Dependency analysis on package monocle

General information

Bioconductor link link
Package version2.24.0
Number of strong dependencies83
Number of all dependencies257
Number of parent packages34
Max heaviness from parent packages8
Total heaviness from parent packages33
Number of parent packages (including Suggests and Enhances)40
Max co-heaviness from parent packages ("viridis" and "ggplot2")6

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats graphics grDevices grid tools splines stats4 parallel magrittr glue lattice Matrix pkgconfig rlang lifecycle R6 ellipsis fansi pillar vctrs cli crayon utf8 tibble Rcpp digest gtable scales withr farver labeling munsell RColorBrewer viridisLite colorspace isoband MASS mgcv nlme stringi stringr ggplot2 BiocGenerics irlba RcppEigen BH bitops gridExtra Biobase RCurl generics tidyselect purrr plyr igraph slam sparsesvd docopt graph RBGL XML RUnit BiocManager evaluate yaml jsonlite highr xfun rprojroot rstudioapi data.table survival matrixStats brio callr desc pkgload praise processx ps waldo diffobj rematch2 nnet knitr foreign backports cluster rpart viridis htmltools base64enc png htmlwidgets fastmap SummarizedExperiment SingleCellExperiment RcppHNSW MatrixGenerics GenomicRanges S4Vectors IRanges GenomeInfoDb DelayedArray XVector GenomeInfoDbData zlibbioc ggrepel Rtsne codetools RSpectra tidyr dplyr cpp11 sp abind lmtest zoo curl Formula latticeExtra htmlTable jpeg checkmate scuttle DelayedMatrixStats beachmat BiocNeighbors BiocSingular BiocParallel ggbeeswarm RcppML sparseMatrixStats ScaledMatrix rsvd futile.logger snow beeswarm vipor lambda.r futile.options formatR pcaMethods ggplot.multistats ggthemes VIM knn.covertree proxy smoother scatterplot3d hexbin car robustbase vcd e1071 laeken ranger TTR carData pbkrtest quantreg maptools lme4 DEoptimR class boot xts broom numDeriv SparseM MatrixModels minqa nloptr testthat cowplot fitdistrplus future future.apply ggridges httr ica KernSmooth leiden miniUI patchwork pbapply plotly RANN RcppAnnoy reticulate ROCR scattermore sctransform SeuratObject shiny spatstat.core spatstat.geom uwot RcppProgress globals listenv parallelly mime openssl lazyeval crosstalk promises RcppTOML here rappdirs gplots reshape2 RcppArmadillo progressr rgeos httpuv xtable fontawesome sourcetools later commonmark bslib cachem spatstat.data spatstat.random spatstat.utils spatstat.sparse tensor goftest deldir polyclip FNN dqrng askpass gtools caTools sass jquerylib sitmo sys fs 0 10 20 Imported methods 0 50 100 150 Required packages 0 20 40 60 80 Heaviness from parents methods VGAM Biobase Matrix DDRTree ggplot2 parallel HSMMSingleCell combinat fastICA grid matrixStats stats RANN slam proxy Rcpp plyr BiocGenerics cluster Rtsne MASS limma stringr irlba igraph reshape2 leidenbase qlcMatrix tibble biocViews pheatmap dplyr viridis knitr testthat Hmisc scater destiny Seurat In total 83 packages are required directly or indirectly (257) when installing 'monocle' (2.24.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'monocle' Imported functions The whole namespace is imported Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on monocle
DDRTree Depends The whole set of functions/methods/classes from parent package is imported to the namespace of monocle. 12 2
VGAM Depends The whole set of functions/methods/classes from parent package is imported to the namespace of monocle. 4 1
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of monocle. 0 0
Biobase Depends 11 0 0 5 0
Matrix Depends The whole set of functions/methods/classes from parent package is imported to the namespace of monocle. 7 0
ggplot2 Depends 1 0 0 37 0
biocViews Imports Parent package is listed in Imports of monocle but no object from parent package is imported. 16 8
dplyr Imports 11 0 0 20 4
qlcMatrix Imports 1 0 0 11 3
viridis Imports 1 0 0 39 2
parallel Imports 10 0 0 0 1
HSMMSingleCell Imports The whole set of functions/methods/classes from parent package is imported to the namespace of monocle. 0 1
combinat Imports 1 0 0 0 1
fastICA Imports 2 0 0 0 1
matrixStats Imports 1 0 0 0 1
RANN Imports 1 0 0 0 1
proxy Imports Parent package is listed in Imports of monocle but no object from parent package is imported. 2 1
cluster Imports 1 0 0 4 1
Rtsne Imports The whole set of functions/methods/classes from parent package is imported to the namespace of monocle. 4 1
limma Imports 1 0 0 5 1
reshape2 Imports 2 0 0 10 1
leidenbase Imports 1 0 0 11 1
pheatmap Imports The whole set of functions/methods/classes from parent package is imported to the namespace of monocle. 18 1
grid Imports The whole set of functions/methods/classes from parent package is imported to the namespace of monocle. 0 0
stats Imports 20 0 0 0 0
slam Imports The whole set of functions/methods/classes from parent package is imported to the namespace of monocle. 1 0
Rcpp Imports Parent package is listed in Imports of monocle but no object from parent package is imported. 2 0
plyr Imports 2 0 0 3 0
BiocGenerics Imports 4 0 0 4 0
MASS Imports Parent package is listed in Imports of monocle but no object from parent package is imported. 5 0
stringr Imports 4 0 0 7 0
irlba Imports The whole set of functions/methods/classes from parent package is imported to the namespace of monocle. 8 0
igraph Imports 28 0 0 10 0
tibble Imports 1 0 0 15 0
Seurat Suggests No object is imported into the namespace of monocle. 145 87
destiny Suggests No object is imported into the namespace of monocle. 130 75
scater Suggests No object is imported into the namespace of monocle. 85 33
Hmisc Suggests No object is imported into the namespace of monocle. 67 24
testthat Suggests No object is imported into the namespace of monocle. 36 15
knitr Suggests No object is imported into the namespace of monocle. 12 5

Analysis was done with pkgndep.