Dependency analysis on package CATALYST

General information

Bioconductor link link
Package version1.20.1
Number of strong dependencies235
Number of all dependencies256
Number of parent packages31
Max heaviness from parent packages69
Total heaviness from parent packages106
Number of parent packages (including Suggests and Enhances)40
Max co-heaviness from parent packages ("FlowSOM" and "drc")42

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats grDevices graphics grid tools stats4 splines parallel tcltk magrittr glue rlang R6 lattice digest Matrix colorspace lifecycle crayon Rcpp RColorBrewer tibble ellipsis fansi pillar pkgconfig vctrs cli utf8 BiocGenerics gtable farver labeling munsell viridisLite withr scales isoband MASS mgcv nlme S4Vectors Biobase matrixStats ggplot2 IRanges jsonlite DelayedArray MatrixGenerics zlibbioc BH stringr stringi generics tidyselect purrr evaluate base64enc RCurl bitops plyr cytolib RcppArmadillo RProtoBufLib RcppParallel Rhdf5lib png dplyr highr yaml xfun cluster RcppEigen knitr flowCore XML data.table RBGL Rgraphviz graph xml2 latticeExtra aws.s3 aws.signature ncdfFlow jpeg curl httr mime openssl askpass sys GenomicRanges GenomeInfoDb XVector GenomeInfoDbData clue codetools gridExtra gtools mvtnorm brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 flowWorkspace hexbin FNN SummarizedExperiment GlobalOptions shape ALL ggrepel Rtsne car carData abind nnet pbkrtest quantreg maptools lme4 survival broom numDeriv SparseM MatrixModels sp foreign boot minqa nloptr backports tidyr testthat cpp11 corpcor flowViz flowStats flowClust ks rrcov R.utils KernSmooth IDPmisc fda mnormt kernlab mclust multicool plot3D pracma robustbase pcaPP R.oo R.methodsS3 fds deSolve misc3d DEoptimR rainbow hdrcde locfit ash circlize GetoptLong foreach doParallel rjson iterators irlba multcomp TH.data sandwich zoo igraph colorRamps ConsensusClusterPlus CytoML ggforce ggnewscale ggpointdensity ggpubr pheatmap scattermore openCyto ggcyto RUnit tweenr polyclip ggsci cowplot ggsignif polynom rstatix corrplot SingleCellExperiment scuttle DelayedMatrixStats beachmat BiocNeighbors BiocSingular BiocParallel ggbeeswarm viridis RcppML sparseMatrixStats RcppHNSW ScaledMatrix rsvd futile.logger snow beeswarm vipor lambda.r futile.options formatR plotrix htmltools jquerylib tinytex bslib fastmap sass fs rappdirs RSpectra RcppAnnoy RcppProgress dqrng sitmo bookdown rmarkdown BiocManager FlowSOM limma edgeR reshape2 ComplexHeatmap 0 5 10 15 Imported methods 0 100 200 Required packages 0 20 40 60 Heaviness from parents SingleCellExperiment graphics grDevices grid magrittr matrixStats methods nnls RColorBrewer stats data.table purrr Rtsne gridExtra S4Vectors Matrix circlize ConsensusClusterPlus reshape2 scales flowCore dplyr SummarizedExperiment ComplexHeatmap ggplot2 cowplot ggrepel ggridges scater drc FlowSOM knitr uwot rmarkdown BiocStyle testthat flowWorkspace ggcyto openCyto diffcyt In total 235 packages are required directly or indirectly (256) when installing 'CATALYST' (1.20.1) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'CATALYST' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on CATALYST
SingleCellExperiment Depends 10 0 0 25 0
FlowSOM Imports 2 0 0 187 69
scater Imports 10 0 0 85 22
ComplexHeatmap Imports 4 0 0 28 6
drc Imports 2 0 0 96 6
nnls Imports 1 0 0 0 1
reshape2 Imports 1 0 0 10 1
ggridges Imports 2 0 0 40 1
graphics Imports 2 0 0 0 0
grDevices Imports 5 0 0 0 0
grid Imports 3 0 0 0 0
magrittr Imports 2 0 0 0 0
matrixStats Imports 9 0 0 0 0
methods Imports 3 0 0 0 0
RColorBrewer Imports 1 0 0 0 0
stats Imports 15 0 0 0 0
data.table Imports 1 0 0 1 0
purrr Imports 2 0 0 3 0
Rtsne Imports 1 0 0 4 0
gridExtra Imports 1 0 0 5 0
S4Vectors Imports 3 0 0 6 0
Matrix Imports 5 0 0 7 0
circlize Imports 1 0 0 9 0
ConsensusClusterPlus Imports The whole set of functions/methods/classes from parent package is imported to the namespace of CATALYST. 9 0
scales Imports 1 0 0 15 0
flowCore Imports 16 0 0 17 0
dplyr Imports 17 0 0 20 0
SummarizedExperiment Imports 8 0 0 24 0
ggplot2 Imports The whole set of functions/methods/classes from parent package is imported to the namespace of CATALYST. 37 0
cowplot Imports 2 0 0 38 0
ggrepel Imports 2 0 0 39 0
BiocStyle Suggests No object is imported into the namespace of CATALYST. 30 12
rmarkdown Suggests No object is imported into the namespace of CATALYST. 27 9
uwot Suggests No object is imported into the namespace of CATALYST. 18 6
diffcyt Suggests No object is imported into the namespace of CATALYST. 210 3
knitr Suggests No object is imported into the namespace of CATALYST. 12 0
testthat Suggests No object is imported into the namespace of CATALYST. 36 0
flowWorkspace Suggests No object is imported into the namespace of CATALYST. 80 0
ggcyto Suggests No object is imported into the namespace of CATALYST. 84 0
openCyto Suggests No object is imported into the namespace of CATALYST. 120 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 CATALYST Co-heaviness as Jaccard coeffcient
drc FlowSOM 42 0.359

Analysis was done with pkgndep.