Dependency analysis on package CNEr

General information

Bioconductor link link
Package version1.32.0
Number of strong dependencies116
Number of all dependencies184
Number of parent packages22
Max heaviness from parent packages15
Total heaviness from parent packages42
Number of parent packages (including Suggests and Enhances)32
Max co-heaviness from parent packages ("rtracklayer" and "GenomicAlignments")15

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats graphics tools grDevices stats4 parallel grid splines BiocGenerics S4Vectors IRanges crayon zlibbioc RCurl GenomeInfoDbData bitops XVector GenomeInfoDb glue Biostrings rlang R6 Biobase yaml magrittr Matrix lattice pkgconfig vctrs cli jsonlite GenomicRanges Rsamtools BiocParallel Rhtslib SummarizedExperiment futile.logger snow codetools BH MatrixGenerics DelayedArray lambda.r futile.options matrixStats formatR XML fastmap GenomicAlignments BiocIO restfulr rjson Rcpp stringr stringi bit64 bit digest blob DBI memoise plogr cachem httr curl mime openssl png askpass sys lifecycle tibble ellipsis fansi pillar withr utf8 AnnotationDbi RSQLite KEGGREST hms tidyselect progress purrr prettyunits gtable isoband MASS mgcv scales nlme farver labeling munsell RColorBrewer viridisLite colorspace R.oo R.methodsS3 pracma plyr clipr vroom cpp11 tzdb xtable rtracklayer evaluate BSgenome highr xfun rappdirs htmltools base64enc knitr jquerylib tinytex bslib sass fs rstudioapi biomaRt GenomicFeatures BiocFileCache xml2 dbplyr dplyr filelock assertthat generics bookdown rmarkdown BiocManager brio callr desc pkgload praise processx ps waldo rprojroot diffobj rematch2 ensembldb biovizBase latticeExtra AnnotationFilter ProtGenerics Hmisc dichromat VariantAnnotation jpeg lazyeval survival Formula ggplot2 cluster rpart nnet foreign gridExtra data.table htmlTable viridis checkmate htmlwidgets backports 0 10 20 30 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents methods tools parallel DBI BiocGenerics R.utils S4Vectors IRanges poweRlaw XVector reshape2 GenomeInfoDb GenomicRanges Biostrings RSQLite KEGGREST readr ggplot2 GenomicAlignments rtracklayer GO.db annotate knitr rmarkdown BiocStyle testthat BSgenome.Drerio.UCSC.danRer10 BSgenome.Hsapiens.UCSC.hg38 BSgenome.Hsapiens.UCSC.hg19 BSgenome.Ggallus.UCSC.galGal3 TxDb.Drerio.UCSC.danRer10.refGene Gviz In total 116 packages are required directly or indirectly (184) when installing 'CNEr' (1.32.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'CNEr' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on CNEr
ggplot2 Imports 17 0 0 37 15
readr Imports 1 0 0 31 10
rtracklayer Imports 1 4 0 44 5
reshape2 Imports 1 0 0 10 4
R.utils Imports 2 0 0 5 3
poweRlaw Imports 2 0 0 7 2
annotate Imports 1 0 0 47 2
GO.db Imports 9 0 0 45 1
methods Imports 5 2 4 0 0
tools Imports 1 0 0 0 0
parallel Imports 1 0 0 0 0
DBI Imports 0 1 0 1 0
BiocGenerics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of CNEr. 4 0
S4Vectors Imports 10 17 4 6 0
IRanges Imports 3 3 0 7 0
XVector Imports 0 1 0 10 0
GenomeInfoDb Imports 1 7 0 11 0
GenomicRanges Imports 1 8 1 15 0
Biostrings Imports 4 1 1 17 0
RSQLite Imports 1 3 0 17 0
KEGGREST Imports 1 0 0 27 0
GenomicAlignments Imports 3 1 0 38 0
Gviz Suggests No object is imported into the namespace of CNEr. 142 42
BiocStyle Suggests No object is imported into the namespace of CNEr. 30 16
testthat Suggests No object is imported into the namespace of CNEr. 36 14
rmarkdown Suggests No object is imported into the namespace of CNEr. 27 13
TxDb.Drerio.UCSC.danRer10.refGene Suggests No object is imported into the namespace of CNEr. 97 11
knitr Suggests No object is imported into the namespace of CNEr. 12 4
BSgenome.Drerio.UCSC.danRer10 Suggests No object is imported into the namespace of CNEr. 46 2
BSgenome.Hsapiens.UCSC.hg38 Suggests No object is imported into the namespace of CNEr. 46 2
BSgenome.Hsapiens.UCSC.hg19 Suggests No object is imported into the namespace of CNEr. 46 2
BSgenome.Ggallus.UCSC.galGal3 Suggests No object is imported into the namespace of CNEr. 46 2

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 CNEr Co-heaviness as Jaccard coeffcient
GenomicAlignments rtracklayer 15 0.75

Analysis was done with pkgndep.