Dependency analysis on package Biostrings

General information

Bioconductor link link
Package version2.64.0
Number of strong dependencies17
Number of all dependencies112
Number of parent packages11
Max heaviness from parent packages4
Total heaviness from parent packages8
Number of parent packages (including Suggests and Enhances)24
Max co-heaviness from parent packages ("crayon" and "grDevices")1

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests Enhances methods utils graphics stats stats4 grDevices tools parallel grid BiocGenerics S4Vectors zlibbioc IRanges RCurl GenomeInfoDbData bitops Biobase GenomeInfoDb Biostrings XVector crayon GenomicRanges rtracklayer matrixStats Rsamtools XML GenomicAlignments BiocIO restfulr BiocParallel Rhtslib SummarizedExperiment rjson yaml futile.logger snow codetools BH MatrixGenerics Matrix DelayedArray lambda.r futile.options lattice formatR AnnotationDbi DBI RSQLite KEGGREST bit64 blob memoise pkgconfig Rcpp plogr httr png bit rlang vctrs cachem curl jsonlite mime openssl R6 cli glue fastmap askpass sys BSgenome affyio BiocManager preprocessCore affy biomaRt progress stringr digest BiocFileCache rappdirs xml2 hms prettyunits magrittr stringi dbplyr dplyr filelock ellipsis lifecycle assertthat pillar purrr tibble tidyselect withr generics fansi utf8 0 2 4 6 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents methods BiocGenerics S4Vectors IRanges XVector GenomeInfoDb utils grDevices graphics stats crayon RUnit affy affydata BSgenome drosophila2probe hgu95av2probe hgu133aprobe hgu95av2cdf BSgenome.Celegans.UCSC.ce2 BSgenome.Dmelanogaster.UCSC.dm3 BSgenome.Hsapiens.UCSC.hg18 GenomicFeatures Rmpi In total 17 packages are required directly or indirectly (112) when installing 'Biostrings' (2.64.0) 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 'Biostrings' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on Biostrings
GenomeInfoDb Depends 4 0 0 11 4
XVector Depends The whole set of functions/methods/classes from parent package is imported to the namespace of Biostrings. 10 3
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of Biostrings. 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of Biostrings. 4 0
S4Vectors Depends The whole set of functions/methods/classes from parent package is imported to the namespace of Biostrings. 6 0
IRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of Biostrings. 7 0
crayon Imports 2 0 0 3 1
utils Imports 2 0 0 0 0
grDevices Imports 1 0 0 0 0
graphics Imports 7 0 0 0 0
stats Imports 5 0 0 0 0
GenomicFeatures Suggests No object is imported into the namespace of Biostrings. 96 80
BSgenome.Celegans.UCSC.ce2 Suggests No object is imported into the namespace of Biostrings. 46 30
BSgenome.Dmelanogaster.UCSC.dm3 Suggests No object is imported into the namespace of Biostrings. 46 30
BSgenome.Hsapiens.UCSC.hg18 Suggests No object is imported into the namespace of Biostrings. 46 30
BSgenome Suggests No object is imported into the namespace of Biostrings. 45 29
drosophila2probe Suggests No object is imported into the namespace of Biostrings. 45 29
hgu95av2probe Suggests No object is imported into the namespace of Biostrings. 45 29
hgu133aprobe Suggests No object is imported into the namespace of Biostrings. 45 29
hgu95av2cdf Suggests No object is imported into the namespace of Biostrings. 45 29
affydata Suggests No object is imported into the namespace of Biostrings. 12 6
affy Suggests No object is imported into the namespace of Biostrings. 11 5
RUnit Suggests No object is imported into the namespace of Biostrings. 3 1
Rmpi Enhances No object is imported into the namespace of Biostrings. 1 2

Analysis was done with pkgndep.