Dependency analysis on package muscData

General information

Bioconductor link link
Package version1.10.0
Number of strong dependencies96
Number of all dependencies281
Number of parent packages3
Max heaviness from parent packages70
Total heaviness from parent packages79
Number of parent packages (including Suggests and Enhances)18
Max co-heaviness from parent packages ("ExperimentHub" and "SingleCellExperiment")16

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils grDevices stats tools graphics grid stats4 parallel splines glue magrittr R6 rlang pkgconfig lifecycle tibble vctrs pillar cli crayon ellipsis fansi utf8 BiocGenerics Biobase bitops lattice S4Vectors IRanges XVector GenomeInfoDb zlibbioc RCurl GenomeInfoDbData Matrix matrixStats yaml Rcpp jsonlite generics tidyselect purrr digest SummarizedExperiment GenomicRanges DelayedArray MatrixGenerics dplyr withr fastmap curl rappdirs htmltools bslib jquerylib base64enc sass fs httr bit64 mime openssl bit cachem png xtable askpass sys BiocManager RSQLite AnnotationDbi DBI blob memoise plogr KEGGREST shiny Biostrings httpuv fontawesome sourcetools later promises commonmark htmlwidgets crosstalk lazyeval AnnotationHub BiocFileCache BiocVersion interactiveDisplayBase dbplyr filelock DT assertthat stringr stringi xfun evaluate highr cpp11 data.table SingleCellExperiment BH codetools R.oo R.methodsS3 hms progress prettyunits knitr limma tidyr plyr BiocParallel DelayedMatrixStats beachmat scuttle futile.logger snow sparseMatrixStats lambda.r futile.options formatR ggplot2 scales colorspace RColorBrewer gtable isoband MASS mgcv nlme RcppEigen farver labeling munsell viridisLite gridExtra Rtsne ggrepel irlba tinytex R.utils edgeR dqrng locfit sitmo viridis BiocNeighbors BiocSingular ggbeeswarm RcppML RcppHNSW ScaledMatrix rsvd beeswarm vipor sctransform RcppArmadillo future.apply future reshape2 gplots cluster survival globals listenv parallelly gtools caTools KernSmooth rprojroot cellranger rematch bookdown rmarkdown readr xml2 clipr vroom tzdb xgboost pROC HDF5Array rhdf5 Rhdf5lib rhdf5filters cowplot fitdistrplus ggridges ica igraph leiden lmtest miniUI patchwork pbapply plotly RANN RcppAnnoy reticulate ROCR scattermore SeuratObject spatstat.core spatstat.geom uwot RcppProgress zoo RcppTOML here progressr sp rgeos spatstat.data spatstat.random rpart spatstat.utils spatstat.sparse abind tensor goftest deldir polyclip FNN RSpectra blme ComplexHeatmap DESeq2 glmmTMB lmerTest lme4 scater variancePartition circlize GetoptLong clue GlobalOptions foreach doParallel genefilter geneplotter TMB numDeriv boot minqa nloptr pbkrtest iterators RhpcBLASctl aod Rdpack shape rjson annotate testthat broom rbibutils XML brio callr desc pkgload praise processx ps waldo backports rstudioapi diffobj rematch2 0 0.5 1 Imported methods 0 50 100 150 Required packages 0 50 100 Heaviness from parents SingleCellExperiment ExperimentHub utils matrixStats methods R.utils Matrix knitr dplyr readxl rmarkdown BiocStyle GEOquery scds DropletUtils scater Seurat muscat In total 96 packages are required directly or indirectly (281) when installing 'muscData' (1.10.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'muscData' Imported functions Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on muscData
ExperimentHub Depends 1 0 0 86 70
SingleCellExperiment Depends Parent package is listed in Depends of muscData but no object from parent package is imported. 25 9
utils Imports 1 0 0 0 0
muscat Suggests No object is imported into the namespace of muscData. 187 119
Seurat Suggests No object is imported into the namespace of muscData. 145 85
scater Suggests No object is imported into the namespace of muscData. 85 43
DropletUtils Suggests No object is imported into the namespace of muscData. 52 26
GEOquery Suggests No object is imported into the namespace of muscData. 45 16
BiocStyle Suggests No object is imported into the namespace of muscData. 30 10
rmarkdown Suggests No object is imported into the namespace of muscData. 27 8
readxl Suggests No object is imported into the namespace of muscData. 23 7
knitr Suggests No object is imported into the namespace of muscData. 12 6
scds Suggests No object is imported into the namespace of muscData. 50 5
R.utils Suggests No object is imported into the namespace of muscData. 5 3
matrixStats Suggests No object is imported into the namespace of muscData. 0 0
methods Suggests No object is imported into the namespace of muscData. 0 0
Matrix Suggests No object is imported into the namespace of muscData. 7 0
dplyr Suggests No object is imported into the namespace of muscData. 20 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 muscData Co-heaviness as Jaccard coeffcient
SingleCellExperiment ExperimentHub 16 0.168

Analysis was done with pkgndep.