Dependency analysis on package muscat

General information

Bioconductor link link
Package version1.10.0
Number of strong dependencies187
Number of all dependencies230
Number of parent packages29
Max heaviness from parent packages25
Total heaviness from parent packages75
Number of parent packages (including Suggests and Enhances)42
Max co-heaviness from parent packages ("scater" and "scuttle")4

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats grDevices graphics grid tools splines parallel stats4 glue magrittr rlang R6 lattice crayon lifecycle digest cli ellipsis pkgconfig vctrs fansi tibble pillar utf8 Matrix Rcpp withr nlme MASS colorspace RColorBrewer farver labeling munsell viridisLite jsonlite gtable isoband mgcv scales BiocGenerics ggplot2 evaluate bitops codetools IRanges matrixStats S4Vectors Biobase stringr stringi GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc yaml futile.logger snow BH lambda.r futile.options formatR generics tidyselect purrr GenomicRanges MatrixGenerics DelayedArray RcppEigen brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 fastmap xfun SummarizedExperiment BiocParallel gridExtra boot minqa nloptr testthat dplyr plyr highr limma png lme4 xtable mime cachem knitr locfit numDeriv RcppArmadillo reshape2 AnnotationDbi DBI RSQLite KEGGREST httr bit64 blob memoise plogr Biostrings curl openssl bit askpass sys caTools hms prettyunits foreach doParallel iterators SingleCellExperiment DelayedMatrixStats beachmat sparseMatrixStats genefilter geneplotter annotate survival XML gplots gtools KernSmooth tidyr cpp11 circlize GetoptLong clue GlobalOptions shape rjson cluster TMB future.apply future globals listenv parallelly scuttle BiocNeighbors BiocSingular ggbeeswarm viridis Rtsne RcppML ggrepel RcppHNSW ScaledMatrix irlba rsvd beeswarm vipor pbkrtest lmerTest RhpcBLASctl progress aod Rdpack broom rbibutils backports htmltools jquerylib bslib base64enc sass fs rappdirs tinytex DT htmlwidgets crosstalk promises lazyeval later rmarkdown BiocManager shiny httpuv fontawesome sourcetools commonmark ape bookdown shinydashboard shinyBS ROCR UpSetR markdown AnnotationHub BiocFileCache BiocVersion interactiveDisplayBase dbplyr filelock assertthat edgeR DESeq2 randtests 0 5 10 Imported methods 0 50 100 Required packages 0 10 20 Heaviness from parents grDevices grid matrixStats methods stats data.table purrr limma S4Vectors Matrix edgeR BiocParallel progress scales dplyr SummarizedExperiment SingleCellExperiment ComplexHeatmap ggplot2 scuttle viridis lme4 blme glmmTMB sctransform lmerTest scater DESeq2 variancePartition RColorBrewer statmod reshape2 knitr phylogram rmarkdown BiocStyle testthat cowplot UpSetR iCOBRA ExperimentHub countsimQC In total 187 packages are required directly or indirectly (230) when installing 'muscat' (1.10.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'muscat' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on muscat
DESeq2 Imports 6 0 0 93 25
variancePartition Imports 3 0 0 106 18
scater Imports 2 0 0 85 13
ComplexHeatmap Imports 3 0 0 28 8
sctransform Imports 1 0 0 58 6
glmmTMB Imports 2 0 0 52 2
data.table Imports 1 0 0 1 1
edgeR Imports 11 0 0 10 1
blme Imports 2 0 0 50 1
grDevices Imports 1 0 0 0 0
grid Imports 1 0 0 0 0
matrixStats Imports 5 0 0 0 0
methods Imports 1 0 0 0 0
stats Imports 10 0 0 0 0
purrr Imports 6 0 0 3 0
limma Imports 9 0 0 5 0
S4Vectors Imports 6 0 0 6 0
Matrix Imports 5 0 0 7 0
BiocParallel Imports 3 0 0 11 0
progress Imports 1 0 0 14 0
scales Imports 1 0 0 15 0
dplyr Imports 14 0 0 20 0
SummarizedExperiment Imports 9 0 0 24 0
SingleCellExperiment Imports 9 0 0 25 0
ggplot2 Imports The whole set of functions/methods/classes from parent package is imported to the namespace of muscat. 37 0
scuttle Imports 1 0 0 39 0
viridis Imports 1 0 0 39 0
lme4 Imports 2 0 0 49 0
lmerTest Imports 2 0 0 62 0
ExperimentHub Suggests No object is imported into the namespace of muscat. 86 27
iCOBRA Suggests No object is imported into the namespace of muscat. 85 24
countsimQC Suggests No object is imported into the namespace of muscat. 126 17
BiocStyle Suggests No object is imported into the namespace of muscat. 30 12
rmarkdown Suggests No object is imported into the namespace of muscat. 27 9
phylogram Suggests No object is imported into the namespace of muscat. 12 2
statmod Suggests No object is imported into the namespace of muscat. 2 1
cowplot Suggests No object is imported into the namespace of muscat. 38 1
UpSetR Suggests No object is imported into the namespace of muscat. 41 1
RColorBrewer Suggests No object is imported into the namespace of muscat. 0 0
reshape2 Suggests No object is imported into the namespace of muscat. 10 0
knitr Suggests No object is imported into the namespace of muscat. 12 0
testthat Suggests No object is imported into the namespace of muscat. 36 0

Analysis was done with pkgndep.