Dependency analysis on package oligo

General information

Bioconductor link link
Package version1.60.0
Number of strong dependencies52
Number of all dependencies142
Number of parent packages17
Max heaviness from parent packages13
Total heaviness from parent packages16
Number of parent packages (including Suggests and Enhances)38
Max co-heaviness from parent packages ("RSQLite" and "oligoClasses")13

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests Enhances methods utils stats graphics tools grDevices stats4 grid splines parallel compiler BiocGenerics zlibbioc bitops glue IRanges S4Vectors GenomeInfoDb XVector crayon RCurl GenomeInfoDbData Biobase bit rlang fastmap Biostrings DBI bit64 blob memoise pkgconfig Rcpp plogr vctrs cachem cli RSQLite codetools foreach Matrix iterators lattice GenomicRanges SummarizedExperiment BiocManager MatrixGenerics DelayedArray matrixStats affyio ff oligoClasses oligo affxparser preprocessCore jsonlite R6 yaml stringr magrittr stringi KEGGREST httr png curl mime openssl askpass sys XML xfun evaluate highr digest rappdirs AnnotationDbi bookdown knitr rmarkdown htmltools jquerylib tinytex bslib base64enc sass fs BSgenome rtracklayer Rsamtools GenomicAlignments BiocIO restfulr BiocParallel Rhtslib rjson futile.logger snow BH lambda.r futile.options formatR annotate survival xtable progress BiocFileCache xml2 hms prettyunits dbplyr dplyr filelock ellipsis lifecycle assertthat pillar purrr tibble tidyselect withr generics fansi utf8 Rmpi 0 10 20 30 Imported methods 0 20 40 60 Required packages 0 10 20 30 Heaviness from parents BiocGenerics Biobase Biostrings oligoClasses affxparser graphics methods splines stats stats4 utils zlibbioc DBI preprocessCore affyio ff RSQLite hapmap100kxba maqcExpression4plex RColorBrewer RCurl RUnit limma ACME knitr BiocStyle AnnotationDbi BSgenome.Hsapiens.UCSC.hg18 pd.hg.u95av2 pd.mapping50k.xba240 pd.huex.1.0.st.v2 pd.hg18.60mer.expr pd.hugene.1.0.st.v1 genefilter oligoData biomaRt doMC doMPI In total 52 packages are required directly or indirectly (142) when installing 'oligo' (1.60.0) Depends Imports Suggests Enhances Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'oligo' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on oligo
oligoClasses Depends 15 10 11 48 13
BiocGenerics Depends 6 8 0 4 0
Biobase Depends 5 27 1 5 0
Biostrings Depends 1 0 0 17 0
affxparser Imports 4 0 0 0 1
splines Imports 1 0 0 0 1
preprocessCore Imports 17 0 0 1 1
graphics Imports 9 0 0 0 0
methods Imports 6 0 7 0 0
stats Imports 20 0 0 0 0
stats4 Imports 0 2 0 0 0
utils Imports 7 0 0 0 0
zlibbioc Imports The whole set of functions/methods/classes from parent package is imported to the namespace of oligo. 0 0
DBI Imports 0 3 0 1 0
affyio Imports 2 0 0 2 0
ff Imports 8 0 0 2 0
RSQLite Imports 0 1 0 17 0
biomaRt Suggests No object is imported into the namespace of oligo. 70 37
BiocStyle Suggests No object is imported into the namespace of oligo. 30 22
BSgenome.Hsapiens.UCSC.hg18 Suggests No object is imported into the namespace of oligo. 46 19
genefilter Suggests No object is imported into the namespace of oligo. 53 16
AnnotationDbi Suggests No object is imported into the namespace of oligo. 44 11
knitr Suggests No object is imported into the namespace of oligo. 12 8
pd.hg.u95av2 Suggests No object is imported into the namespace of oligo. 53 2
pd.mapping50k.xba240 Suggests No object is imported into the namespace of oligo. 53 2
pd.huex.1.0.st.v2 Suggests No object is imported into the namespace of oligo. 53 2
pd.hg18.60mer.expr Suggests No object is imported into the namespace of oligo. 53 2
pd.hugene.1.0.st.v1 Suggests No object is imported into the namespace of oligo. 53 2
oligoData Suggests No object is imported into the namespace of oligo. 53 2
hapmap100kxba Suggests No object is imported into the namespace of oligo. 0 1
maqcExpression4plex Suggests No object is imported into the namespace of oligo. 0 1
RColorBrewer Suggests No object is imported into the namespace of oligo. 0 1
RUnit Suggests No object is imported into the namespace of oligo. 3 1
limma Suggests No object is imported into the namespace of oligo. 5 1
ACME Suggests No object is imported into the namespace of oligo. 6 1
RCurl Suggests No object is imported into the namespace of oligo. 2 0
doMPI Enhances No object is imported into the namespace of oligo. 7 4
doMC Enhances No object is imported into the namespace of oligo. 5 2

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 oligo Co-heaviness as Jaccard coeffcient
oligoClasses RSQLite 13 0.500
Biostrings oligoClasses 11 0.458

Analysis was done with pkgndep.