Dependency analysis on package Seurat

General information

CRAN link link
Package version4.1.1
Number of strong dependencies145
Number of all dependencies266
Number of parent packages50
Max heaviness from parent packages8
Total heaviness from parent packages52
Number of parent packages (including Suggests and Enhances)73
Max co-heaviness from parent packages ("miniUI" and "shiny")11

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports LinkingTo Suggests utils methods stats graphics grDevices grid tools splines parallel stats4 lattice Matrix R6 magrittr rlang Rcpp digest glue lifecycle crayon pkgconfig ellipsis withr MASS fansi pillar vctrs cli utf8 nlme tibble farver labeling munsell RColorBrewer viridisLite colorspace mgcv gtable scales isoband ggplot2 jsonlite bitops codetools matrixStats mime globals listenv parallelly curl openssl askpass sys survival png rappdirs BH fastmap plyr dplyr purrr tidyselect generics future rprojroot RcppEigen htmltools xtable later promises cachem base64enc reshape2 RcppArmadillo stringr stringi httr zoo spatstat.data spatstat.utils deldir polyclip RcppTOML here irlba igraph abind future.apply httpuv fontawesome sourcetools commonmark bslib sass jquerylib fs gridExtra data.table yaml cpp11 gplots gtools caTools KernSmooth FNN RSpectra RcppAnnoy RcppProgress dqrng sitmo reticulate spatstat.geom spatstat.random rpart spatstat.sparse tensor goftest progressr sp rgeos shiny htmlwidgets tidyr lazyeval crosstalk BiocGenerics S4Vectors RCurl IRanges GenomeInfoDbData Biobase GenomeInfoDb XVector zlibbioc MatrixGenerics GenomicRanges DelayedArray SummarizedExperiment XML bit64 bit RANN BiocParallel futile.logger snow lambda.r futile.options formatR Biostrings rjson Rfast RcppZiggurat RcppGSL kernlab segmented brio callr desc evaluate pkgload praise processx ps waldo rstudioapi diffobj rematch2 Rsamtools GenomicAlignments BiocIO restfulr Rhtslib Cairo ggbeeswarm ragg beeswarm vipor systemfonts textshaping Rdpack TFisher mutoss mathjaxr qqconf rbibutils sn mvtnorm plotrix multtest multcomp robustbase mnormt numDeriv quantreg TH.data sandwich DEoptimR SparseM MatrixModels SingleCellExperiment progress hms prettyunits VGAM DDRTree HSMMSingleCell cluster combinat fastICA Rtsne leidenbase limma qlcMatrix pheatmap proxy slam viridis biocViews sparsesvd docopt graph RBGL RUnit BiocManager genefilter locfit geneplotter AnnotationDbi annotate DBI RSQLite KEGGREST blob memoise plogr 0 20 40 60 80 Imported methods 0 20 40 60 80 Required packages 0 10 20 30 Heaviness from parents methods graphics grDevices grid ica matrixStats png RANN RColorBrewer stats tools utils jsonlite KernSmooth pbapply rlang Rcpp RcppAnnoy cluster Rtsne MASS lmtest Matrix future irlba future.apply httr igraph ROCR fitdistrplus spatstat.geom scales tibble reticulate uwot leiden spatstat.core SeuratObject shiny miniUI ggplot2 cowplot patchwork scattermore ggrepel ggridges sctransform plotly RcppProgress RcppEigen BiocGenerics VGAM Biobase limma hdf5r S4Vectors IRanges rsvd ape GenomeInfoDb Rfast2 mixtools GenomicRanges SummarizedExperiment SingleCellExperiment testthat rtracklayer enrichR ggrastr metap MAST monocle DESeq2 In total 145 packages are required directly or indirectly (266) when installing 'Seurat' (4.1.1) Depends Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'Seurat' 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 Seurat.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on Seurat
methods Depends 14 0 0 0 0
plotly Imports 4 0 0 63 8
spatstat.core Imports 1 0 0 22 7
uwot Imports 2 0 0 18 6
sctransform Imports 4 0 0 58 6
ROCR Imports 2 0 0 10 5
SeuratObject Imports 60 0 8 23 4
lmtest Imports 1 0 0 7 2
fitdistrplus Imports 1 0 0 11 2
ica Imports 3 0 0 0 1
RANN Imports 1 0 0 0 1
pbapply Imports 3 0 0 1 1
cluster Imports 1 0 0 4 1
Rtsne Imports 1 0 0 4 1
leiden Imports 1 0 0 20 1
miniUI Imports 5 0 0 35 1
cowplot Imports 3 0 0 38 1
patchwork Imports 1 0 0 38 1
scattermore Imports 1 0 0 38 1
ggrepel Imports 2 0 0 39 1
ggridges Imports 2 0 0 40 1
graphics Imports 8 0 0 0 0
grDevices Imports 4 0 0 0 0
grid Imports 11 0 0 0 0
matrixStats Imports 4 0 0 0 0
png Imports 1 0 0 0 0
RColorBrewer Imports 2 0 0 0 0
stats Imports 36 0 0 0 0
tools Imports 1 0 0 0 0
utils Imports 16 0 0 0 0
jsonlite Imports 1 0 0 1 0
KernSmooth Imports 1 0 0 1 0
rlang Imports 3 0 0 1 0
Rcpp Imports 1 0 0 2 0
RcppAnnoy Imports 4 0 0 3 0
MASS Imports 2 0 0 5 0
Matrix Imports 11 1 1 7 0
future Imports 2 0 0 8 0
irlba Imports 1 0 0 8 0
future.apply Imports 2 0 0 9 0
httr Imports 7 0 0 9 0
igraph Imports 5 0 0 10 0
spatstat.geom Imports 1 0 0 12 0
scales Imports 5 0 0 15 0
tibble Imports 1 0 0 15 0
reticulate Imports 3 0 0 16 0
shiny Imports 19 0 0 34 0
ggplot2 Imports 89 0 0 37 0
RcppProgress LinkingTo Parent package is listed in LinkingTo of Seurat but no object from parent package is imported. 0 0
RcppEigen LinkingTo Parent package is listed in LinkingTo of Seurat but no object from parent package is imported. 9 0
DESeq2 Suggests No object is imported into the namespace of Seurat. 93 36
rtracklayer Suggests No object is imported into the namespace of Seurat. 44 29
monocle Suggests No object is imported into the namespace of Seurat. 83 25
metap Suggests No object is imported into the namespace of Seurat. 56 24
MAST Suggests No object is imported into the namespace of Seurat. 67 19
SingleCellExperiment Suggests No object is imported into the namespace of Seurat. 25 15
SummarizedExperiment Suggests No object is imported into the namespace of Seurat. 24 14
testthat Suggests No object is imported into the namespace of Seurat. 36 13
GenomicRanges Suggests No object is imported into the namespace of Seurat. 15 10
ggrastr Suggests No object is imported into the namespace of Seurat. 47 8
GenomeInfoDb Suggests No object is imported into the namespace of Seurat. 11 7
IRanges Suggests No object is imported into the namespace of Seurat. 7 4
Rfast2 Suggests No object is imported into the namespace of Seurat. 11 4
hdf5r Suggests No object is imported into the namespace of Seurat. 6 3
S4Vectors Suggests No object is imported into the namespace of Seurat. 6 3
mixtools Suggests No object is imported into the namespace of Seurat. 14 3
VGAM Suggests No object is imported into the namespace of Seurat. 4 2
Biobase Suggests No object is imported into the namespace of Seurat. 5 2
enrichR Suggests No object is imported into the namespace of Seurat. 47 2
BiocGenerics Suggests No object is imported into the namespace of Seurat. 4 1
limma Suggests No object is imported into the namespace of Seurat. 5 1
rsvd Suggests No object is imported into the namespace of Seurat. 8 1
ape Suggests No object is imported into the namespace of Seurat. 11 1

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 Seurat Co-heaviness as Jaccard coeffcient
shiny miniUI 11 0.917

Analysis was done with pkgndep.