Dependency analysis on package HDCytoData

General information

Bioconductor link link
Package version1.16.0
Number of strong dependencies102
Number of all dependencies241
Number of parent packages5
Max heaviness from parent packages69
Total heaviness from parent packages83
Number of parent packages (including Suggests and Enhances)13
Max co-heaviness from parent packages ("ExperimentHub" and "SummarizedExperiment")8

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils stats methods grDevices graphics tools stats4 grid splines parallel tcltk glue magrittr Rcpp yaml jsonlite R6 rlang digest BiocGenerics S4Vectors Biobase Matrix lattice rappdirs withr base64enc matrixStats IRanges zlibbioc RCurl bitops pkgconfig openssl lifecycle tibble vctrs pillar cli png htmltools crayon fastmap bslib ellipsis jquerylib askpass fansi utf8 sass sys fs cytolib RcppArmadillo BH RProtoBufLib RcppParallel Rhdf5lib XVector GenomeInfoDb GenomeInfoDbData MatrixGenerics DelayedArray BiocManager curl httr dplyr mime generics tidyselect purrr GenomicRanges AnnotationHub BiocFileCache RSQLite BiocVersion AnnotationDbi interactiveDisplayBase dbplyr DBI filelock bit64 blob memoise plogr KEGGREST shiny DT assertthat bit cachem Biostrings httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk lazyeval xfun evaluate highr stringr stringi knitr RcppEigen rprojroot tinytex gtable isoband MASS mgcv scales nlme farver labeling munsell RColorBrewer viridisLite colorspace reticulate RSpectra RcppTOML here bookdown rmarkdown igraph colorRamps ConsensusClusterPlus CytoML flowCore flowWorkspace ggforce ggnewscale ggplot2 ggpointdensity ggpubr ggrepel pheatmap Rtsne tidyr XML scattermore ALL cluster openCyto data.table RBGL Rgraphviz graph plyr ggcyto corpcor RUnit xml2 latticeExtra aws.s3 aws.signature ncdfFlow tweenr polyclip ggsci cowplot ggsignif gridExtra polynom rstatix cpp11 gtools flowViz flowStats flowClust clue ks rrcov R.utils hexbin jpeg broom corrplot car KernSmooth IDPmisc fda mnormt FNN kernlab mclust multicool mvtnorm plot3D pracma robustbase pcaPP R.oo R.methodsS3 backports carData abind nnet pbkrtest quantreg maptools lme4 fds deSolve misc3d DEoptimR numDeriv SparseM MatrixModels survival sp foreign boot minqa nloptr rainbow testthat hdrcde brio callr desc pkgload praise processx ps waldo locfit ash rstudioapi diffobj rematch2 0 2 4 6 Imported methods 0 50 100 150 Required packages 0 50 100 Heaviness from parents flowCore SummarizedExperiment ExperimentHub utils methods Rtsne mclust knitr umap rmarkdown BiocStyle ggplot2 FlowSOM In total 102 packages are required directly or indirectly (241) when installing 'HDCytoData' (1.16.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'HDCytoData' Imported functions


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on HDCytoData
ExperimentHub Depends 1 0 0 86 69
flowCore Depends 6 0 0 17 7
SummarizedExperiment Depends 1 0 0 24 7
utils Imports 3 0 0 0 0
methods Imports 1 0 0 0 0
FlowSOM Suggests No object is imported into the namespace of HDCytoData. 187 130
ggplot2 Suggests No object is imported into the namespace of HDCytoData. 37 14
BiocStyle Suggests No object is imported into the namespace of HDCytoData. 30 10
rmarkdown Suggests No object is imported into the namespace of HDCytoData. 27 8
umap Suggests No object is imported into the namespace of HDCytoData. 22 7
knitr Suggests No object is imported into the namespace of HDCytoData. 12 6
Rtsne Suggests No object is imported into the namespace of HDCytoData. 4 1
mclust Suggests No object is imported into the namespace of HDCytoData. 4 1

Analysis was done with pkgndep.