Dependency analysis on package gwascat

General information

Bioconductor link link
Package version2.28.1
Number of strong dependencies129
Number of all dependencies197
Number of parent packages13
Max heaviness from parent packages22
Total heaviness from parent packages32
Number of parent packages (including Suggests and Enhances)29
Max co-heaviness from parent packages ("VariantAnnotation" and "GenomicFeatures")26

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests Enhances methods utils stats graphics grDevices stats4 tools grid parallel splines BiocGenerics S4Vectors IRanges crayon RCurl GenomeInfoDbData bitops zlibbioc rlang R6 glue GenomeInfoDb XVector jsonlite magrittr fastmap pkgconfig vctrs cli Biostrings yaml bit64 bit Biobase Rcpp DBI RSQLite blob memoise plogr httr cachem curl mime openssl askpass sys digest Matrix lattice ellipsis lifecycle pillar tibble withr fansi utf8 KEGGREST png rappdirs BH purrr tidyselect AnnotationDbi GenomicRanges stringr BiocParallel Rhtslib stringi futile.logger snow codetools MatrixGenerics lambda.r futile.options matrixStats formatR dbplyr dplyr filelock assertthat generics BiocIO XML Rsamtools GenomicAlignments restfulr SummarizedExperiment rjson DelayedArray progress hms prettyunits BiocFileCache htmltools base64enc rtracklayer biomaRt xml2 htmlwidgets jquerylib lazyeval BSgenome GenomicFeatures survival BiocManager bslib sass fs cpp11 later promises crosstalk clipr vroom tzdb BiocVersion interactiveDisplayBase shiny DT httpuv xtable fontawesome sourcetools commonmark evaluate highr xfun knitr rstudioapi graph tinytex RColorBrewer ensembldb biovizBase latticeExtra AnnotationFilter ProtGenerics scales Hmisc dichromat VariantAnnotation jpeg farver labeling munsell viridisLite Formula ggplot2 cluster rpart nnet foreign gtable gridExtra data.table htmlTable viridis colorspace isoband MASS mgcv checkmate nlme backports bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot diffobj rematch2 reshape2 OrganismDbi GGally plyr RBGL forcats reshape tidyr 0 2 4 6 8 Imported methods 0 50 100 150 Required packages 0 20 40 Heaviness from parents methods S4Vectors IRanges GenomeInfoDb snpStats GenomicRanges Biostrings readr AnnotationDbi BiocFileCache AnnotationHub GenomicFeatures VariantAnnotation graph RBGL knitr DelayedArray DT rmarkdown Rsamtools BiocStyle testthat rtracklayer DO.db org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene Gviz ggbio SNPlocs.Hsapiens.dbSNP144.GRCh37 In total 129 packages are required directly or indirectly (197) when installing 'gwascat' (2.28.1) Depends Imports Suggests Enhances Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'gwascat' Imported functions Imported S4 classes The whole namespace is imported Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on gwascat
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of gwascat. 0 0
AnnotationHub Imports Parent package is listed in Imports of gwascat but no object from parent package is imported. 85 22
readr Imports The whole set of functions/methods/classes from parent package is imported to the namespace of gwascat. 31 5
snpStats Imports The whole set of functions/methods/classes from parent package is imported to the namespace of gwascat. 12 3
VariantAnnotation Imports The whole set of functions/methods/classes from parent package is imported to the namespace of gwascat. 98 2
S4Vectors Imports 4 0 0 6 0
IRanges Imports 2 0 1 7 0
GenomeInfoDb Imports 9 0 0 11 0
GenomicRanges Imports 1 0 1 15 0
Biostrings Imports Parent package is listed in Imports of gwascat but no object from parent package is imported. 17 0
AnnotationDbi Imports 1 0 0 44 0
BiocFileCache Imports The whole set of functions/methods/classes from parent package is imported to the namespace of gwascat. 46 0
GenomicFeatures Imports 1 0 0 96 0
ggbio Suggests No object is imported into the namespace of gwascat. 153 47
Gviz Suggests No object is imported into the namespace of gwascat. 142 38
testthat Suggests No object is imported into the namespace of gwascat. 36 14
BiocStyle Suggests No object is imported into the namespace of gwascat. 30 8
rmarkdown Suggests No object is imported into the namespace of gwascat. 27 6
knitr Suggests No object is imported into the namespace of gwascat. 12 4
RBGL Suggests No object is imported into the namespace of gwascat. 8 2
graph Suggests No object is imported into the namespace of gwascat. 6 1
DO.db Suggests No object is imported into the namespace of gwascat. 45 1
org.Hs.eg.db Suggests No object is imported into the namespace of gwascat. 45 1
TxDb.Hsapiens.UCSC.hg19.knownGene Suggests No object is imported into the namespace of gwascat. 97 1
DelayedArray Suggests No object is imported into the namespace of gwascat. 14 0
DT Suggests No object is imported into the namespace of gwascat. 20 0
Rsamtools Suggests No object is imported into the namespace of gwascat. 29 0
rtracklayer Suggests No object is imported into the namespace of gwascat. 44 0
SNPlocs.Hsapiens.dbSNP144.GRCh37 Enhances No object is imported into the namespace of gwascat. 46 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 gwascat Co-heaviness as Jaccard coeffcient
GenomicFeatures VariantAnnotation 26 0.929

Analysis was done with pkgndep.