Dependency analysis on package affycoretools

General information

Bioconductor link link
Package version1.68.1
Number of strong dependencies188
Number of all dependencies201
Number of parent packages21
Max heaviness from parent packages65
Total heaviness from parent packages75
Number of parent packages (including Suggests and Enhances)28
Max co-heaviness from parent packages ("ReportingTools" and "Glimma")14

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils stats methods graphics grDevices tools stats4 grid splines parallel glue BiocGenerics rlang fastmap Biobase zlibbioc R6 bitops Rcpp pkgconfig vctrs cli crayon jsonlite DBI bit64 blob memoise plogr bit cachem IRanges S4Vectors RCurl Biostrings XVector GenomeInfoDb GenomeInfoDbData magrittr RSQLite lattice BiocManager digest KEGGREST httr png curl mime openssl askpass sys yaml Matrix AnnotationDbi htmltools base64enc evaluate highr stringr xfun stringi affyio knitr limma locfit preprocessCore gtable isoband MASS mgcv scales tibble withr nlme farver labeling lifecycle munsell RColorBrewer viridisLite ellipsis fansi pillar colorspace utf8 GenomicRanges SummarizedExperiment MatrixGenerics DelayedArray codetools matrixStats annotate genefilter BH XML xtable survival htmlwidgets rappdirs affy Category graph GO.db RBGL AnnotationForge Rgraphviz GSEABase edgeR DESeq2 ggplot2 BiocParallel geneplotter RcppArmadillo futile.logger snow lambda.r futile.options formatR gtools caTools KernSmooth foreach ff iterators hwriter GOstats PFAM.db R.utils ggbio R.oo R.methodsS3 gridExtra reshape2 Hmisc biovizBase Rsamtools GenomicAlignments BSgenome VariantAnnotation rtracklayer GenomicFeatures OrganismDbi GGally ensembldb AnnotationFilter plyr Formula latticeExtra cluster rpart nnet foreign data.table htmlTable viridis dichromat Rhtslib BiocIO restfulr biomaRt dplyr forcats progress reshape tidyr ProtGenerics lazyeval jpeg checkmate rstudioapi rjson BiocFileCache xml2 generics tidyselect hms prettyunits purrr cpp11 backports dbplyr filelock assertthat jquerylib tinytex bslib sass fs bookdown rmarkdown org.Hs.eg.db 0 5 10 Imported methods 0 50 100 150 Required packages 0 20 40 60 Heaviness from parents methods Biobase splines hwriter DBI xtable BiocGenerics limma lattice S4Vectors gplots edgeR affy RSQLite gcrma ggplot2 AnnotationDbi oligoClasses GOstats Glimma ReportingTools affydata knitr rgl rmarkdown BiocStyle hgfocuscdf hgu95av2.db In total 188 packages are required directly or indirectly (201) when installing 'affycoretools' (1.68.1) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'affycoretools' Imported functions Imported S4 methods The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on affycoretools
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of affycoretools. 0 0
Biobase Depends 4 8 0 5 0
ReportingTools Imports 7 0 0 174 65
gplots Imports 4 0 0 7 4
oligoClasses Imports 1 0 0 48 4
gcrma Imports 1 0 0 24 1
Glimma Imports 1 0 0 100 1
splines Imports 1 0 0 0 0
hwriter Imports 5 0 0 0 0
DBI Imports The whole set of functions/methods/classes from parent package is imported to the namespace of affycoretools. 1 0
xtable Imports 1 0 0 2 0
BiocGenerics Imports 1 0 0 4 0
limma Imports 6 0 0 5 0
lattice Imports 8 0 0 5 0
S4Vectors Imports 1 0 0 6 0
edgeR Imports 5 0 0 10 0
affy Imports 6 2 0 11 0
RSQLite Imports The whole set of functions/methods/classes from parent package is imported to the namespace of affycoretools. 17 0
ggplot2 Imports 11 0 0 37 0
AnnotationDbi Imports 0 5 0 44 0
GOstats Imports 1 0 0 62 0
BiocStyle Suggests No object is imported into the namespace of affycoretools. 30 8
rmarkdown Suggests No object is imported into the namespace of affycoretools. 27 6
hgu95av2.db Suggests No object is imported into the namespace of affycoretools. 46 2
affydata Suggests No object is imported into the namespace of affycoretools. 12 1
rgl Suggests No object is imported into the namespace of affycoretools. 23 1
hgfocuscdf Suggests No object is imported into the namespace of affycoretools. 45 1
knitr Suggests No object is imported into the namespace of affycoretools. 12 0

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 affycoretools Co-heaviness as Jaccard coeffcient
Glimma ReportingTools 14 0.175

Analysis was done with pkgndep.