Dependency analysis on package tximeta

General information

Bioconductor link link
Package version1.14.0
Number of strong dependencies123
Number of all dependencies194
Number of parent packages18
Max heaviness from parent packages21
Total heaviness from parent packages25
Number of parent packages (including Suggests and Enhances)28
Max co-heaviness from parent packages ("ensembldb" and "GenomicFeatures")25

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats graphics grDevices tools stats4 grid parallel splines BiocGenerics glue S4Vectors rlang crayon IRanges RCurl GenomeInfoDbData bitops pkgconfig vctrs cli magrittr jsonlite R6 GenomeInfoDb XVector zlibbioc ellipsis lifecycle pillar fansi utf8 Rcpp fastmap Biobase memoise httr cachem curl mime openssl askpass sys tibble withr digest lattice DBI RSQLite bit64 blob plogr bit KEGGREST png Biostrings rappdirs yaml stringr stringi MatrixGenerics GenomicRanges Matrix DelayedArray matrixStats purrr AnnotationDbi dbplyr dplyr filelock assertthat tidyselect generics SummarizedExperiment BiocFileCache fs XML xml2 BiocParallel prettyunits futile.logger snow codetools BH lambda.r futile.options formatR lazyeval xtable htmltools commonmark bslib jquerylib base64enc sass BiocIO rtracklayer biomaRt Rsamtools GenomicAlignments restfulr progress Rhtslib rjson hms BiocManager BiocVersion interactiveDisplayBase shiny DT httpuv fontawesome sourcetools later promises htmlwidgets crosstalk GenomicFeatures AnnotationFilter ProtGenerics evaluate highr xfun locfit knitr brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 ggplot2 RColorBrewer gtable isoband MASS mgcv scales nlme farver labeling munsell viridisLite colorspace limma tinytex abind gtools qvalue svMisc SingleCellExperiment reshape2 plyr usethis pkgbuild rcmdcheck remotes roxygen2 rversions sessioninfo testthat clipr gert gh whisker xopen brew cpp11 credentials zip gitcreds ini genefilter geneplotter RcppArmadillo annotate survival 0 2 4 6 8 Imported methods 0 50 100 Required packages 0 10 20 30 Heaviness from parents tools utils methods jsonlite tximport S4Vectors IRanges Matrix GenomeInfoDb GenomicRanges tibble Biostrings SummarizedExperiment AnnotationDbi BiocFileCache AnnotationHub GenomicFeatures ensembldb tximportData limma edgeR knitr rmarkdown testthat org.Dm.eg.db fishpond devtools DESeq2 In total 123 packages are required directly or indirectly (194) when installing 'tximeta' (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 'tximeta' Imported functions


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on tximeta
AnnotationHub Imports 4 0 0 85 21
ensembldb Imports 2 0 0 100 3
tximport Imports 2 0 0 3 1
tools Imports 2 0 0 0 0
utils Imports 5 0 0 0 0
methods Imports 2 0 0 0 0
jsonlite Imports 2 0 0 1 0
S4Vectors Imports 4 0 0 6 0
IRanges Imports 2 0 0 7 0
Matrix Imports 1 0 0 7 0
GenomeInfoDb Imports 6 0 0 11 0
GenomicRanges Imports 1 0 0 15 0
tibble Imports 1 0 0 15 0
Biostrings Imports 2 0 0 17 0
SummarizedExperiment Imports 8 0 0 24 0
AnnotationDbi Imports 5 0 0 44 0
BiocFileCache Imports 6 0 0 46 0
GenomicFeatures Imports 6 0 0 96 0
devtools Suggests No object is imported into the namespace of tximeta. 76 36
fishpond Suggests No object is imported into the namespace of tximeta. 66 22
DESeq2 Suggests No object is imported into the namespace of tximeta. 93 21
testthat Suggests No object is imported into the namespace of tximeta. 36 14
rmarkdown Suggests No object is imported into the namespace of tximeta. 27 6
knitr Suggests No object is imported into the namespace of tximeta. 12 4
edgeR Suggests No object is imported into the namespace of tximeta. 10 3
tximportData Suggests No object is imported into the namespace of tximeta. 0 1
limma Suggests No object is imported into the namespace of tximeta. 5 1
org.Dm.eg.db Suggests No object is imported into the namespace of tximeta. 45 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 tximeta Co-heaviness as Jaccard coeffcient
GenomicFeatures ensembldb 25 0.893

Analysis was done with pkgndep.