Dependency analysis on package glmGamPoi

General information

Bioconductor link link
Package version1.8.0
Number of strong dependencies35
Number of all dependencies179
Number of parent packages13
Max heaviness from parent packages9
Total heaviness from parent packages18
Number of parent packages (including Suggests and Enhances)29
Max co-heaviness from parent packages ("SummarizedExperiment" and "HDF5Array")1

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports LinkingTo Suggests utils stats methods grDevices graphics grid tools stats4 parallel splines lattice Matrix MatrixGenerics matrixStats S4Vectors IRanges BiocGenerics DelayedArray Rcpp GenomicRanges Biobase GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops sparseMatrixStats rhdf5 rhdf5filters Rhdf5lib magrittr glue rlang pkgconfig digest R6 cli crayon ellipsis lifecycle fansi tibble pillar vctrs utf8 jsonlite yaml fastmap withr evaluate bslib htmltools jquerylib sass base64enc fs rappdirs SummarizedExperiment locfit futile.logger snow codetools BH lambda.r futile.options formatR highr stringr xfun stringi BiocManager SingleCellExperiment AnnotationDbi DBI RSQLite KEGGREST xtable httr bit64 blob memoise plogr png Biostrings curl mime openssl bit cachem askpass sys limma knitr tinytex RColorBrewer gtable isoband MASS mgcv scales nlme farver labeling munsell viridisLite colorspace BiocParallel AnnotationHub ExperimentHub BiocFileCache BiocVersion interactiveDisplayBase dplyr dbplyr filelock shiny DT generics tidyselect assertthat purrr httpuv fontawesome sourcetools later promises commonmark htmlwidgets crosstalk lazyeval profmem bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 scuttle edgeR igraph statmod DelayedMatrixStats BiocSingular bluster metapod dqrng beachmat ScaledMatrix irlba rsvd cluster BiocNeighbors sitmo RcppHNSW genefilter geneplotter ggplot2 RcppArmadillo annotate survival XML HDF5Array 0 1 2 3 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents matrixStats methods stats utils splines Rcpp BiocGenerics DelayedArray DelayedMatrixStats HDF5Array SummarizedExperiment RcppArmadillo beachmat statmod limma MASS zoo edgeR BiocParallel knitr bench rmarkdown BiocStyle testthat ggplot2 scran DESeq2 muscData TENxPBMCData In total 35 packages are required directly or indirectly (179) when installing 'glmGamPoi' (1.8.0) Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'glmGamPoi' 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 glmGamPoi.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on glmGamPoi
SummarizedExperiment Imports 1 0 0 24 9
HDF5Array Imports Parent package is listed in Imports of glmGamPoi but no object from parent package is imported. 19 4
DelayedMatrixStats Imports Parent package is listed in Imports of glmGamPoi but no object from parent package is imported. 17 2
splines Imports Parent package is listed in Imports of glmGamPoi but no object from parent package is imported. 0 1
matrixStats Imports Parent package is listed in Imports of glmGamPoi but no object from parent package is imported. 0 0
methods Imports 3 0 0 0 0
stats Imports The whole set of functions/methods/classes from parent package is imported to the namespace of glmGamPoi. 0 0
utils Imports 1 0 0 0 0
Rcpp Imports The whole set of functions/methods/classes from parent package is imported to the namespace of glmGamPoi. 2 0
BiocGenerics Imports 2 0 0 4 0
DelayedArray Imports Parent package is listed in Imports of glmGamPoi but no object from parent package is imported. 14 0
RcppArmadillo LinkingTo Parent package is listed in LinkingTo of glmGamPoi but no object from parent package is imported. 4 1
beachmat LinkingTo Parent package is listed in LinkingTo of glmGamPoi but no object from parent package is imported. 16 1
muscData Suggests No object is imported into the namespace of glmGamPoi. 96 71
TENxPBMCData Suggests No object is imported into the namespace of glmGamPoi. 100 71
DESeq2 Suggests No object is imported into the namespace of glmGamPoi. 93 66
testthat Suggests No object is imported into the namespace of glmGamPoi. 36 31
scran Suggests No object is imported into the namespace of glmGamPoi. 58 30
ggplot2 Suggests No object is imported into the namespace of glmGamPoi. 37 29
BiocStyle Suggests No object is imported into the namespace of glmGamPoi. 30 26
rmarkdown Suggests No object is imported into the namespace of glmGamPoi. 27 23
bench Suggests No object is imported into the namespace of glmGamPoi. 18 15
BiocParallel Suggests No object is imported into the namespace of glmGamPoi. 11 9
knitr Suggests No object is imported into the namespace of glmGamPoi. 12 9
edgeR Suggests No object is imported into the namespace of glmGamPoi. 10 3
statmod Suggests No object is imported into the namespace of glmGamPoi. 2 1
limma Suggests No object is imported into the namespace of glmGamPoi. 5 1
MASS Suggests No object is imported into the namespace of glmGamPoi. 5 1
zoo Suggests No object is imported into the namespace of glmGamPoi. 6 1

Analysis was done with pkgndep.