Dependency analysis on package destiny

General information

Bioconductor link link
Package version3.10.0
Number of strong dependencies130
Number of all dependencies252
Number of parent packages28
Max heaviness from parent packages49
Total heaviness from parent packages63
Number of parent packages (including Suggests and Enhances)43
Max co-heaviness from parent packages ("SingleCellExperiment" and "SummarizedExperiment")14

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests utils methods stats grDevices graphics grid tools splines stats4 parallel lattice glue rlang Matrix magrittr R6 vctrs cli pkgconfig ellipsis lifecycle crayon digest fansi pillar utf8 tibble Rcpp withr MASS farver labeling munsell RColorBrewer viridisLite colorspace gtable jsonlite BiocGenerics isoband mgcv scales nlme stringr stringi Biobase purrr ggplot2 evaluate yaml S4Vectors IRanges GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops highr xfun curl dplyr tidyselect generics MatrixGenerics GenomicRanges DelayedArray matrixStats knitr RcppEigen cpp11 SummarizedExperiment callr processx ps rstudioapi rematch2 zoo data.table broom backports tidyr brio desc pkgload praise waldo rprojroot diffobj TTR xts hexbin car robustbase sp vcd nnet e1071 laeken ranger carData abind pbkrtest quantreg maptools lme4 DEoptimR lmtest class proxy boot numDeriv SparseM MatrixModels survival foreign minqa nloptr testthat fastmap htmltools base64enc memoise cachem bslib jquerylib sass fs rappdirs httr blob DBI mime openssl askpass bit64 sys bit htmlwidgets tinytex AnnotationDbi RSQLite KEGGREST Biostrings plogr png SingleCellExperiment BiocParallel futile.logger snow codetools BH lambda.r futile.options formatR dbplyr hms xml2 assertthat progress prettyunits gridExtra scuttle edgeR limma igraph statmod DelayedMatrixStats BiocSingular bluster metapod dqrng beachmat locfit sparseMatrixStats ScaledMatrix irlba rsvd cluster BiocNeighbors sitmo RcppHNSW dtplyr forcats googledrive googlesheets4 haven lubridate modelr readr readxl reprex rvest gargle uuid cellranger ids clipr vroom tzdb rmarkdown selectr rematch ExperimentHub AnnotationHub ensembldb GenomicFeatures BiocFileCache BiocManager BiocVersion interactiveDisplayBase AnnotationFilter rtracklayer Rsamtools ProtGenerics BiocIO biomaRt filelock shiny DT lazyeval XML GenomicAlignments restfulr Rhtslib httpuv xtable fontawesome sourcetools later promises commonmark crosstalk rjson 0 10 20 30 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents methods graphics grDevices grid utils stats Rcpp proxy RcppHNSW scatterplot3d BiocGenerics Biobase Matrix irlba RcppEigen pcaMethods tidyselect RSpectra knn.covertree smoother scales tidyr SummarizedExperiment SingleCellExperiment ggplot2 ggplot.multistats ggthemes VIM FNN gridExtra conflicted igraph knitr repr rgl rmarkdown testthat cowplot viridis org.Mm.eg.db scran tidyverse scRNAseq In total 130 packages are required directly or indirectly (252) when installing 'destiny' (3.10.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'destiny' Imported functions Imported S4 methods Imported S4 classes Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on destiny
VIM Imports 1 0 0 99 49
smoother Imports 1 0 0 11 4
ggplot.multistats Imports 1 0 0 39 2
RcppHNSW Imports 3 0 0 3 1
scatterplot3d Imports 1 0 0 3 1
irlba Imports 1 0 0 8 1
pcaMethods Imports 2 0 0 9 1
RSpectra Imports 2 0 0 10 1
knn.covertree Imports Parent package is listed in Imports of destiny but no object from parent package is imported. 10 1
SingleCellExperiment Imports 3 0 0 25 1
ggthemes Imports 2 0 0 42 1
methods Imports 17 0 0 0 0
graphics Imports 11 0 0 0 0
grDevices Imports 4 0 0 0 0
grid Imports 2 0 0 0 0
utils Imports 10 0 0 0 0
stats Imports 3 0 0 0 0
Rcpp Imports 1 0 0 2 0
proxy Imports 2 0 0 2 0
BiocGenerics Imports 5 0 0 4 0
Biobase Imports 12 0 0 5 0
Matrix Imports 15 1 16 7 0
RcppEigen Imports 1 0 0 9 0
tidyselect Imports 1 0 0 9 0
scales Imports 3 0 0 15 0
tidyr Imports 1 0 0 22 0
SummarizedExperiment Imports 2 0 0 24 0
ggplot2 Imports 27 0 0 37 0
scRNAseq Suggests No object is imported into the namespace of destiny. 124 72
tidyverse Suggests No object is imported into the namespace of destiny. 107 46
scran Suggests No object is imported into the namespace of destiny. 58 27
org.Mm.eg.db Suggests No object is imported into the namespace of destiny. 45 19
rmarkdown Suggests No object is imported into the namespace of destiny. 27 10
rgl Suggests No object is imported into the namespace of destiny. 23 5
conflicted Suggests No object is imported into the namespace of destiny. 5 4
repr Suggests No object is imported into the namespace of destiny. 18 4
viridis Suggests No object is imported into the namespace of destiny. 39 2
FNN Suggests No object is imported into the namespace of destiny. 0 1
gridExtra Suggests No object is imported into the namespace of destiny. 5 1
igraph Suggests No object is imported into the namespace of destiny. 10 1
cowplot Suggests No object is imported into the namespace of destiny. 38 1
knitr Suggests No object is imported into the namespace of destiny. 12 0
testthat Suggests No object is imported into the namespace of destiny. 36 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 destiny Co-heaviness as Jaccard coeffcient
SummarizedExperiment SingleCellExperiment 14 0.933

Analysis was done with pkgndep.