Dependency analysis on package SummarizedExperiment

General information

Bioconductor link link
Package version1.26.1
Number of strong dependencies24
Number of all dependencies136
Number of parent packages13
Max heaviness from parent packages3
Total heaviness from parent packages5
Number of parent packages (including Suggests and Enhances)28
Max co-heaviness from parent packages ("GenomeInfoDb" and "GenomicRanges")4

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics stats4 tools grDevices grid parallel BiocGenerics S4Vectors IRanges RCurl GenomeInfoDbData bitops GenomeInfoDb XVector zlibbioc matrixStats lattice Matrix MatrixGenerics glue jsonlite R6 rlang fastmap magrittr Biobase pkgconfig vctrs crayon cli stringr yaml stringi digest DBI httr RSQLite KEGGREST curl mime openssl bit64 blob memoise Rcpp plogr png Biostrings askpass bit cachem sys evaluate DelayedArray rappdirs AnnotationDbi xfun highr GenomicRanges SummarizedExperiment ellipsis lifecycle pillar tibble withr fansi utf8 XML rhdf5filters Rhdf5lib knitr htmltools jquerylib tinytex bslib base64enc sass fs BiocIO rtracklayer biomaRt Rsamtools GenomicAlignments restfulr progress BiocFileCache xml2 BiocParallel Rhtslib rjson hms prettyunits dbplyr dplyr filelock futile.logger snow codetools BH assertthat purrr tidyselect generics lambda.r futile.options formatR rhdf5 bookdown rmarkdown BiocManager brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 org.Hs.eg.db xtable GenomicFeatures 0 1 2 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents methods MatrixGenerics Biobase GenomicRanges utils stats tools BiocGenerics S4Vectors Matrix IRanges GenomeInfoDb DelayedArray jsonlite digest rhdf5 RUnit knitr HDF5Array airway rmarkdown BiocStyle testthat AnnotationDbi hgu95av2.db annotate GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene In total 24 packages are required directly or indirectly (136) when installing 'SummarizedExperiment' (1.26.1) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'SummarizedExperiment' Imported functions Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on SummarizedExperiment
GenomicRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of SummarizedExperiment. 15 3
Biobase Depends The whole set of functions/methods/classes from parent package is imported to the namespace of SummarizedExperiment. 5 1
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of SummarizedExperiment. 0 0
MatrixGenerics Depends 1 0 0 2 0
DelayedArray Imports The whole set of functions/methods/classes from parent package is imported to the namespace of SummarizedExperiment. 14 1
utils Imports 2 0 0 0 0
stats Imports 1 0 0 0 0
tools Imports 1 0 0 0 0
BiocGenerics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of SummarizedExperiment. 4 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of SummarizedExperiment. 6 0
Matrix Imports 0 0 1 7 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of SummarizedExperiment. 7 0
GenomeInfoDb Imports The whole set of functions/methods/classes from parent package is imported to the namespace of SummarizedExperiment. 11 0
TxDb.Hsapiens.UCSC.hg19.knownGene Suggests No object is imported into the namespace of SummarizedExperiment. 97 74
GenomicFeatures Suggests No object is imported into the namespace of SummarizedExperiment. 96 73
testthat Suggests No object is imported into the namespace of SummarizedExperiment. 36 31
annotate Suggests No object is imported into the namespace of SummarizedExperiment. 47 31
hgu95av2.db Suggests No object is imported into the namespace of SummarizedExperiment. 46 30
AnnotationDbi Suggests No object is imported into the namespace of SummarizedExperiment. 44 28
BiocStyle Suggests No object is imported into the namespace of SummarizedExperiment. 30 26
rmarkdown Suggests No object is imported into the namespace of SummarizedExperiment. 27 23
knitr Suggests No object is imported into the namespace of SummarizedExperiment. 12 9
HDF5Array Suggests No object is imported into the namespace of SummarizedExperiment. 19 4
rhdf5 Suggests No object is imported into the namespace of SummarizedExperiment. 3 3
airway Suggests No object is imported into the namespace of SummarizedExperiment. 25 2
jsonlite Suggests No object is imported into the namespace of SummarizedExperiment. 1 1
digest Suggests No object is imported into the namespace of SummarizedExperiment. 1 1
RUnit Suggests No object is imported into the namespace of SummarizedExperiment. 3 1

Analysis was done with pkgndep.