Dependency analysis on package scran

General information

Bioconductor link link
Package version1.24.0
Number of strong dependencies58
Number of all dependencies222
Number of parent packages23
Max heaviness from parent packages4
Total heaviness from parent packages15
Number of parent packages (including Suggests and Enhances)37
Max co-heaviness from parent packages ("bluster" and "igraph")3

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports LinkingTo Suggests methods utils stats graphics grDevices grid stats4 tools parallel splines lattice BiocGenerics Matrix S4Vectors matrixStats MatrixGenerics IRanges DelayedArray Rcpp magrittr BH Biobase RCurl bitops futile.logger snow codetools lambda.r futile.options formatR pkgconfig GenomicRanges GenomeInfoDb XVector GenomeInfoDbData zlibbioc BiocParallel SummarizedExperiment SingleCellExperiment beachmat sparseMatrixStats irlba DelayedMatrixStats limma locfit cluster igraph BiocNeighbors RcppHNSW ScaledMatrix rsvd sitmo glue R6 rlang digest lifecycle stringr stringi jsonlite cli crayon ellipsis withr fansi tibble pillar vctrs utf8 evaluate yaml RColorBrewer gtable scales farver labeling munsell viridisLite colorspace fastmap xfun highr htmltools jquerylib bslib base64enc sass fs rappdirs BiocManager XML ggplot2 isoband MASS mgcv nlme knitr tinytex dplyr generics tidyselect purrr Rtsne viridis RcppEigen gridExtra AnnotationDbi curl RSQLite httr DBI KEGGREST Biostrings bit64 blob memoise plogr mime openssl png bit cachem xtable askpass sys rhdf5 rhdf5filters Rhdf5lib bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 VGAM DDRTree HSMMSingleCell plyr combinat fastICA reshape2 leidenbase qlcMatrix pheatmap proxy slam biocViews RANN sparsesvd docopt graph RBGL RUnit scuttle BiocSingular ggbeeswarm RcppML ggrepel beeswarm vipor genefilter geneplotter RcppArmadillo annotate survival ExperimentHub AnnotationHub ensembldb GenomicFeatures BiocFileCache BiocVersion interactiveDisplayBase AnnotationFilter rtracklayer Rsamtools ProtGenerics BiocIO biomaRt dbplyr filelock shiny DT lazyeval GenomicAlignments restfulr Rhtslib progress xml2 assertthat httpuv fontawesome sourcetools later promises commonmark htmlwidgets crosstalk rjson hms prettyunits 0 10 20 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents SingleCellExperiment scuttle stats methods utils Rcpp statmod metapod BiocGenerics limma dqrng S4Vectors Matrix edgeR igraph BiocParallel DelayedArray beachmat DelayedMatrixStats SummarizedExperiment bluster BiocSingular BH dynamicTreeCut Biobase knitr ResidualMatrix ScaledMatrix pheatmap HDF5Array rmarkdown BiocStyle testthat monocle scater DESeq2 scRNAseq In total 58 packages are required directly or indirectly (222) when installing 'scran' (1.24.0) 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 'scran' 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 scran.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on scran
scuttle Depends 18 0 0 39 1
SingleCellExperiment Depends 6 0 1 25 0
bluster Imports 5 0 0 27 4
BiocSingular Imports 4 0 0 29 4
dqrng Imports 1 0 0 5 2
edgeR Imports 14 0 0 10 2
statmod Imports 1 0 0 2 1
metapod Imports 3 0 0 3 1
stats Imports 22 0 0 0 0
methods Imports 3 0 0 0 0
utils Imports 2 0 0 0 0
Rcpp Imports 1 0 0 2 0
BiocGenerics Imports 4 0 0 4 0
limma Imports 12 0 0 5 0
S4Vectors Imports 11 1 2 6 0
Matrix Imports 5 0 2 7 0
igraph Imports 3 0 0 10 0
BiocParallel Imports 7 0 0 11 0
DelayedArray Imports 5 0 0 14 0
beachmat Imports 3 0 0 16 0
DelayedMatrixStats Imports 11 0 0 17 0
SummarizedExperiment Imports 5 0 0 24 0
BH LinkingTo Parent package is listed in LinkingTo of scran but no object from parent package is imported. 0 0
scRNAseq Suggests No object is imported into the namespace of scran. 124 87
monocle Suggests No object is imported into the namespace of scran. 83 60
DESeq2 Suggests No object is imported into the namespace of scran. 93 56
scater Suggests No object is imported into the namespace of scran. 85 38
testthat Suggests No object is imported into the namespace of scran. 36 29
BiocStyle Suggests No object is imported into the namespace of scran. 30 25
rmarkdown Suggests No object is imported into the namespace of scran. 27 22
pheatmap Suggests No object is imported into the namespace of scran. 18 13
knitr Suggests No object is imported into the namespace of scran. 12 8
HDF5Array Suggests No object is imported into the namespace of scran. 19 4
dynamicTreeCut Suggests No object is imported into the namespace of scran. 1 1
ResidualMatrix Suggests No object is imported into the namespace of scran. 15 1
Biobase Suggests No object is imported into the namespace of scran. 5 0
ScaledMatrix Suggests No object is imported into the namespace of scran. 15 0

Analysis was done with pkgndep.