Dependency analysis on package TFBSTools

General information

Bioconductor link link
Package version1.34.0
Number of strong dependencies123
Number of all dependencies155
Number of parent packages23
Max heaviness from parent packages57
Total heaviness from parent packages63
Number of parent packages (including Suggests and Enhances)30
Max co-heaviness from parent packages ("CNEr" and "RSQLite")13

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats graphics stats4 tools grDevices grid parallel splines BiocGenerics S4Vectors IRanges bitops zlibbioc RCurl GenomeInfoDbData XVector GenomeInfoDb crayon glue yaml rlang magrittr futile.logger snow codetools BH lambda.r futile.options formatR fastmap Biostrings R6 stringr digest stringi jsonlite Rcpp pkgconfig cli vctrs GenomicRanges matrixStats Rsamtools XML GenomicAlignments BiocIO restfulr BiocParallel Rhtslib SummarizedExperiment rjson MatrixGenerics Biobase Matrix DelayedArray lattice DBI bit64 blob memoise plogr bit cachem rtracklayer lifecycle tibble withr ellipsis fansi pillar utf8 RSQLite readr reshape2 ggplot2 poweRlaw annotate GO.db R.utils KEGGREST clipr hms vroom cpp11 tzdb plyr gtable isoband MASS mgcv scales pracma AnnotationDbi xtable httr R.oo R.methodsS3 png tidyselect progress nlme farver labeling munsell RColorBrewer viridisLite curl mime openssl purrr prettyunits colorspace askpass sys evaluate xfun highr knitr htmltools jquerylib tinytex bslib base64enc sass fs rappdirs bookdown rmarkdown BiocManager brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 0 5 10 15 20 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents grid methods parallel caTools DBI XML gtools TFMPvalue BiocGenerics seqLogo Biobase S4Vectors IRanges DirichletMultinomial XVector BiocParallel GenomeInfoDb GenomicRanges Biostrings RSQLite rtracklayer BSgenome CNEr JASPAR2016 JASPAR2018 knitr JASPAR2014 rmarkdown BiocStyle testthat In total 123 packages are required directly or indirectly (155) when installing 'TFBSTools' (1.34.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'TFBSTools' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on TFBSTools
CNEr Imports 0 4 1 116 57
caTools Imports 1 0 0 1 1
gtools Imports 1 0 0 3 1
TFMPvalue Imports 1 0 0 3 1
seqLogo Imports 2 0 0 4 1
DirichletMultinomial Imports 3 1 0 8 1
BSgenome Imports 0 1 0 45 1
grid Imports 10 0 0 0 0
methods Imports 4 2 4 0 0
parallel Imports 1 0 0 0 0
DBI Imports 0 1 0 1 0
XML Imports 2 0 0 2 0
BiocGenerics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of TFBSTools. 4 0
Biobase Imports 2 0 0 5 0
S4Vectors Imports 3 5 5 6 0
IRanges Imports 1 10 0 7 0
XVector Imports 0 1 0 10 0
BiocParallel Imports 2 0 0 11 0
GenomeInfoDb Imports 0 1 0 11 0
GenomicRanges Imports 2 5 2 15 0
Biostrings Imports 10 7 3 17 0
RSQLite Imports 1 2 0 17 0
rtracklayer Imports 0 2 0 44 0
BiocStyle Suggests No object is imported into the namespace of TFBSTools. 30 16
testthat Suggests No object is imported into the namespace of TFBSTools. 36 14
rmarkdown Suggests No object is imported into the namespace of TFBSTools. 27 13
knitr Suggests No object is imported into the namespace of TFBSTools. 12 4
JASPAR2016 Suggests No object is imported into the namespace of TFBSTools. 1 1
JASPAR2018 Suggests No object is imported into the namespace of TFBSTools. 1 1
JASPAR2014 Suggests No object is imported into the namespace of TFBSTools. 18 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 TFBSTools Co-heaviness as Jaccard coeffcient
RSQLite CNEr 13 0.186

Analysis was done with pkgndep.