Dependency analysis on package Glimma

General information

Bioconductor link link
Package version2.6.0
Number of strong dependencies100
Number of all dependencies199
Number of parent packages9
Max heaviness from parent packages63
Total heaviness from parent packages68
Number of parent packages (including Suggests and Enhances)20
Max co-heaviness from parent packages ("DESeq2" and "SummarizedExperiment")15

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats grDevices graphics tools stats4 grid parallel splines magrittr BiocGenerics rlang glue digest S4Vectors jsonlite Rcpp IRanges GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops R6 yaml fastmap lattice Biobase pkgconfig crayon htmltools base64enc GenomicRanges MatrixGenerics Matrix DelayedArray matrixStats codetools tibble withr lifecycle ellipsis fansi pillar vctrs cli utf8 SummarizedExperiment BiocParallel futile.logger snow BH lambda.r futile.options formatR locfit AnnotationDbi DBI RSQLite KEGGREST xtable httr bit64 blob memoise plogr png Biostrings curl mime openssl bit cachem askpass sys limma ggplot2 RColorBrewer gtable isoband MASS mgcv scales XML nlme farver labeling munsell viridisLite colorspace genefilter geneplotter RcppArmadillo annotate survival stringr stringi evaluate bslib jquerylib sass fs rappdirs highr xfun BiocManager SingleCellExperiment knitr tinytex scuttle DelayedMatrixStats beachmat BiocNeighbors BiocSingular sparseMatrixStats RcppHNSW ScaledMatrix irlba rsvd BiocFileCache BiocVersion interactiveDisplayBase dplyr dbplyr filelock shiny DT generics tidyselect assertthat purrr httpuv fontawesome sourcetools later promises commonmark htmlwidgets crosstalk lazyeval lobstr bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 edgeR igraph statmod bluster metapod dqrng cluster sitmo gridExtra ggbeeswarm viridis Rtsne RcppML ggrepel beeswarm vipor RcppEigen ExperimentHub AnnotationHub ensembldb GenomicFeatures AnnotationFilter rtracklayer Rsamtools ProtGenerics BiocIO biomaRt GenomicAlignments restfulr Rhtslib progress xml2 rjson hms prettyunits 0 2 4 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents stats methods jsonlite limma S4Vectors htmlwidgets edgeR SummarizedExperiment DESeq2 IRanges knitr pryr GenomicRanges rmarkdown BiocStyle testthat scran AnnotationHub scater scRNAseq In total 100 packages are required directly or indirectly (199) when installing 'Glimma' (2.6.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'Glimma' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on Glimma
DESeq2 Imports 2 0 0 93 63
htmlwidgets Imports The whole set of functions/methods/classes from parent package is imported to the namespace of Glimma. 10 4
edgeR Imports 2 0 0 10 1
stats Imports 4 0 0 0 0
methods Imports 1 0 0 0 0
jsonlite Imports 1 0 0 1 0
limma Imports 1 0 0 5 0
S4Vectors Imports 1 0 0 6 0
SummarizedExperiment Imports 1 0 0 24 0
scRNAseq Suggests No object is imported into the namespace of Glimma. 124 48
AnnotationHub Suggests No object is imported into the namespace of Glimma. 85 27
scater Suggests No object is imported into the namespace of Glimma. 85 21
scran Suggests No object is imported into the namespace of Glimma. 58 19
BiocStyle Suggests No object is imported into the namespace of Glimma. 30 16
testthat Suggests No object is imported into the namespace of Glimma. 36 14
rmarkdown Suggests No object is imported into the namespace of Glimma. 27 13
knitr Suggests No object is imported into the namespace of Glimma. 12 6
pryr Suggests No object is imported into the namespace of Glimma. 14 4
IRanges Suggests No object is imported into the namespace of Glimma. 7 0
GenomicRanges Suggests No object is imported into the namespace of Glimma. 15 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 Glimma Co-heaviness as Jaccard coeffcient
SummarizedExperiment DESeq2 15 0.192

Analysis was done with pkgndep.