Dependency analysis on package diffcyt

General information

Bioconductor link link
Package version1.16.0
Number of strong dependencies210
Number of all dependencies282
Number of parent packages20
Max heaviness from parent packages103
Total heaviness from parent packages120
Number of parent packages (including Suggests and Enhances)26
Max co-heaviness from parent packages ("FlowSOM" and "lme4")22

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats grDevices graphics tools grid stats4 splines parallel tcltk magrittr glue rlang R6 crayon digest BiocGenerics Rcpp lattice pkgconfig tibble lifecycle vctrs pillar ellipsis fansi cli utf8 jsonlite evaluate stringr stringi Matrix matrixStats S4Vectors yaml Biobase generics tidyselect purrr IRanges withr base64enc highr xfun colorspace MASS cytolib RcppArmadillo BH RProtoBufLib RcppParallel Rhdf5lib dplyr DelayedArray zlibbioc MatrixGenerics RCurl bitops png brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 knitr GlobalOptions shape locfit plyr mvtnorm survival codetools cpp11 GenomicRanges GenomeInfoDb XVector GenomeInfoDbData RColorBrewer cluster clue RcppEigen nlme boot minqa nloptr testthat flowCore curl httr mime openssl askpass sys TH.data sandwich zoo circlize GetoptLong foreach doParallel rjson iterators igraph colorRamps ConsensusClusterPlus CytoML flowWorkspace ggforce ggnewscale ggplot2 ggpointdensity ggpubr ggrepel pheatmap Rtsne tidyr XML scattermore ALL openCyto data.table RBGL Rgraphviz graph ggcyto corpcor RUnit xml2 latticeExtra scales aws.s3 aws.signature ncdfFlow tweenr gtable polyclip isoband mgcv ggsci cowplot ggsignif gridExtra polynom rstatix gtools flowViz flowStats flowClust ks rrcov R.utils hexbin jpeg farver labeling munsell viridisLite broom corrplot car KernSmooth IDPmisc fda mnormt FNN kernlab mclust multicool plot3D pracma robustbase pcaPP R.oo R.methodsS3 backports carData abind nnet pbkrtest quantreg maptools lme4 fds deSolve misc3d DEoptimR numDeriv SparseM MatrixModels sp foreign rainbow hdrcde ash limma htmltools jquerylib bslib fastmap sass fs rappdirs tinytex BiocManager SummarizedExperiment bookdown rmarkdown ExperimentHub 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 SingleCellExperiment ComplexHeatmap drc FlowSOM ggridges nnls reshape2 scater multcomp plotrix scuttle DelayedMatrixStats beachmat BiocNeighbors BiocSingular BiocParallel ggbeeswarm viridis RcppML sparseMatrixStats RcppHNSW ScaledMatrix irlba rsvd futile.logger snow beeswarm vipor lambda.r futile.options formatR 0 2 4 6 8 Imported methods 0 100 200 Required packages 0 50 100 Heaviness from parents magrittr stats methods utils grDevices graphics grid limma S4Vectors circlize edgeR reshape2 multcomp flowCore dplyr tidyr SummarizedExperiment ComplexHeatmap lme4 FlowSOM knitr rmarkdown BiocStyle testthat HDCytoData CATALYST In total 210 packages are required directly or indirectly (282) when installing 'diffcyt' (1.16.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'diffcyt' Imported functions


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on diffcyt
FlowSOM Imports 4 0 0 187 103
ComplexHeatmap Imports 7 0 0 28 6
SummarizedExperiment Imports 8 0 0 24 5
multcomp Imports 1 0 0 16 4
edgeR Imports 6 0 0 10 1
reshape2 Imports 2 0 0 10 1
magrittr Imports 1 0 0 0 0
stats Imports 6 0 0 0 0
methods Imports 2 0 0 0 0
utils Imports 1 0 0 0 0
grDevices Imports 2 0 0 0 0
graphics Imports 1 0 0 0 0
grid Imports 1 0 0 0 0
limma Imports 7 0 0 5 0
S4Vectors Imports 3 0 0 6 0
circlize Imports 1 0 0 9 0
flowCore Imports 3 0 0 17 0
dplyr Imports 3 0 0 20 0
tidyr Imports 1 0 0 22 0
lme4 Imports 2 0 0 49 0
HDCytoData Suggests No object is imported into the namespace of diffcyt. 102 40
CATALYST Suggests No object is imported into the namespace of diffcyt. 235 28
BiocStyle Suggests No object is imported into the namespace of diffcyt. 30 12
rmarkdown Suggests No object is imported into the namespace of diffcyt. 27 9
knitr Suggests No object is imported into the namespace of diffcyt. 12 0
testthat Suggests No object is imported into the namespace of diffcyt. 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 diffcyt Co-heaviness as Jaccard coeffcient
lme4 FlowSOM 22 0.176

Analysis was done with pkgndep.