Dependency analysis on package DEXSeq

General information

Bioconductor link link
Package version1.42.0
Number of strong dependencies114
Number of all dependencies152
Number of parent packages18
Max heaviness from parent packages15
Total heaviness from parent packages33
Number of parent packages (including Suggests and Enhances)25
Max co-heaviness from parent packages ("biomaRt" and "DESeq2")8

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests stats methods utils graphics tools stats4 grDevices grid parallel splines BiocGenerics S4Vectors glue IRanges GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops rlang R6 jsonlite Biobase crayon fastmap magrittr pkgconfig vctrs Biostrings cli lattice Rcpp DBI RSQLite KEGGREST httr bit64 blob memoise plogr png curl mime openssl bit cachem askpass sys digest stringi GenomicRanges Matrix AnnotationDbi XML stringr futile.logger snow codetools BH lambda.r futile.options formatR MatrixGenerics DelayedArray matrixStats tibble withr lifecycle ellipsis fansi pillar utf8 rappdirs SummarizedExperiment BiocParallel annotate xtable survival RColorBrewer Rhtslib progress BiocFileCache xml2 hms prettyunits dbplyr dplyr filelock assertthat purrr tidyselect generics genefilter locfit geneplotter ggplot2 RcppArmadillo gtable isoband MASS mgcv scales nlme farver labeling munsell viridisLite colorspace yaml evaluate xfun highr knitr htmltools jquerylib tinytex bslib base64enc sass fs biomaRt Rsamtools bookdown rmarkdown BiocManager brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 BiocIO rtracklayer GenomicAlignments restfulr rjson DEXSeq DESeq2 hwriter statmod 0 0.5 1 Imported methods 0 50 100 Required packages 0 5 10 15 Heaviness from parents RColorBrewer Biobase S4Vectors IRanges BiocParallel GenomicRanges SummarizedExperiment AnnotationDbi DESeq2 hwriter methods statmod BiocGenerics stringr Rsamtools geneplotter genefilter biomaRt knitr parathyroidSE rmarkdown BiocStyle testthat GenomicFeatures pasilla In total 114 packages are required directly or indirectly (152) when installing 'DEXSeq' (1.42.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'DEXSeq' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on DEXSeq
DESeq2 Depends The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 93 15
RColorBrewer Depends 1 0 0 0 0
Biobase Depends The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 5 0
S4Vectors Depends The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 6 0
IRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 7 0
BiocParallel Depends The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 11 0
GenomicRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 15 0
SummarizedExperiment Depends The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 24 0
AnnotationDbi Depends 1 0 0 44 0
biomaRt Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 70 14
Rsamtools Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 29 2
hwriter Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 0 1
statmod Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 2 1
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 0 0
BiocGenerics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 4 0
stringr Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 7 0
geneplotter Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 51 0
genefilter Imports The whole set of functions/methods/classes from parent package is imported to the namespace of DEXSeq. 53 0
BiocStyle Suggests No object is imported into the namespace of DEXSeq. 30 16
testthat Suggests No object is imported into the namespace of DEXSeq. 36 14
rmarkdown Suggests No object is imported into the namespace of DEXSeq. 27 13
GenomicFeatures Suggests No object is imported into the namespace of DEXSeq. 96 7
knitr Suggests No object is imported into the namespace of DEXSeq. 12 5
pasilla Suggests No object is imported into the namespace of DEXSeq. 115 2
parathyroidSE Suggests No object is imported into the namespace of DEXSeq. 25 1

Analysis was done with pkgndep.