Dependency analysis on package karyoploteR

General information

Bioconductor link link
Package version1.22.0
Number of strong dependencies145
Number of all dependencies174
Number of parent packages19
Max heaviness from parent packages43
Total heaviness from parent packages46
Number of parent packages (including Suggests and Enhances)32
Max co-heaviness from parent packages ("biovizBase" and "VariantAnnotation")1

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils stats methods tools graphics stats4 grDevices parallel grid splines BiocGenerics S4Vectors IRanges RCurl GenomeInfoDbData bitops GenomeInfoDb XVector zlibbioc crayon Biostrings rlang fastmap yaml Biobase glue GenomicRanges Rhtslib R6 jsonlite cachem BiocParallel futile.logger snow codetools BH lambda.r futile.options formatR memoise matrixStats Rsamtools XML GenomicAlignments BiocIO restfulr SummarizedExperiment rjson MatrixGenerics Matrix DelayedArray lattice Rcpp pkgconfig vctrs mime cli magrittr rtracklayer DBI RSQLite KEGGREST curl png bit64 blob plogr httr bit openssl askpass sys digest stringr stringi AnnotationDbi rappdirs lifecycle tibble withr ellipsis fansi pillar utf8 BSgenome biomaRt progress BiocFileCache xml2 hms prettyunits dbplyr dplyr filelock assertthat purrr tidyselect generics evaluate xfun GenomicFeatures highr htmltools base64enc knitr rstudioapi scales Hmisc RColorBrewer dichromat VariantAnnotation ensembldb AnnotationFilter farver labeling munsell viridisLite survival Formula ggplot2 latticeExtra cluster rpart nnet foreign gtable gridExtra data.table htmlTable viridis ProtGenerics lazyeval colorspace isoband MASS mgcv jpeg checkmate htmlwidgets nlme backports jquerylib tinytex bslib sass fs bookdown rmarkdown BiocManager brio callr desc pkgload praise processx ps waldo rprojroot diffobj rematch2 BSgenome.Hsapiens.UCSC.hg19 0 2 4 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents methods GenomicRanges regioneR stats graphics bezier grDevices digest memoise S4Vectors IRanges GenomeInfoDb bamsignals Rsamtools rtracklayer AnnotationDbi GenomicFeatures VariantAnnotation biovizBase magrittr pasillaBamSubset markdown knitr rmarkdown BiocStyle testthat org.Hs.eg.db org.Mm.eg.db BSgenome.Hsapiens.UCSC.hg19 BSgenome.Hsapiens.UCSC.hg19.masked TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene In total 145 packages are required directly or indirectly (174) when installing 'karyoploteR' (1.22.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'karyoploteR' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on karyoploteR
regioneR Depends The whole set of functions/methods/classes from parent package is imported to the namespace of karyoploteR. 50 1
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of karyoploteR. 0 0
GenomicRanges Depends 1 0 0 15 0
biovizBase Imports 1 0 0 141 43
bezier Imports 1 0 0 0 1
bamsignals Imports 1 0 0 18 1
stats Imports 4 0 0 0 0
graphics Imports 3 0 0 0 0
grDevices Imports 4 0 0 0 0
digest Imports 1 0 0 1 0
memoise Imports 1 0 0 4 0
S4Vectors Imports 3 0 0 6 0
IRanges Imports 5 0 0 7 0
GenomeInfoDb Imports 5 0 0 11 0
Rsamtools Imports 4 0 0 29 0
rtracklayer Imports 4 0 0 44 0
AnnotationDbi Imports 2 0 0 44 0
GenomicFeatures Imports 5 0 0 96 0
VariantAnnotation Imports 3 0 0 98 0
testthat Suggests No object is imported into the namespace of karyoploteR. 36 12
BiocStyle Suggests No object is imported into the namespace of karyoploteR. 30 9
rmarkdown Suggests No object is imported into the namespace of karyoploteR. 27 6
BSgenome.Hsapiens.UCSC.hg19.masked Suggests No object is imported into the namespace of karyoploteR. 47 2
pasillaBamSubset Suggests No object is imported into the namespace of karyoploteR. 0 1
markdown Suggests No object is imported into the namespace of karyoploteR. 5 1
org.Hs.eg.db Suggests No object is imported into the namespace of karyoploteR. 45 1
org.Mm.eg.db Suggests No object is imported into the namespace of karyoploteR. 45 1
BSgenome.Hsapiens.UCSC.hg19 Suggests No object is imported into the namespace of karyoploteR. 46 1
TxDb.Hsapiens.UCSC.hg19.knownGene Suggests No object is imported into the namespace of karyoploteR. 97 1
TxDb.Mmusculus.UCSC.mm10.knownGene Suggests No object is imported into the namespace of karyoploteR. 97 1
magrittr Suggests No object is imported into the namespace of karyoploteR. 0 0
knitr Suggests No object is imported into the namespace of karyoploteR. 12 0

Analysis was done with pkgndep.