Dependency analysis on package GenomicAlignments

General information

Bioconductor link link
Package version1.32.0
Number of strong dependencies38
Number of all dependencies148
Number of parent packages12
Max heaviness from parent packages8
Total heaviness from parent packages10
Number of parent packages (including Suggests and Enhances)26
Max co-heaviness from parent packages ("BiocParallel" and "Rsamtools")9

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics stats4 tools grDevices grid parallel splines BiocGenerics S4Vectors IRanges RCurl GenomeInfoDbData bitops GenomeInfoDb XVector zlibbioc crayon GenomicRanges lattice futile.logger snow codetools BH lambda.r futile.options formatR MatrixGenerics Biobase Matrix DelayedArray matrixStats Biostrings BiocParallel Rhtslib SummarizedExperiment yaml Rsamtools GenomicAlignments XML BiocIO restfulr rjson rtracklayer Rcpp digest rlang R6 glue magrittr jsonlite fastmap png stringr rappdirs stringi AnnotationDbi DBI RSQLite KEGGREST bit64 blob memoise pkgconfig plogr httr bit vctrs cachem curl mime openssl cli ellipsis lifecycle askpass pillar tibble withr sys fansi utf8 biomaRt progress BiocFileCache xml2 hms prettyunits dbplyr dplyr filelock assertthat purrr tidyselect generics locfit RColorBrewer BSgenome GenomicFeatures limma bookdown knitr rmarkdown BiocManager htmltools jquerylib xfun tinytex evaluate highr bslib base64enc sass fs hwriter latticeExtra jpeg genefilter geneplotter ggplot2 RcppArmadillo annotate survival gtable isoband MASS mgcv scales xtable nlme farver labeling munsell viridisLite colorspace 0 0.5 1 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents methods BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges Biostrings SummarizedExperiment Rsamtools utils stats BiocParallel RNAseqData.HNRNPC.bam.chr14 pasillaBamSubset RUnit edgeR BiocStyle ShortRead rtracklayer BSgenome BSgenome.Dmelanogaster.UCSC.dm3 BSgenome.Hsapiens.UCSC.hg19 DESeq2 GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Dmelanogaster.UCSC.dm3.ensGene In total 38 packages are required directly or indirectly (148) when installing 'GenomicAlignments' (1.32.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'GenomicAlignments' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on GenomicAlignments
SummarizedExperiment Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicAlignments. 24 8
Rsamtools Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicAlignments. 29 2
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicAlignments. 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicAlignments. 4 0
S4Vectors Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicAlignments. 6 0
IRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicAlignments. 7 0
GenomeInfoDb Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicAlignments. 11 0
GenomicRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicAlignments. 15 0
Biostrings Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicAlignments. 17 0
utils Imports 1 0 0 0 0
stats Imports 1 0 0 0 0
BiocParallel Imports 1 0 0 11 0
TxDb.Hsapiens.UCSC.hg19.knownGene Suggests No object is imported into the namespace of GenomicAlignments. 97 60
TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests No object is imported into the namespace of GenomicAlignments. 97 60
GenomicFeatures Suggests No object is imported into the namespace of GenomicAlignments. 96 59
DESeq2 Suggests No object is imported into the namespace of GenomicAlignments. 93 58
BiocStyle Suggests No object is imported into the namespace of GenomicAlignments. 30 26
BSgenome.Dmelanogaster.UCSC.dm3 Suggests No object is imported into the namespace of GenomicAlignments. 46 9
BSgenome.Hsapiens.UCSC.hg19 Suggests No object is imported into the namespace of GenomicAlignments. 46 9
BSgenome Suggests No object is imported into the namespace of GenomicAlignments. 45 8
ShortRead Suggests No object is imported into the namespace of GenomicAlignments. 44 7
rtracklayer Suggests No object is imported into the namespace of GenomicAlignments. 44 7
edgeR Suggests No object is imported into the namespace of GenomicAlignments. 10 4
RNAseqData.HNRNPC.bam.chr14 Suggests No object is imported into the namespace of GenomicAlignments. 0 1
pasillaBamSubset Suggests No object is imported into the namespace of GenomicAlignments. 0 1
RUnit Suggests No object is imported into the namespace of GenomicAlignments. 3 1

Analysis was done with pkgndep.