Dependency analysis on package motifStack

General information

Bioconductor link link
Package version1.40.0
Number of strong dependencies130
Number of all dependencies152
Number of parent packages13
Max heaviness from parent packages70
Total heaviness from parent packages76
Number of parent packages (including Suggests and Enhances)23
Max co-heaviness from parent packages ("TFBSTools" and "ggplot2")27

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils grDevices stats graphics grid tools stats4 splines parallel yaml digest rlang glue magrittr lattice jsonlite base64enc fastmap crayon R6 XML stringr stringi MASS htmltools BiocGenerics S4Vectors IRanges XVector GenomeInfoDb zlibbioc RCurl GenomeInfoDbData bitops Matrix gtable isoband mgcv scales tibble withr nlme farver labeling lifecycle munsell RColorBrewer viridisLite ellipsis fansi pillar pkgconfig vctrs colorspace cli utf8 Biobase Biostrings BiocParallel GenomicRanges rtracklayer futile.logger snow codetools BH matrixStats Rsamtools GenomicAlignments BiocIO restfulr lambda.r futile.options Rhtslib SummarizedExperiment png rjson formatR MatrixGenerics DelayedArray pixmap sp BSgenome caTools CNEr DirichletMultinomial gtools DBI RSQLite seqLogo TFMPvalue readr reshape2 ggplot2 poweRlaw annotate GO.db R.utils KEGGREST bit64 blob memoise Rcpp plogr clipr hms vroom cpp11 tzdb plyr pracma AnnotationDbi xtable httr R.oo R.methodsS3 bit cachem tidyselect progress curl mime openssl purrr prettyunits askpass sys xfun evaluate highr knitr jquerylib tinytex bslib sass fs rappdirs jpeg bookdown rmarkdown BiocManager splitstackshape data.table 0 10 20 30 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents methods grid grDevices graphics stats stats4 utils XML ade4 htmlwidgets Biostrings ggplot2 TFBSTools RColorBrewer JASPAR2020 RUnit BiocGenerics grImport grImport2 knitr rmarkdown BiocStyle MotifDb In total 130 packages are required directly or indirectly (152) when installing 'motifStack' (1.40.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'motifStack' Imported functions Imported S4 methods The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on motifStack
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of motifStack. 0 0
grid Depends 30 0 0 0 0
TFBSTools Imports 0 4 0 123 70
ade4 Imports 2 0 0 10 3
htmlwidgets Imports 3 0 0 10 3
grDevices Imports 7 0 0 0 0
graphics Imports 16 0 0 0 0
stats Imports 10 0 0 0 0
stats4 Imports 1 0 0 0 0
utils Imports 4 0 0 0 0
XML Imports 2 0 0 2 0
Biostrings Imports 1 0 0 17 0
ggplot2 Imports 4 0 0 37 0
BiocStyle Suggests No object is imported into the namespace of motifStack. 30 14
rmarkdown Suggests No object is imported into the namespace of motifStack. 27 11
knitr Suggests No object is imported into the namespace of motifStack. 12 4
MotifDb Suggests No object is imported into the namespace of motifStack. 47 3
grImport2 Suggests No object is imported into the namespace of motifStack. 8 2
JASPAR2020 Suggests No object is imported into the namespace of motifStack. 1 1
RUnit Suggests No object is imported into the namespace of motifStack. 3 1
grImport Suggests No object is imported into the namespace of motifStack. 6 1
RColorBrewer Suggests No object is imported into the namespace of motifStack. 0 0
BiocGenerics Suggests No object is imported into the namespace of motifStack. 4 0

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 motifStack Co-heaviness as Jaccard coeffcient
ggplot2 TFBSTools 27 0.278
Biostrings TFBSTools 11 0.136

Analysis was done with pkgndep.