Dependency analysis on package ReportingTools

General information

Bioconductor link link
Package version2.36.0
Number of strong dependencies174
Number of all dependencies197
Number of parent packages22
Max heaviness from parent packages58
Total heaviness from parent packages71
Number of parent packages (including Suggests and Enhances)31
Max co-heaviness from parent packages ("ggbio" and "DESeq2")13

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats graphics grDevices tools stats4 grid splines parallel glue BiocGenerics R6 rlang Rcpp crayon jsonlite mime fastmap S4Vectors pkgconfig vctrs cli Biobase cachem DBI IRanges RSQLite KEGGREST httr bit64 blob memoise plogr png Biostrings curl openssl bit XVector GenomeInfoDb askpass zlibbioc RCurl GenomeInfoDbData sys bitops AnnotationDbi magrittr lattice XML xtable Matrix digest withr lifecycle ellipsis annotate BH survival stringr xfun stringi RColorBrewer gtable isoband MASS mgcv scales tibble nlme farver labeling munsell viridisLite fansi pillar colorspace utf8 graph genefilter rappdirs evaluate highr yaml locfit RBGL GenomicRanges SummarizedExperiment BiocParallel ggplot2 MatrixGenerics DelayedArray futile.logger snow codetools matrixStats lambda.r futile.options formatR htmltools base64enc GSEABase geneplotter RcppArmadillo Rsamtools Rhtslib biomaRt dplyr progress knitr BiocFileCache xml2 generics tidyselect hms prettyunits purrr dbplyr filelock assertthat R.oo R.methodsS3 limma Category GO.db AnnotationForge Rgraphviz gridExtra reshape2 Hmisc biovizBase GenomicAlignments BSgenome VariantAnnotation rtracklayer GenomicFeatures OrganismDbi GGally ensembldb AnnotationFilter plyr Formula latticeExtra cluster rpart nnet foreign data.table htmlTable viridis dichromat BiocIO restfulr BiocManager forcats reshape tidyr ProtGenerics lazyeval jpeg checkmate htmlwidgets rstudioapi rjson cpp11 backports bslib sass jquerylib fs tinytex httpuv fontawesome sourcetools later promises commonmark org.Hs.eg.db DEXSeq DESeq2 hwriter statmod 0 5 10 Imported methods 0 50 100 150 Required packages 0 20 40 60 Heaviness from parents methods utils knitr hwriter grid XML BiocGenerics Biobase limma lattice R.utils IRanges edgeR ggplot2 AnnotationDbi PFAM.db annotate GSEABase Category GOstats DESeq2 ggbio RUnit markdown ALL rmarkdown shiny org.Mm.eg.db org.Sc.sgd.db hgu95av2.db pasilla In total 174 packages are required directly or indirectly (197) when installing 'ReportingTools' (2.36.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'ReportingTools' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on ReportingTools
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ReportingTools. 0 0
utils Depends 3 0 0 0 0
knitr Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ReportingTools. 12 0
ggbio Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ReportingTools. 153 58
GOstats Imports 3 1 1 62 4
R.utils Imports 1 0 0 5 3
DESeq2 Imports 2 0 2 93 3
hwriter Imports 5 0 0 0 1
edgeR Imports 2 0 3 10 1
PFAM.db Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ReportingTools. 45 1
grid Imports 5 0 0 0 0
XML Imports 13 1 0 2 0
BiocGenerics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ReportingTools. 4 0
Biobase Imports 0 0 1 5 0
limma Imports 1 0 1 5 0
lattice Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ReportingTools. 5 0
IRanges Imports 0 1 0 7 0
ggplot2 Imports 1 0 0 37 0
AnnotationDbi Imports 0 4 0 44 0
annotate Imports 2 0 0 47 0
GSEABase Imports 0 2 1 49 0
Category Imports 0 3 2 58 0
shiny Suggests No object is imported into the namespace of ReportingTools. 34 11
rmarkdown Suggests No object is imported into the namespace of ReportingTools. 27 6
pasilla Suggests No object is imported into the namespace of ReportingTools. 115 3
hgu95av2.db Suggests No object is imported into the namespace of ReportingTools. 46 2
RUnit Suggests No object is imported into the namespace of ReportingTools. 3 1
markdown Suggests No object is imported into the namespace of ReportingTools. 5 1
ALL Suggests No object is imported into the namespace of ReportingTools. 6 1
org.Mm.eg.db Suggests No object is imported into the namespace of ReportingTools. 45 1
org.Sc.sgd.db Suggests No object is imported into the namespace of ReportingTools. 45 1

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 ReportingTools Co-heaviness as Jaccard coeffcient
DESeq2 ggbio 13 0.176

Analysis was done with pkgndep.