace of GenomeInfoDb. 12 10
GenomicRanges Suggests No object is imported into the namespace of GenomeInfoDb. 15 5
RUnit Suggests No object is imported into the namespace of GenomeInfoDb. 3 1

Analysis was done with pkgndep.