Dependency analysis on package Rsamtools

General information

Bioconductor link link
Package version2.12.0
Number of strong dependencies29
Number of all dependencies123
Number of parent packages14
Max heaviness from parent packages9
Total heaviness from parent packages14
Number of parent packages (including Suggests and Enhances)23

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports LinkingTo Suggests methods utils stats graphics stats4 tools grDevices parallel grid BiocGenerics S4Vectors IRanges zlibbioc RCurl GenomeInfoDbData bitops GenomeInfoDb XVector crayon futile.logger snow codetools BH lambda.r futile.options formatR GenomicRanges SummarizedExperiment Biostrings Rsamtools BiocParallel MatrixGenerics Biobase Matrix DelayedArray Rhtslib matrixStats lattice yaml GenomicAlignments stringr digest rappdirs rlang R6 glue magrittr stringi jsonlite fastmap png BiocIO rtracklayer XML restfulr rjson AnnotationDbi DBI RSQLite biomaRt KEGGREST bit64 blob memoise pkgconfig Rcpp plogr progress httr BiocFileCache xml2 bit vctrs cachem hms prettyunits curl mime openssl dbplyr dplyr filelock cli ellipsis lifecycle askpass assertthat pillar purrr tibble tidyselect withr generics sys fansi utf8 GenomicFeatures bookdown knitr rmarkdown BiocManager htmltools jquerylib xfun tinytex evaluate highr bslib base64enc sass fs hwriter latticeExtra jpeg RColorBrewer BSgenome 0 10 20 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents methods GenomeInfoDb GenomicRanges Biostrings utils zlibbioc bitops stats BiocGenerics S4Vectors IRanges XVector BiocParallel Rhtslib RNAseqData.HNRNPC.bam.chr14 RUnit BiocStyle GenomicAlignments ShortRead BSgenome.Hsapiens.UCSC.hg19 GenomicFeatures TxDb.Dmelanogaster.UCSC.dm3.ensGene TxDb.Hsapiens.UCSC.hg18.knownGene In total 29 packages are required directly or indirectly (123) when installing 'Rsamtools' (2.12.0) 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 'Rsamtools' Imported functions Imported S4 methods Imported S4 classes 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 Rsamtools.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on Rsamtools
Biostrings Depends 9 0 3 17 3
GenomicRanges Depends 2 2 2 15 1
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of Rsamtools. 0 0
GenomeInfoDb Depends 4 0 1 11 0
BiocParallel Imports 1 0 0 11 9
utils Imports 1 0 0 0 0
zlibbioc Imports The whole set of functions/methods/classes from parent package is imported to the namespace of Rsamtools. 0 0
bitops Imports 1 0 0 0 0
stats Imports 2 0 0 0 0
BiocGenerics Imports 17 0 4 4 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of Rsamtools. 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of Rsamtools. 7 0
XVector Imports The whole set of functions/methods/classes from parent package is imported to the namespace of Rsamtools. 10 0
Rhtslib LinkingTo Parent package is listed in LinkingTo of Rsamtools but no object from parent package is imported. 1 1
TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests No object is imported into the namespace of Rsamtools. 97 69
TxDb.Hsapiens.UCSC.hg18.knownGene Suggests No object is imported into the namespace of Rsamtools. 97 69
GenomicFeatures Suggests No object is imported into the namespace of Rsamtools. 96 68
BiocStyle Suggests No object is imported into the namespace of Rsamtools. 30 26
BSgenome.Hsapiens.UCSC.hg19 Suggests No object is imported into the namespace of Rsamtools. 46 18
ShortRead Suggests No object is imported into the namespace of Rsamtools. 44 16
GenomicAlignments Suggests No object is imported into the namespace of Rsamtools. 38 10
RNAseqData.HNRNPC.bam.chr14 Suggests No object is imported into the namespace of Rsamtools. 0 1
RUnit Suggests No object is imported into the namespace of Rsamtools. 3 1

Analysis was done with pkgndep.