Dependency analysis on package countsimQC

General information

Bioconductor link link
Package version1.14.0
Number of strong dependencies126
Number of all dependencies139
Number of parent packages17
Max heaviness from parent packages12
Total heaviness from parent packages36
Number of parent packages (including Suggests and Enhances)19
Max co-heaviness from parent packages ("DESeq2" and "genefilter")23

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils grDevices stats graphics tools grid stats4 splines parallel rlang glue magrittr R6 pkgconfig vctrs cli crayon lattice tibble lifecycle ellipsis fansi pillar utf8 jsonlite digest bitops Rcpp fastmap Matrix yaml S4Vectors IRanges BiocGenerics Biobase GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc evaluate withr locfit generics tidyselect purrr htmltools jquerylib base64enc GenomicRanges MatrixGenerics DelayedArray matrixStats stringr xfun highr stringi RColorBrewer gtable isoband MASS mgcv scales nlme farver labeling munsell viridisLite colorspace AnnotationDbi annotate survival DBI RSQLite KEGGREST XML xtable httr bit64 blob memoise plogr png Biostrings curl mime openssl bit cachem askpass sys limma htmlwidgets crosstalk promises lazyeval later dplyr cpp11 bslib knitr tinytex sass fs rappdirs SummarizedExperiment BiocParallel genefilter geneplotter ggplot2 RcppArmadillo futile.logger snow codetools BH lambda.r futile.options formatR brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 0 2 4 Imported methods 0 20 40 60 80 Required packages 0 5 10 Heaviness from parents grDevices tools GenomeInfoDbData randtests stats utils methods caTools edgeR dplyr DT tidyr SummarizedExperiment rmarkdown ggplot2 genefilter DESeq2 knitr testthat In total 126 packages are required directly or indirectly (139) when installing 'countsimQC' (1.14.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'countsimQC' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on countsimQC
rmarkdown Imports 3 0 0 27 12
DESeq2 Imports The whole set of functions/methods/classes from parent package is imported to the namespace of countsimQC. 93 12
DT Imports The whole set of functions/methods/classes from parent package is imported to the namespace of countsimQC. 20 6
edgeR Imports 1 0 0 10 2
tidyr Imports The whole set of functions/methods/classes from parent package is imported to the namespace of countsimQC. 22 2
randtests Imports 1 0 0 0 1
caTools Imports 1 0 0 1 1
grDevices Imports 1 0 0 0 0
tools Imports 2 0 0 0 0
GenomeInfoDbData Imports The whole set of functions/methods/classes from parent package is imported to the namespace of countsimQC. 0 0
stats Imports 5 0 0 0 0
utils Imports 1 0 0 0 0
methods Imports 1 0 0 0 0
dplyr Imports The whole set of functions/methods/classes from parent package is imported to the namespace of countsimQC. 20 0
SummarizedExperiment Imports The whole set of functions/methods/classes from parent package is imported to the namespace of countsimQC. 24 0
ggplot2 Imports The whole set of functions/methods/classes from parent package is imported to the namespace of countsimQC. 37 0
genefilter Imports 1 0 0 53 0
testthat Suggests No object is imported into the namespace of countsimQC. 36 13
knitr Suggests No object is imported into the namespace of countsimQC. 12 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 countsimQC Co-heaviness as Jaccard coeffcient
genefilter DESeq2 23 0.657
ggplot2 DESeq2 14 0.538

Analysis was done with pkgndep.