Dependency analysis on package ShortRead

General information

Bioconductor link link
Package version1.54.0
Number of strong dependencies44
Number of all dependencies118
Number of parent packages17
Max heaviness from parent packages6
Total heaviness from parent packages11
Number of parent packages (including Suggests and Enhances)22
Max co-heaviness from parent packages ("GenomicAlignments" and "Rsamtools")1

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports LinkingTo Suggests utils stats methods graphics stats4 grDevices tools parallel grid BiocGenerics S4Vectors IRanges zlibbioc RCurl GenomeInfoDbData bitops XVector GenomeInfoDb crayon futile.logger snow codetools BH lambda.r futile.options formatR Biostrings GenomicRanges BiocParallel Rhtslib Biobase lattice png SummarizedExperiment Rsamtools MatrixGenerics Matrix DelayedArray matrixStats jpeg RColorBrewer stringr jsonlite digest rlang fastmap glue magrittr stringi R6 rappdirs yaml XML AnnotationDbi progress httr BiocFileCache xml2 DBI RSQLite KEGGREST hms prettyunits curl mime openssl dbplyr dplyr filelock bit64 blob memoise pkgconfig Rcpp plogr ellipsis lifecycle vctrs askpass assertthat cli pillar purrr tibble tidyselect withr generics bit cachem sys fansi utf8 bookdown knitr rmarkdown BiocManager htmltools jquerylib xfun tinytex evaluate highr bslib base64enc sass fs BiocIO rtracklayer biomaRt GenomicAlignments restfulr rjson 0 5 10 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents BiocGenerics BiocParallel Biostrings Rsamtools GenomicAlignments hwriter methods zlibbioc Biobase lattice S4Vectors IRanges latticeExtra GenomeInfoDb GenomicRanges Rhtslib XVector yeastNagalakshmi RUnit BiocStyle biomaRt GenomicFeatures In total 44 packages are required directly or indirectly (118) when installing 'ShortRead' (1.54.0) Depends Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'ShortRead' Imported functions The whole namespace is imported Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on ShortRead
GenomicAlignments Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ShortRead. 38 6
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ShortRead. 4 0
BiocParallel Depends 1 0 0 11 0
Biostrings Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ShortRead. 17 0
Rsamtools Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ShortRead. 29 0
latticeExtra Imports 1 0 0 9 4
hwriter Imports 2 0 0 0 1
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ShortRead. 0 0
zlibbioc Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ShortRead. 0 0
Biobase Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ShortRead. 5 0
lattice Imports 14 0 0 5 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ShortRead. 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ShortRead. 7 0
GenomeInfoDb Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ShortRead. 11 0
GenomicRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ShortRead. 15 0
Rhtslib LinkingTo Parent package is listed in LinkingTo of ShortRead but no object from parent package is imported. 1 0
XVector LinkingTo Parent package is listed in LinkingTo of ShortRead but no object from parent package is imported. 10 0
GenomicFeatures Suggests No object is imported into the namespace of ShortRead. 96 57
biomaRt Suggests No object is imported into the namespace of ShortRead. 70 51
BiocStyle Suggests No object is imported into the namespace of ShortRead. 30 26
yeastNagalakshmi Suggests No object is imported into the namespace of ShortRead. 0 1
RUnit Suggests No object is imported into the namespace of ShortRead. 3 1

Analysis was done with pkgndep.