Dependency analysis on package zinbwave

General information

Bioconductor link link
Package version1.18.0
Number of strong dependencies73
Number of all dependencies171
Number of parent packages9
Max heaviness from parent packages33
Total heaviness from parent packages47
Number of parent packages (including Suggests and Enhances)20
Max co-heaviness from parent packages ("SingleCellExperiment" and "SummarizedExperiment")5

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats grDevices graphics tools grid stats4 parallel splines lattice glue R6 rlang Matrix jsonlite Biobase BiocGenerics S4Vectors IRanges GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops Rcpp pkgconfig vctrs crayon cli fastmap MatrixGenerics GenomicRanges DelayedArray matrixStats AnnotationDbi DBI RSQLite KEGGREST XML httr bit64 blob memoise plogr png Biostrings curl mime openssl bit cachem askpass sys SummarizedExperiment futile.logger snow codetools BH lambda.r futile.options formatR xtable locfit annotate survival limma magrittr digest stringr stringi ellipsis lifecycle withr fansi tibble pillar utf8 evaluate yaml rappdirs highr xfun bslib htmltools jquerylib sass base64enc fs knitr tinytex BiocManager gtable isoband MASS mgcv scales nlme farver labeling munsell RColorBrewer viridisLite colorspace BiocFileCache dplyr dbplyr filelock generics tidyselect progress xml2 assertthat purrr hms prettyunits BiocParallel bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 genefilter geneplotter ggplot2 RcppArmadillo SingleCellExperiment ExperimentHub AnnotationHub ensembldb GenomicFeatures BiocVersion interactiveDisplayBase AnnotationFilter rtracklayer Rsamtools ProtGenerics BiocIO biomaRt shiny DT lazyeval GenomicAlignments restfulr Rhtslib httpuv fontawesome sourcetools later promises commonmark htmlwidgets crosstalk rjson 0 5 10 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents methods SummarizedExperiment SingleCellExperiment stats Matrix softImpute edgeR BiocParallel genefilter matrixStats magrittr Rtsne knitr rmarkdown BiocStyle testthat ggplot2 biomaRt DESeq2 scRNAseq In total 73 packages are required directly or indirectly (171) when installing 'zinbwave' (1.18.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'zinbwave' Imported functions Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on zinbwave
SingleCellExperiment Depends The whole set of functions/methods/classes from parent package is imported to the namespace of zinbwave. 25 1
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of zinbwave. 0 0
SummarizedExperiment Depends The whole set of functions/methods/classes from parent package is imported to the namespace of zinbwave. 24 0
genefilter Imports 1 0 0 53 33
BiocParallel Imports The whole set of functions/methods/classes from parent package is imported to the namespace of zinbwave. 11 9
edgeR Imports 2 0 0 10 3
softImpute Imports 1 0 0 8 1
stats Imports 13 0 0 0 0
Matrix Imports 0 0 1 7 0
scRNAseq Suggests No object is imported into the namespace of zinbwave. 124 60
biomaRt Suggests No object is imported into the namespace of zinbwave. 70 25
DESeq2 Suggests No object is imported into the namespace of zinbwave. 93 25
testthat Suggests No object is imported into the namespace of zinbwave. 36 23
ggplot2 Suggests No object is imported into the namespace of zinbwave. 37 22
BiocStyle Suggests No object is imported into the namespace of zinbwave. 30 21
rmarkdown Suggests No object is imported into the namespace of zinbwave. 27 18
knitr Suggests No object is imported into the namespace of zinbwave. 12 8
magrittr Suggests No object is imported into the namespace of zinbwave. 0 1
Rtsne Suggests No object is imported into the namespace of zinbwave. 4 1
matrixStats Suggests No object is imported into the namespace of zinbwave. 0 0

Analysis was done with pkgndep.